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Изменения, происходящие в окружающей среде, заставляют популяции организмов адаптироваться к новым условиям либо за счет фенотипической пластичности, либо за счет генетических или эпигенетических изменений. Следы отбора, такие как специфические изменения частот аллелей и гаплотипов, снижение или повышение генетического разнообразия, помогают выявить изменения генома крупного рогатого скота в ответ на искусственный и естественный отбор, а также локусы и варианты, непосредственно влияющие на адаптивные и экономически важные признаки. Достижения генетики и биотехнологии дают возможность быстрого переноса уникальных генетических вариантов, возникших у местных пород крупного рогатого скота в процессе адаптации к локальной среде обитания, в геномы интернациональных высокопроизводительных пород с целью сохранения их выдающихся свойств в новых условиях обитания. Возможно и использование методов геномной селекции для повышения частот адаптивных аллелей у интернациональных пород. В обзоре рассмотрены недавние работы по истории происхождения и эволюции турано-монгольских пород крупного рогатого скота, адаптации турано-монгольского скота к экстремальным условиям среды. Сделано обобщение имеющихся сведений о потенциальных генах-кандидатах адаптации в геномах турано-монгольских пород, включая гены устойчивости к холоду, гены иммунного ответа и гены адаптации к высокогорью. Авторы приходят к выводу, что имеющиеся данные литературы не позволяют отдать предпочтение одному из двух возможных сценариев происхождения турано-монгольских пород – в результате доместикации дикого тура на территории Восточной Азии или вследствие миграции тауринной протопопуляции из Ближнего Востока. Турано-монгольским породам свойственна высокая адаптация к экстремальным климатическим условиям (холод, жара и недостаток кислорода в горах) и паразитам (гнус, клещи, бактериальные и вирусные инфекции). В результате высокопроизводительного генотипирования и секвенирования геномов и транскриптомов представителей этих пород в последнее время были выявлены перспективные гены-кандидаты и генетические варианты, участвующие в адаптации к факторам внешней среды.

Made available in DSpace on 2021-06-25T15:03:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-04-27 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Context. Indicine breeds are the main source of beef products in tropical and subtropical regions. However, genetic improvement for carcass- and meat-quality traits in zebu cattle have been limited and genomics studies concerning structural variations that influence these traits are essential. Aim. The aim of this study was to perform a genome-wide association study between copy number variation regions (CNVRs) and carcass- and meat quality-traits in Nellore cattle. Methods. In total, 3794 animals, males and females included, were genotyped using a 777 962 single-nucleotide polymorphism platform of BovineHD BeadChip (777k; Illumina Inc.). Of these, 1751 Nellore bulls were slaughtered at 24 months of age for further carcass beef analysis. The following traits were studied: beef tenderness, marbling, rib-eye area, backfat thickness and meat colour (lightness, redness and yellowness). The CNV detection was conducted through PennCNV software. The association analyses were performed using CNVRuler software. Key results. Several identified genomic regions were linked to quantitative trait loci associated with fat deposition (FABP7) and lipid metabolism (PPARA; PLA2 family; BCHE), extracellular matrix (INS; COL10A1), contraction (SLC34A3; TRDN) and muscle development (CAPZP). The gene-enrichment analyses highlighted biological mechanisms directly related to the metabolism and synthesis of lipids and fatty acids. Conclusions. The large number of potential candidate genes identified within the CNVRs, as well as the functions and pathways identified, should help better elucidate the genetic mechanisms involved in the expression of beef and carcass traits in Nellore cattle. Several CNVRs harboured genes that might have a functional impact to improve the beef and carcass traits. Implications. The results obtained contribute to upgrade the sensorial and organoleptic attributes of Nellore cattle and make feasible the genetic improvement of carcass- and meat-quality traits. Univ Estadual Paulista, Dept Zootecnia, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane, BR-14884900 Jaboticabal, SP, Brazil Univ Guelph, Ctr Genet Improvement Livestock, 50 Stone Rd East,Bldg 70, Guelph, ON N1G 2W1, Canada Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Rua Duque Caxias Norte 225, BR-13635900 Pirassununga, SP, Brazil USDA ARS, ANRI, Bovine Funct Genom Lab, Beltsville, MD 20705 USA Univ Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 USA Univ Estadual Paulista, Dept Zootecnia, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2009/16118-5 CAPES: 001

L’amélioration du potentiel génétique des bovins au Burkina Faso s’appuie sur des programmes de croisements avec des races exotiques par la promotion de l’insémination artificielle (IA) depuis un quart de siècle. Néanmoins, l’adaptation des veaux métis obtenus est controversée aussi bien en élevage périurbain que traditionnel. L’objectif de cette étude a été de déterminer le taux de survie et les aptitudes de métis F1 issus de croisements entre des bovins de races Brune des Alpes et Zébu Peul dans des élevages de la région des Cascades au Burkina Faso. L’étude a été menée sur 142 veaux répartis dans 60 élevages extensifs et semi-intensifs entre octobre 2013 et août 2017. Les animaux ont fait l’objet d’un suivi sanitaire rigoureux et d’une alimentation améliorée grâce à la production locale de fourrages. Le taux de survie des veaux à 42 mois a été estimé à 88 % avec une différence significative (p < 0,05) entre saisons avant sevrage, et entre systèmes d’élevage après sevrage. Au total, 26,76 % des métis F1 ont été atteints de cowdriose, dermatophilose, fièvre aphteuse ou trypanosomoses avant et après le sevrage. Rustiques (82,4 %) avec un rythme cardiaque normal (85,6 %), les croisés ont été dociles et affectueux (64,8 %). Les mâles et les femelles F1 ont été respectivement de potentiels reproducteurs et de véritables conductrices de troupeaux. Les femelles sont d’emblée utilisées pour améliorer la production laitière mais l’utilisation des mâles dans les croisements doit éviter la consanguinité dans les élevages. La survie des métis nécessite un suivi sanitaire permanent et une bonne conduite d’élevage. Cependant, considérant le taux de survie élevé, la bonne adaptation et la docilité des métis, l’IA est en mesure d’améliorer les productions animales bovines au Burkina Faso.

The aim was to develop a program for resynchronization of ovulation (ReBreed21) that allowed reinsemination of non-pregnant Bos indicus heifers every 21 d using timed AI (TAI) without the need for detection of estrus. The Rebreed21 program begins 12 d after previous TAI (Day 0) by inserting an intravaginal P4 implant (Day 12) that is removed 7 d later (Day 19) combined with treatment with 300 IU of eCG. On Day 21, early pregnancy diagnosis (Doppler PD) is performed based on CL vascularity. Nonpregnant (NP) heifers immediately received AI combined with 100 mg of GnRH. The program is replicated 12 d after second TAI to produce a breeding season (BS) of 42 d with 3 potential TAIs. Two experiments were conducted as a proof of concept for this rapid rebreeding program. In Experiment 1, 76 heifers were enrolled in ReBreed21, as explained above. In Experiment 2, 300 Nellore heifers were synchronized for 1st TAI and randomly assigned to one of two groups: ReBreed21 (n = 147) or another early resynchronization procedure, Resynch14 (n = 153) with P4 implant inserted 14 d after previous TAI plus 50 mg of long-acting injectable P4; 8 d later P4 implant removed (Day 22) and early Doppler PD performed; NP heifers received 150 mg of cloprostenol, 0.5 mg of ECP, and 300 IU of eCG with TAI on Day 24. In both experiments, the largest follicle (LF) was measured at each Resynch TAI. Ultrasound was later used to confirm the early Doppler PD and to determine ovulation (OV) to Resynch at 12 d after TAI in ReBreed21 (Day 33 of pregnancy) and 14 d after TAI in Resynch14 (Day 38 of pregnancy). Final PD was performed 40 d after 3rd TAI. Results for Experiment 1 were: diameter of LF 11.8 ± 0.23 mm; 88.9% OV; 20.5% false positives; 38.1% P/AI at 1st TAI; 44.4% overall P/AI for ReBreed21 TAIs; 72.3% total pregnant at end of BS. In experiment 2, Rebreed21 vs. Resynch14 were different for: diameter of LF (10.9 ± 0.17 vs. 10.0 ± 0.17 mm, P = 0.0003), heifers with LF < 8.5 mm (10.2 vs. 26.4%, P = 0.04), or LF 11 mm (50.0 vs. 37.2%, P = 0.001), and P/AI at first TAI (29.3% [43/147] vs. 20.3% [31/153], P = 0.074) but similar for OV (overall 86.8% [239/275], P = 0.82), false positives (P = 0.52) overall P/AI for Resynch TAIs (33.6 vs. 28.8%, P = 0.4), and total pregnant at end of BS (58.5% [86/147] vs. 55.6% [85/153], P = 0.64). In addition, median time to pregnancy was 9 d earlier (P = 0.0007) for ReBreed21 than Resynch14. Thus, ReBreed21 is a novel protocol that allows earlier reinseminations than Resynch14 but with similar fertility. Made available in DSpace on 2020-09-01T04:41:18Z (GMT). No. of bitstreams: 1 27022.pdf: 619959 bytes, checksum: f81e68c3fc6a7c4f263b7f44073036e9 (MD5) Previous issue date: 2020

Made available in DSpace on 2020-12-12T01:30:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value

The objective of this study was to identify sexually precocious heifers by observing ovulation (presence of corpus luteum - CL) and correlating it with the plasma progesterone concentration, as well as to verify the accuracy of the ultrasound examination (US) in this class of animals. The animals were kept in Brachiaria brizantha pastures in an extensive system with water and mineralized salt ad libitum . Nelore heifers (n=50) with initial age and weight of 10 months old and 210 kg, respectively, were used. Only 14% (7/50; p

Puberty is a whole‐body event, driven by the hypothalamic integration of peripheral signals such as leptin or IGF‐1. In the process of puberty, reproductive development is simultaneous to growth, including muscle growth. To enhance our understanding of muscle function related to puberty, we performed transcriptome analyses of muscle samples from six pre‐ and six post‐pubertal Brahman heifers (Bos indicus). Our aims were to perform differential expression analyses and co‐expression analyses to derive a regulatory gene network associate with puberty. As a result, we identified 431 differentially expressed (DEx) transcripts (genes and non‐coding RNAs) when comparing pre‐ to post‐pubertal average gene expression. The DEx transcripts were compared with all expressed transcripts in our samples (over 14,000 transcripts) for functional enrichment analyses. The DEx transcripts were associated with “extracellular region,” “inflammatory response” and “hormone activity” (adjusted p, Puberty is a whole‐body event. In the process of puberty, reproductive development is simultaneous to muscle growth. To enhance our understanding of muscle function related to puberty, we performed whole‐genome gene expression analyses. As a result, we identified 431 differentially expressed genes and predicted a gene network. In the derived co‐expression gene network, TCF3 was also a key regulator. In short, we described how puberty may affect muscle gene expression in cattle.

Summary Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

Made available in DSpace on 2020-12-12T02:44:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 The energy content of finishing diets offered to feedlot cattle may vary across countries. We assumed that the lower is the energy content of the finishing diet, the shorter can be the adaptation period to high-concentrate diets without negatively impacting rumen health while still improving feedlot performance. This study was designed to determine the effects of adaptation periods of 6, 9, 14 and 21 days on feedlot performance, feeding behaviour, blood gas profile, carcass characteristics and rumen morphometrics of Nellore cattle. The experiment was designed as a completely randomised block, replicated 6 times, in which 96 20-month-old yearling Nellore bulls (391.1 ± 30.9 kg) were fed in 24 pens (4 animals/pen) according to the adaptation period adopted: 6, 9, 14 or 21 days. The adaptation diets contained 70%, 75% and 80.5% concentrate, and the finishing diet contained 86% concentrate. After adaptation, one animal per pen was slaughtered (n = 24) for rumen morphometric evaluations and the remaining 72 animals were harvested after 88 days on feed. Orthogonal contrasts were used to assess linear, quadratic and cubic relationships between days of adaptation and the dependent variable. Overall, as days of adaptation increased, final BW (P = 0.06), average daily gain (ADG) (P = 0.07), hot carcass weight (P = 0.04) and gain to feed ratio (G: F) (P = 0.07) were affected quadratically, in which yearling bulls adapted by 14 days presented greater final BW, ADG, hot carcass weight and improved G: F. No significant (P > 0.10) days of adaptation effect was observed for any of feeding behaviour variables. As days of adaptation increased, the absorptive surface area of the rumen was affected cubically, where yearling bulls adapted by 14 days presented greater absorptive surface area (P = 0.03). Thus, Nellore yearling bulls should be adapted by 14 days because it led to improved feedlot performance and greater development of rumen epithelium without increasing rumenitis scores. School of Veterinary Medicine and Animal Science São Paulo State University (UNESP) College of Agricultural and Technological Sciences São Paulo State University (UNESP) School of Veterinary Medicine and Animal Science São Paulo State University (UNESP) College of Agricultural and Technological Sciences São Paulo State University (UNESP)

Made available in DSpace on 2020-12-12T02:26:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação para o Desenvolvimento da UNESP (FUNDUNESP) Universidade Estadual Paulista The aim of this research was to evaluate the effect of recombinant bovine somatotropin (bST) on pregnancy per artificial insemination (P/AI), cellular composition of the corpus luteum (CL) and endometrial gland morphometry. In Experiment 1, Nelore cows (n = 587) received a fixed-time artificial insemination (FTAI) protocol and, at insemination, received 0, 250 or 500 mg of bST subcutaneously (SC). In Experiment 2, Nelore cows (n = 243) received 0 or 500 mg of bST, SC, on D7 (D0 = day of FTAI). Blood samples were collected on D7 and D16 to measure progesterone (P4) concentrations. In Experiments 1 and 2, pregnancy diagnosis was performed 30 days after FTAI. In Experiment 3, Nelore heifers (n = 20) received a FTAI protocol, but were not inseminated, and on D0 (ovulation day), they received 0 (bST 0; n = 9) or 500 mg of bST (bST 500; n = 11), SC. The heifers were slaughtered on D15 (D0 = ovulation day), at which time the CL was evaluated for diameter, weight, a percentage of large (LLC) and small (SLC) luteal cells, and the concentration of progesterone in plasma measured. The number, perimeter and area of superficial and deep endometrial glands were evaluated. There was no difference in P/AI when bST was applied on D0 and D7. In Experiment 1, P/AI did not differ among treatments, with 59.28% (115/194), 58.38% (115/197) and 65.82% (129/196) for the bST 0, 250 and 500 treatments, respectively. In Experiment 2, P/AI did not differ between treatments, with 57.3% (71/124) and 60.5% (62/119) for the bST 0 and 500 treatments, respectively. Plasma progesterone concentrations on D16 was greater in the bST 500 (11.63 ± 0.84 ng/mL) than bST 0 (9.83 ± 0.88 ng/mL). In Experiment 3, there was no difference in ovarian diameter and weight, CL diameter, percentage of SLC, P4 concentrations and endometrial gland morphology. Heifers in the bST 500 treatment had heavier CL (3.11 ± 0.32 vs. 2.25 ± 0.20 g); however, the bST 0 treatment heifers had a greater percentage of LLC than did the bST 500 treatment (13.72 ± 1.16% vs. 8.60 ± 1.52). It was concluded that the doses of bST used in this study do not increase P/AI; however, they do cause changes in P4 concentration and the cellular composition of the CL. São Paulo State University - UNESP University of Florida North Florida Research & Education Center Institute of Food and Agricultural Sciences University of São Paulo RG Advanced Genetics University of São Paulo West São Paulo State University - UNESP

A Produção in vitro de embriões (PIVE) depende das etapas de maturação, fertilização e cultivo in vitro, sendo a maturação a etapa decisiva para o oócito atingir o estádio de mórula e blastocisto. Neste trabalho objetivou-se avaliar a qualidade de maturação in vitro, de acordo com a distribuição mitocondrial de oócitos provenientes de ovários de fêmeas de abatedouro, com baixa ou alta contagem de folículos antrais (CFA). Foram aspirados 243 ovários dos quais selecionou-se 334 oócitos perante de cinco repetições para cada grupo. Os ovários foram separados em dois grupos: 1- baixa CFA (n=19), 2- alta CFA (n= 53) e os oócitos recuperados corados com a sonda MitoTracker Red. Os dados obtidos foram analisados pelo teste não paramétrico exato de Fisher (α=5%) mediante o software Statistical Analysis System for Windows (SAS Inst., Inc., Cary, NC). Em relação a localização das mitocôndrias o presente trabalho apresentou diferenças (p

Simple Summary After a brief introduction establishing the importance of parturition and the establishment of the mother-young bond, this review summarizes knowledge on the maternal behavior of Zebu type cows, including maternal and young behavioral patterns, the protective behavior of the mother and how maternal behavior might be influenced by experience and weather conditions. In addition, the effect of some nutrition, heat stress, calf presence around parturition and its effects on cattle reproductive performance, welfare issues on reproductive behavior and calf performance are reviewed. Finally, some conclusions and practical implications are established. Abstract The behaviors associated with domestic cattle such as maternal care are quite similar to those behaviors observed in wild ungulates. These behaviors allow the cow to bond with her calf, protect and provide it with nourishment and ultimately reduce the bond at weaning. Although maternal behavior is an important factor influencing the survival and early development of the newborn calf, Zebu type cows around calving have not been studied extensively. Herein, we consider the four main aspects of maternal behavior in cattle and particularly Bos indicus cows and calves. Firstly, we provide a brief description of the behavior of cows around parturition and the behavior of the first stages of the calves’ lives. In the second part, the protective behavior of the mother is analyzed. Subsequently, examples of animal welfare implications followed by an analysis of some factors that affect calf survival, including mother experience and weather conditions, are discussed, and in the last part, reproduction along with some peculiarities of reproductive behavior, and the wellbeing of mother and calves are examined. We concluded that knowledge of maternal behavior of Zebu type cows around calving and interactions with calves might contribute to an enhanced reproductive efficiency of the mother and the welfare of the calf.

This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne. RESUMO: Os objetivos deste estudo foram analisar o pedigree (41.521 registros de 1958 a 2019) da raça Sardo Negro para avaliar a estrutura, evolução e variabilidade genética (VG) da população. Os parâmetros genéticos populacionais utilizados foram: número efetivo de fundadores (fe) e ancestrais (fa); integridade do pedigree; relação genética aditiva (RGA); número de gerações completas (NGC), máximo plotado (NGT) e equivalentes (NGE); tamanho efetivo (Ne); consanguinidade (F); intervalo geracional (IG). O IG médio foi de 7,45 anos. Foram identificados 7.804 fundadores e 4.856 ancestrais, para fe 185 e 97 na fa. As médias e máximas para NGC, NGE e NGT foram 1,6 e 5,0, 2,5 e 6,5, 4,3 e 12, com estimativas de Ne 15,9, 25,9 e 69,0, respectivamente. O aumento de F, vinculado ao Ne, ficou na faixa de 0,72% a 3,1% por geração. A média para F 3,6% e 1,0% em RGA; a proporção de consanguíneos foi de 32,0%, com F na faixa de 0,01 a 62,2% e média de 11,3%. A taxa da população consanguínea foi de 1,3% ao ano. No RGA, a taxa ao ano era de 0,04%. Para a continuidade e projeção da raça, deve-se considerar a evolução de F em função de Ne e as possíveis implicações dos esquemas de seleção. A variabilidade genética sustentada ao longo do tempo resulta do Ne.

Made available in DSpace on 2022-04-28T17:30:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-10-26 Nutricorp This experiment evaluated the effects of feeding whole cottonseed (WC) and/or calcium salts of fatty acids (CSFA) on dry matter intake (DMI), performance, and carcass characteristics of Bos indicus animals receiving a high-concentrate diet during the finishing phase. On day 0, 96 Nellore bulls were blocked according to initial shrunk body weight (BW; 302 +/- 26.7 kg) into group pens (four animals/pen) and, within blocks, pens were randomly assigned to receive: 1) 15% of WC and 2% of CSFA (dry matter [DM] basis) of palm, cottonseed, and soybean oil (15WC; n = 6); 2) 10% of WC and 3% of CSFA (DM basis) of palm, cottonseed, and soybean oil (10WC; n = 6); 3) 5% of WC and 4% of CSFA (DM basis) of palm, cottonseed, and soybean oil (5WC; n = 6); and 4) 0% of WC and 5% of CSFA (DM basis) of palm, cottonseed, and soybean oil (0WC; n = 6). Diets were formulated to be isocaloric, isonitrogenous, and isolipidic. Experimental period lasted 108 d; DMI was evaluated daily, whereas blood samples and carcass measurements were obtained on days 0, 55, and 108 of the study. Upon slaughter on day 109, steaks were collected for determination of the chemical and fatty acid (FA) profile of the meat. No treatment effects (P >= 0.35) were observed on DMI, performance, average daily gain (ADG), carcass ultrasound measurements, and chemical variables of the steak. Nonetheless, including WC into the diets decreased C12:0, C16:0, C16:1 trans-9, C17:0, C18:0, C18:1 cis-9, C18:2 cis-9, cis-12, C18:3 cis-9, cis-12, cis-15, saturated, and unsaturated FA intake (P < 0.01). Moreover, adding WC increased DMI fluctuation and feed efficiency (FE; P = 0.03) but decreased marbling (P

Background Metabolic profile evaluation is a tool widely used in ruminant nutrition as metabolic cues that relate nutrition to physiology. Metabolic and hormonal traits change during pre-partum and lactation according to parity in dairy cows, but studies of beef cows under grazing are scarce. The present study aimed to evaluate how metabolic and hormonal traits change over time, their relationship to performance, and determine if these factors differ according to the parity order of grazing beef cows. Thirty-six pregnant Nellore cows (12 nulliparous, 12 primiparous, and 12 multiparous) were used. The study started at 60 d prepartum until 203 d of lactation. Results The initial body weight (BW) and final BW were higher for multiparous cows (P > 0.05). An interaction occurred between parity and day (P P P > 0.05). Calf BW, final BW, and average daily gain did not differ between parities (P > 0.05). Effect of day (P P P P > 0.05). Conclusions Hormonal and metabolic profile is strongly influenced by the stage of lactation. Time effects (pre-partum and lactation period) were more pronounced in nulliparous since they displayed more unbalanced metabolic and hormonal traits and lowered BCS pre- and postpartum.

Made available in DSpace on 2022-04-28T19:42:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-09-01 The objective was to evaluate meat quality of Rubia Gallega x Nelore (RGN) crossbred compared to Nelore (N) cattle, using mRNA analysis of calpain 1 and 2, calpastatin, myostatin, and TGFβ; and protein abundance profile post mortem based on aged beef of the different genetic groups. Sixteen N and 16 RGN were finished in feedlot by 120 days and harvested. RGN beef presented greater tenderness. Transcripts analysis showed increased levels of TGFβ and MSTN in RGN, indicating differences in muscle fiber formation. However, no difference was observed in mRNA for CAPN1, CAPN2 and CAST. Protein analysis demonstrated increased troponin-T degradation in RGN. Interaction for HSP 27 degradation was observed, indicating the degradation of this protein is faster and greater in RGN than N. No difference in myostatin protein abundance was found. In general, RGN cattle improves beef quality and these differences may be explained by TGFβ and MSTN gene expression, troponin-T degradation and HSP abundance. Faculty of Animal Science and Food Engineering – University of São Paulo USP Faculty of Veterinary Medicine and Animal Science – University of São Paulo USP Faculty of Agricultural and Veterinary Sciences – São Paulo State University UNESP Faculty of Agricultural and Veterinary Sciences – São Paulo State University UNESP

Made available in DSpace on 2022-05-01T07:58:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-09-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The objective of this study was to evaluate the effect of previous supplementation strategies (mineral and corn-based supplementation in the growing-phase) on intake and performance of different beef cattle group genotypes in the finishing phase on pasture or feedlot. Two experiments for the finishing phase were conducted simultaneously. For Exp.1, 60 bulls were finished on tropical grass with supplementation. They were distributed in a randomized block design in a 3 × 2 factorial arrangement (three genotypes (Nellore, Senepol x Nellore (½Senepol), Angus x Nellore (½Angus)) and two growing-phase supplementation strategies (mineral and corn-based supplementation)). They were allocated to 12 paddocks with 1.8 ha of Urochloa brizantha ‘Xaraes’ per paddock (5 animals/paddock). The animals were supplemented (corn-based supplement at the rate of 20 g/kg body weight [BW]) for 125 days. For Exp.2 60 bulls were finished in individual pens. They were of three genotypes (Nellore, ½Senepol, ½Angus) from two growing-phase supplementation strategies (mineral and corn-based supplementation) and distributed in a randomized block design allocated to individual pens. In Exp.1 (finish on tropical grass), the genotypes,½ Angus and Nellore bulls showed the greatest initial (end of growing phase treatments) and final body weights (BW), final carcass weight (HCW) and hot carcass yield (HCY) than ½ Senepol bulls. Bulls with corn-based supplementation in the growing phase had greater initial (end of growing phase) and final BW and lower feed efficiency (FE) than animal supplementation with mineral in the growing phase. ½Senepol showed higher total dry matter (DM, percentage of BW) and forage DM intake than Nellore in the finishing phase. For supplement DM intake, higher values were found for the ½ Angus bulls compare ½Senepol. Nellore bulls showed greater DM and OM digestibility than ½ Senepol but no different to ½ Angus. For experiment 2 (finish in feedlot), ½ Angus and ½ Senepol bulls had higher ADG than Nellore bulls. ½ Angus and Nellore bulls presented the greatest HCW while Nellore bulls had the highest HCY. Daily carcass gain (DCG) in the finishing phase was higher in animals that received only mineral supplementation during the growth phase. ½ Angus and ½ Senepol showed higher FE than Nellore bulls. Nellore bulls had lower DMI of forage and supplement than ½ Angus and ½ Senepol. ½ Angus and Nellore bulls had greater BW at the end of the finishing phase than ½ Senepol.The feedlot-finishing system promotes better finishing performance in ½ Angus and ½ Senepol, thus crossing Nellore with a Bos taurus breed may be a strategy to improve finishing performance and carcass characteristics. Corn-based supplement during the growing phase may be a strategy to improve body weight on entry to a finishing phase, although it may reduce carcass gain in the finishing phase. Department of Animal Science School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP) Centro de Investigación El NUS Corporación Colombiana de Investigación Agropecuaria AGROSAVIA ICAA – Instituto de Ciências Agrarias e Ambientais Instituto Nacional de Ciência e Tecnologia/Ciência Animal Conselho Nacional de Desenvolvimento Científico e Tecnológico Department of Animal Science School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP) CAPES: 001 FAPESP: 2015/01147-0 FAPESP: 2017/02034-0

BackgroundSpatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare.ResultsWe generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps.ConclusionsOur findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.

Made available in DSpace on 2022-04-29T08:32:10Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-08-02 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Feedlot cattle are usually adapted to high-concentrate diets containing sodium monensin (MON) in more than 14 days. However, for finishing diets with lower energy content, the use of MON during adaptation may hold dry matter intake (DMI), and virginiamycin (VM) may be an alternative. This study was designed to determine the potential of shortening the adaptation of Nellore cattle to high-concentrate diets using only VM as a sole feed additive relative to feedlot performance, feeding behavior, and ruminal and cecum morphometrics. The experiment was designed as a completely randomized block replicated six times (four animals/pen) in which 120 Nellore bulls (390.4 ± 19.0 kg) were fed in 30 pens for 111 days according to the following treatments: (1) MON and adaptation for 14 days (MON14), (2) MON + VM and adaptation for 14 days (MONVM14), (3) VM and adaptation for 14 days (VM14), (4) VM and adaptation for 9 days (VM9), and (5) VM and adaptation for 6 days (VM6). At the end of the adaptation, 30 animals (n = 1 per pen) were randomly slaughtered for rumen and cecum evaluations. The remaining 90 bulls were harvested at the end of the study. No effects of treatments were observed (P < 0.10) for final body weight, average daily gain (ADG), and hot carcass weight (HCW). Cattle fed VM14 presented a greater (P ≤ 0.03) DMI, expressed as percent of body weight (BW), than animals fed either MON14 or MONVM14; however, cattle fed either MON14 or MONVM14 improved (P ≤ 0.02) the gain-to-feed ratio (G/F) by 10.4 or 8.1%, respectively, when compared to bulls fed VM14. Bulls fed VM14 had smaller (P < 0.05) papillae area (0.34 vs. 0.42 cm2) and rumen absorptive surface area (28.9 vs. 33.8 cm2) than those fed MON14. The shortening of the adaptation period linearly decreased the 12th rib fat (P = 0.02) and biceps femoris fat daily gain (P = 0.02) of Nellore bulls fed only VM, which linearly decreased the final biceps femoris fat thickness (P < 0.01). Feedlot cattle fed VM as a sole feed additive should not be adapted to high-concentrate diets in less than 14 days. Regardless of either adaptation length or feed additive, feedlot cattle need at least 14 days to adapt to finishing diets. Department of Breeding and Animal Nutrition School of Veterinary Medicine and Animal Science São Paulo State University (UNESP) Department of Animal Production College of Agricultural and Technological Sciences São Paulo State University (UNESP) Department of Breeding and Animal Nutrition School of Veterinary Medicine and Animal Science São Paulo State University (UNESP) Department of Animal Production College of Agricultural and Technological Sciences São Paulo State University (UNESP)

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75–0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value &lt, 9.9 × 10−6 at FDR &lt, 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes—BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3—are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus–pituitary–ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide, however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. Made available in DSpace on 2021-08-17T12:02:54Z (GMT). No. of bitstreams: 1 MuscleAlleleSpecific.pdf: 13183203 bytes, checksum: a634e71a998500cd0f7dd0ad1e644846 (MD5) Previous issue date: 2021 Article number: 7321.

Objective Yunnan is not only a frontier zone that connects China with South and Southeast Asia, but also represents an admixture zone between taurine (Bos taurus) and zebu (Bos indicus) cattle. The purpose of this study is to understand the level of genomic diversity and the extent of admixture in each Yunnan native cattle breed. Methods All 120 individuals were genotyped using Illumina BovineHD BeadChip (777,962 single nucleotide polymorphisms [SNPs]). Quality control and genomic diversity indexes were calculated using PLINK software. The principal component analysis (PCA) was assessed using SMARTPCA program implemented in EIGENSOFT software. The ADMIXTURE software was used to reveal admixture patterns among breeds. Results A total of 604,630 SNPs was obtained after quality control procedures. Among six breeds, the highest level of mean heterozygosity was found in Zhaotong cattle from Northeastern Yunnan, whereas the lowest level of heterozygosity was detected in Dehong humped cattle from Western Yunnan. The PCA based on a pruned dataset of 233,788 SNPs clearly separated Dehong humped cattle (supposed to be a pure zebu breed) from other five breeds. The admixture analysis further revealed two clusters (K = 2 with the lowest cross validation error), corresponding to taurine and zebu cattle lineages. All six breeds except for Dehong humped cattle showed different degrees of admixture between taurine and zebu cattle. As expected, Dehong humped cattle showed no signature of taurine cattle influence. Conclusion Overall, considerable genomic diversity was found in six Yunnan native cattle breeds except for Dehong humped cattle from Western Yunnan. Dehong humped cattle is a pure zebu breed, while other five breeds had admixed origins with different extents of admixture between taurine and zebu cattle. Such admixture by crossbreeding between zebu and taurine cattle facilitated the spread of zebu cattle from tropical and subtropical regions to other highland regions in Yunnan.

Per capita meat consumption in Chile is 89.1 kg per year in 2014, of which approximately 25 kg are beef. Some 50% of the beef consumed is imported as vacuum packaged meat from two species, Bos taurus, produced mainly in Chile, Argentina and Paraguay, and Bos indicus, which comes mainly from Brazil and Paraguay. The latter two countries account for the highest levels of beef imports in Chile. The objective of this investigation was to study and compare the fatty acid profiles of beef from Bos Taurus from Chile and Bos indicus from Paraguay and Brazil. Samples of vacuum packaged Longissimus dorsi muscle tissue were collected from private companies, two Chilean, three Paraguayan and two Brazilian. The fatty acid profiles were determined by GLC according to standardized regulations. There were differences in the fat profiles of the analyzed meats, mainly in the content of saturated and monounsaturated fatty acids. Brazilian and Paraguayan beef had similar fat compositions, with higher saturated fat content and lower monounsaturated fat content than the Chilean beef. The saturated and monounsaturated fat contents in the Chilean beef were similar. All the analyzed beef samples had a low content of trans and polyunsaturated fats.

Crossbreeding represents an important technique to improve growth, beef quality and adaptability in beef production systems in tropical countries. The aim of this study was to evaluate sire and dam breed effects on performance and carcass traits of crossbred cattle produced in a tropical environment. Heifers and steers were evaluated during the pre-weaning, the post-weaning (n = 173) and the finishing phase (n = 123). Animals were produced by mating Nellore (N_N), Angus × Nellore (A_N) and Caracu × Nellore (C_N) dams with Braford, Charbray and Caracu sires. After weaning, animals were raised grazing on Marandu grass for 12 months; thereafter they were housed in individual pens and finished in a feedlot, receiving a total mixed ration. Ultrasound carcass evaluations were performed to determine ribeye area (R_A), backfat thickness (B_T) and rump fat thickness (R_T). A_N progeny were heavier at birth than N_N (P < 0.05), and Braford progeny had greater birth BW than Caracu (P < 0.05). Greater weaning BW was observed in the A_N and C_N offspring compared to N_N (P < 0.01). Greater average daily gain during the post-weaning period was verified in the N_N progeny compared to C_N (P < 0.05). No dam or sire breed effects were observed for BW at the end of the post-weaning period (P > 0.05). Progeny of N_N cows had greater B_T (P < 0.05) and R_T (P < 0.01) at the end of the post-weaning period in relation to C_N. Greater R_A was observed in the Caracu progeny than in the Braford (P < 0.05), which showed greater R_T than the Charbray progeny at the end of the post-weaning period (P < 0.05). No dam or sire breed effects were verified for final BW at the feedlot or for feed efficiency traits (P > 0.05). A_N progeny were superior in final B_T compared to C_N (P < 0.01), and Braford progeny had greater R_T at the end of finishing than Charbray (P = 0.05). The use of crossbred dams allows an increase in productivity until weaning, but this is not maintained in the post-weaning and finishing periods. The use of Braford sires produces similar growth performance in the different stages of the production system to those seen with Charbray and Caracu sires but generates animals with higher fat thickness at the end of finishing, which may improve carcass quality and commercial value. Made available in DSpace on 2020-01-23T18:06:21Z (GMT). No. of bitstreams: 1 Crossbreedingappliedtosystemsofbeefcattle.pdf: 160676 bytes, checksum: 8974b11d5875715b99317c0649935e93 (MD5) Previous issue date: 2019

Kazakhstan is the largest landlocked country and contains two important propagation routes for livestock from the Fertile Crescent to Asia. Therefore, genetic information about Kazakhstani cattle can be important for understanding the propagation history and the genetic admixture in Central Asian cattle. In the present study, we analyzed the complete mtDNA D-loop sequence and SRY gene polymorphism in 122 Kazakhstani native cattle. The D-loop sequences revealed 79 mitochondrial haplotypes, with the major haplogroups T and I. The Bos taurus subhaplogroups consisted of T (3.3%), T1 (2.5%), T2 (2.5%), and T4 (0.8%) in addition to the predominant subhaplogroup T3 (86.9%), and the Bos indicus subhaplogroup of I1 (4.1%). Subsequently, we investigated the paternal lineages of Bos taurus and Bos indicus, however, all Kazakhstani cattle were shown to have Y chromosome of Bos taurus origin. While highly divergent mtDNA subhaplogroups in Kazakhstani cattle could be due to the geographical proximity of Kazakhstan with the domestication center of the Fertile Crescent, the absence of Bos indicus Y chromosomes could be explained by a decoupling of the introgression dynamics of maternal and paternal lineages. This genetic information would contribute to understanding the genetic diversity and propagation history of cattle in Central Asia.

The mitigation of enteric methane emission in beef cattle production is important for reducing feed energy loss and increasing environmental sustainability. The main objective of this study was to evaluate the effect of different oilseeds included in fermented total mixed rations (whole soyabean seed (SBS, control), whole kapok seed (KPS) and cracked oil palm fruit (OPF)) on feed intake, digestibility, rumen microbial populations, energy partition and methane emissions in different cattle genotypes (Charolais crossbred v. Japanese Black crossbred). Three Charolais crossbred and three Japanese Black crossbred bulls were studied in a replicated 3×3 Latin square experimental design; genotypes were analysed in separate squares including three periods of 21 days each and three dietary oilseed treatments fed ad libitum. The cattle were placed in a metabolic cage equipped with a ventilated head box respiration system for evaluating digestibility and energy balance. As compared with Charolais crossbred individuals, Japanese Black crossbred bulls showed consistently lower dry matter intake (15.5%, P0.05) or diet (P>0.05) under the experimental conditions and ranged from 5.8% to 6.0% of gross energy intake. This value is lower than that reported by the Intergovernmental Panel on Climate Change (6.5%) for cattle fed with low-quality crop residues or by-products. Thus, our results imply that the Japanese Black crossbred cattle consume less feed and emits less enteric methane than the Charolais crossbred does, mainly owing to its lower ME requirement for maintenance. The OPF diet could be used to replace SBS for high beef production, although further studies are required to evaluate their application across a wide range of beef production systems.

Made available in DSpace on 2021-06-25T10:27:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-04-01 This study was carried out to evaluate the effects of selection criteria for post-weaning daily gain (PWDG) and early sexual heifer precocity (PP14) on the performance, carcass traits and meat quality of Nellore bulls. In year one, 50 animals were selected according to their expected progeny differences (EPDs) for PWDG and grouped as high (HG) or low (LG) groups. In year two, 50 animals were selected according to EPD for PP14 and also grouped as high (HP) or low (LP). After slaughter, samples of the longissimus muscle area (LMA) were used to evaluate meat quality. Most of performance traits were not affected by the selection criteria. However, the HG group had higher dressing percentage (ρ = 0.028), LMA (ρ = 0.02) and fat trim in the forequarter (ρ = 0.04) compared to the LG group. The HP group tended to have greater dry matter intake (ρ = 0.08), LMA (ρ = 0.05), rump fat (ρ = 0.04), heavier striploins (ρ = 0.07), tenderloins (ρ = 0.09) and briskets (ρ = 0.08) compared with LP group. In conclusion, the selection based on divergent groups PWDG or PP14 has a small impact on performance, carcass and meat quality traits. Department of Animal Science University of São Paulo, Duque de Caxias Norte 225 Department of Animal Nutrition and Production Universidade de São Paulo, Duque de Caxias Norte 225 Department of Animal and Poultry Sciences Virginia Polytechnic Institute and State University, 3480 Litton-Reaves Hall Department of Animal Science São Paulo State University (UNESP) AgResearch Grasslands Research Centre, Tennent Drive, 11 Dairy Farm Rd Department of Animal Science São Paulo State University (UNESP)

Made available in DSpace on 2021-06-26T04:30:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The supply of wet distillers grains (WDG) has been growing in Brazil, with the increase in corn ethanol production. However, little is known about de-oiled corn WDG on nutrient digestibility, ruminal fermentation and microbiology of beef cattle. Thus, the aim of the study was to evaluate the effects of the increasing levels of de oiled WDG replacing soybean meal and corn on dry matter (DM) intake, total tract digestibility, ruminal short chain fatty acids and microbiology. Eight ruminally cannulated Nellore bulls (BW = 453 ? 32 kg) were allocated on individual pens and distributed in 4 treatments with 0, 150, 300 and 450 g de-oiled WDG/kg DM in a 4 ? 4 replicated Latin square design. The experimental period lasted 112 days, divided into 4 periods of 28 days (14 days of adaptation plus 14 days of sampling). The DM, organic matter and ether extract intake increased quadratically (P < 0.05), and were greater in animals fed 300 g/kg WDG. Intake and digestibility of crude protein and neutral detergent fiber increased, however, intake and digestibility of non-fiber carbohydrates decreased linearly (P< 0.05) with increasing levels of de-oiled WDG.Gross energy (GE) and digestible energy (DE) intake were quadratically affected by the treatments, whereby animals fed 300 g/kg WDG in the diet showed greater (P < 0.05) GE and DE intake. Moreover, propionate and butyrate concentration increased linearly (P< 0.05) in animals fed de-oiled WDG, which could be associated to greater (P< 0.10) relative abundance of Selonomonas ruminantium, resulting in higher ruminal pH in these animals. Therefore, the inclusion of de-oiled WDG might be used as replacement of soybean meal and ground corn in high concentrate diets of Nellore cattle without compromising ruminal fermentation and nutrient digestibility. Sao Paulo State Univ, Sch Vet Med & Anim Sci, BR-18610307 Botucatu, SP, Brazil Sao Paulo State Univ, Sch Agr & Veterinarian Sci, BR-14884900 Jaboticabal, SP, Brazil Univ Fed Triangulo Mineiro, R-38280000 Iturama, MG, Brazil Sao Paulo State Univ, Sch Vet Med & Anim Sci, BR-18610307 Botucatu, SP, Brazil Sao Paulo State Univ, Sch Agr & Veterinarian Sci, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2016/04478-0 FAPESP: 2017/21354-6 FAPESP: 2018/09731-1

Made available in DSpace on 2021-06-25T10:50:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-01 The objective of this study was to identify genomic regions associated with beef fatty acid (FA) profile in Nellore cattle finished in feedlot, using haplotype based analyzes. Also, the metabolic pathway enrichment analysis was performed to seek for genes with known functions, close to the haplotype blocks, associated with the evaluated traits, providing subsidies for a better understanding of how the genes affect this trait. A total of 963 Nellore bulls with phenotype for FA, were genotyped using the Illumina BovineHD BeadChip. Samples from the Longissimus thoracis muscle were taken for FAs profile measurement by gas chromatography using a SP-2560 capillary column. Haplotype blocks were defined based on the linkage disequilibrium (LD), where pairs of SNPs are in strong LD if the confidence interval is equal to or greater than 95% with D’ equal to 0.98 and the lower limit is above 0.70. The model used to estimate the haplotypes effects for the sum of beef fatty acid groups included the fixed effects of contemporary group, animal age at slaughter (as linear covariable), haplotypes (as linear regression over the number of haplotype copies: 0, 1 e 2), and the additive genetic effect as random (polygenic effect). Genome-wide association analyzes were performed for each haplotype block (single marker association) by a Restricted Maximum Likelihood model (REML) using ASREML v. 4.3 software. A total of 15, 15, 4, 3, 6, 5, and 10 haplotypes were significantly associated (FDR< 0.10) with monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), total amount of saturated fatty acids (SFA), PUFA:SFA ratio, omega 3 (n3), omega 6 (n6), and n6:n3 ratio, respectively. The statistically significant haplotypes harbored 38 genes, among which we highlighted those involved in lipid biosynthesis and metabolism, low-density lipoprotein oxidation, transport of fatty acids and cholesterol, adipocyte functions, biosynthesis of glycoprotein hormones, regulation of serum triglyceride and high-density lipoprotein-cholesterol levels, and adipogenesis. In addition, several novel regions were identified, including a putative quantitative trait locus for lipid metabolism and energy homeostasis. The enrichment analysis by DAVID tool revealed 14 significant (P< 0.05) terms related to fatty acids such as cellular response to retinoic acid, glycerol transport, regulation of Notch signaling pathway, and Ras signaling pathway. These results would contribute to the improvement of nutritional and health value of beef lipids in indicine cattle by including information from causal mutations in genetic evaluation through weighted their effects differently in genomic predictions. Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista Julio de Mesquita Filho (UNESP) Departamento de Nutrição e Produção Animal Faculdade de Medicina Veterinária e Zootecnia Universidade de São Paulo (USP) Department of Animal Biosciences Centre for Genetic Improvement of Livestock University of Guelph Department of Animal and Poultry Science Centre for Genetic Improvement of Livestock University of Guelph Departament of Animal Science University of Purdue Centro de Pesquisa em Bovinos de Corte Instituto de Zootecnia (IZ), Rodovia Carlos Tonanni km 94 Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista Julio de Mesquita Filho (UNESP)

Variability in the production of bovine blastocysts per session of ultrasound-guided follicularaspiration(OPU) is still an obstacle in commercial production.Thus, the objective of the current work was to verify factors that influence in vitro embryo production (PIVE), using data from a commercial laboratory.Data from 2014 to 2016 were analyzed, referring to 799 OPU sessions of adult bovine females of the breeds: Nelore (n=83), Girolando (n=73), Brangus (n=49), HPB (n=20), and Senepol (n=10).The influence of five variables was analyzed: breed, genetic group, frequency of aspiration, type of semen (sexed/conventional), and seasonality (spring/summer vs. autumn/winter) on the rate of viable oocytes, cleavage, and blastocyst production (bl).The protocols for the in vitroproduction of embryos (IVP) followed the routine established by the partner laboratory of the present study. The statistical analysis of the data was performed using SAS, with the Chi-square test.The Girolando and Nelore breeds had a higher (p=0.0001) number of blastocysts/OPU session, as well as the Bos indicus blood group.Blastocyst production was higher (p=0.0059) with sexed semen compared to conventional semen (6.6 x 5.2 bl/OPU session); a higher frequency of aspirations also increased (p=0.005) the number of bl/OPU session (7.7 x 5.9).We conclude that the in vitro production of bovine embryos is influenced by the analyzed factors and knowledge of these variables could guide the commercial use of OPU-PIVE. La variabilidad en la producción de blastocistos bovinos por sesión de aspiración folicular guiada por ultrasonido (OPU) sigue siendo un obstáculo en la producción comercial. Así, el objetivo fue verificar los factores que influyen en la producción de embriones in vitro (PIVE), utilizando datos de un laboratorio comercial. Se analizaron datos del año 2014 al 2016, referidos a 799 sesiones de OPU de hembras bovinas adultas de las razas: Nellore (n = 83), Girolando (n = 73), Brangus (n = 49), HPB (n = 20) y Senepol (n = 10). Se analizó la influencia de cinco variables: raza, grupo genético, frecuencia de aspiración, tipo de semen (sexado / convencional) y estacionalidad (primavera / verano vs otoño / invierno) sobre la tasa de ovocitos viables, clivaje y producción de blastocistos (licenciado en Derecho). Los protocolos para la producción de embriones in vitro (PIV) siguieron la rutina establecida por el laboratorio socio del presente estudio. El análisis estadístico de los datos se realizó mediante el SAS, mediante la prueba de Chi-cuadrado. Las razas Girolando y Nelore tuvieron un mayor número (p = 0,0001) de sesiones de blastocistos / OPU, así como el grupo sanguíneo Bos indicus. La producción de blastocistos fue mayor (p = 0,0059) con semen sexado en comparación con el semen convencional (6,6 x 5,2 bl / sesión de OPU); la mayor frecuencia de aspiraciones también aumentó (p = 0,005) el número de sesiones bl / OPU (7,7 x 5,9). Concluimos que la producción in vitro de embriones bovinos está influenciada por los factores analizados y conocer estas variables puede orientar el uso comercial de OPU-PIVE. A variabilidade na produção de blastocisto bovinos por sessão de aspiração folicular guiada por ultrassom (OPU) ainda é um entrave na produção comercial. Assim,objetivou-se verificar os fatores que influenciam a produção de embrião in vitro(PIVE), utilizando dados de um laboratório comercial. Foram analisados dados do ano de 2014 a 2016, referentes a 799 sessões de OPU de fêmeas bovinas adultas das raças: Nelore (n=83), Girolando (n=73), Brangus (n=49), HPB (n=20) e Senepol (n=10). Analisou-se a influência de cinco variáveis: raça, grupamento genético, frequência de aspiração, tipo de sêmen (sexado/convencional) e sazonalidade (primavera/verão vs outono/inverno) sobre a taxa de oócitos viáveis, clivagem e produção de blastocisto (bl). Os protocolos para a produção de embriões in vitro (PIV)seguiram a rotina estabelecida pelo laboratório parceiro do presente estudo. A análise estatística dos dados foi realizada utilizado o SAS, empregando-se o Teste Qui-quadrado. As raças Girolando e Nelore apresentaram maior (p=0,0001) número de blastocisto/sessão de OPU, assim como o grupamento sanguíneo Bosindicus. A produção de blastocisto foimaior (p=0,0059) com sêmen sexado em relação ao convencional (6,6 x 5,2 bl/sessão OPU); a frequência maior de aspirações também elevou (p=0,005) o número de bl/sessão OPU (7,7 x 5,9). Concluímos que a produção in vitro de embriões bovinos é influenciada pelos fatores analisados e conhecer estas variáveis pode nortear o emprego comercial da OPU-PIVE.

Machine learning (ML) methods have shown promising results in identifying genes when applied to large transcriptome datasets. However, no attempt has been made to compare the performance of combining different ML methods together in the prediction of high feed efficiency (HFE) and low feed efficiency (LFE) animals. In this study, using RNA sequencing data of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle, and pituitary) from nine HFE and nine LFE Nellore bulls, we evaluated the prediction accuracies of five analytical methods in classifying FE animals. These included two conventional methods for differential gene expression (DGE) analysis (t-test and edgeR) as benchmarks, and three ML methods: Random Forests (RFs), Extreme Gradient Boosting (XGBoost), and combination of both RF and XGBoost (RX). Utility of a subset of candidate genes selected from each method for classification of FE animals was assessed by support vector machine (SVM). Among all methods, the smallest subsets of genes (117) identified by RX outperformed those chosen by t-test, edgeR, RF, or XGBoost in classification accuracy of animals. Gene co-expression network analysis confirmed the interactivity existing among these genes and their relevance within the network related to their prediction ranking based on ML. The results demonstrate a great potential for applying a combination of ML methods to large transcriptome datasets to identify biologically important genes for accurately classifying FE animals.

Reliably identifying breed proportions in crossbred cattle in smallholder farms is a crucial step to improve mating decisions and optimizing management in these systems. High‐density genotype information is able to estimate higher‐order breed proportions accurately, but, are too expensive for mass application in smallholder systems. We used high‐density genotype information (777 k SNPs) of 623 crossbred cattle from India that had Holstein‐Friesian (HFX) and/or Jersey and indigenous breeds in their ancestry to select a smaller number of SNPs for breed proportion estimation. The accuracy of estimates obtained from panels with 100–500 SNP was compared to estimates based on all SNPs. Panels were selected for highest absolute allele frequency difference between exotic dairy versus indigenous Bos indicus, or between HFX versus Jersey breeds. A step‐wise pruning approach was developed showing that and increased physical distances between markers of 8.5 Mb improved breed proportion estimation compared to a standard 1 Mb distance. A panel of 500 SNPs optimized to estimate HFX versus Jersey versus indicine ancestry was able to estimate indicine breed proportions with r 2 = .991, HFX proportions with r 2 = .979 and Jersey proportions with r 2 = .949. The number of markers was a deciding factor in estimation accuracy, together with the distribution of markers across the genome.

Made available in DSpace on 2021-06-25T11:17:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-01 Dental classification of carcasses is used as a parameter of cattle maturity at slaughter, and it can influence carcass and meat quality traits. Brazilian beef-packing companies use the number of permanent incisor (PI) teeth as a parameter for bonus and certification of carcasses with superior quality. However, when non-castrated male such as F1 Angus-Nellore (Bos taurus×Bos indicus) are slaughtered, only animals without PI teeth are subsidized by the breed association. We evaluated these animals finished in feedlot for 180 days with zero versus two PI teeth on the carcass and meat quality traits. At the time of slaughter, 88 carcasses were selected, forming two treatments according to dental carcass maturity (0 versus 2 PI teeth; 44 animals per category). It was demonstrated that the number of PI teeth (0 versus 2 PI) did not influence (p>0.05) carcass (weights, yield, cooling loss, ribeye area and the backfat thickness) and meat quality traits (Longissimus thoracis chemical composition, color, cooking losses, shear force and pH). Thus, dental carcass maturity (zero versus two PI teeth) does not influence non-castrated male F1 Angus-Nellore finished in feedlot for 180 days. This is the first study to demonstrate that carcasses of non-castrated male F1 Angus-Nellore with two PI teeth should be subsidized in a similar way to those with zero PI teeth. Moreover, Brazilian beef-packing companies could produce heavier and leaner carcasses of acceptable quality though the use of crossbred cattle such as non-castrated F1 Angus Nellore. School of Agricultural and Veterinarian Sciences São Paulo State University (FCAV UNESP) College of Veterinary Medicine and Animal Science São Paulo State University (FMVZ UNESP) School of Agricultural and Veterinarian Sciences São Paulo State University (FCAV UNESP) College of Veterinary Medicine and Animal Science São Paulo State University (FMVZ UNESP)

Made available in DSpace on 2021-06-25T10:10:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) This study investigated the effects of growth rates and compensatory growth on puberty attainment in Nellore heifers. Nellore heifers (n = 120), weaned at 8 ± 0.75 mo of age, were blocked by sire and BW (180 ± 8.6 kg) and assigned randomly to receive 1 of 4 treatments over a 10-mo period. Treatments included ad libitum feeding (high gain, HG), feed intake to gain 0.6 kg/d (medium gain, MG), restricted feeding (0.2 kg/d) for 4 mo followed by ad libitum feeding for 6 mo (compensatory gain, CG), and alternating periods of ad libitum and restricted feeding for 2 mo each throughout the trial (alternated CG, ACG). Puberty was assessed weekly by transrectal ultrasonography. Blood samples were collected at 8, 11, and 18 mo of age and at puberty to determine circulating concentrations of leptin. At 18 mo of age, nonpubertal heifers were treated with a puberty induction protocol using an intravaginal progestin device. There was no treatment effect (P = 0.17) on the percentage of heifers pubertal by 18 mo of age (HG: 66, MG: 40, CG: 58, and ACG: 52%), BW at puberty, and age at puberty. However, HG heifers had higher ADG (P < 0.01), dry matter intake (P < 0.01), and leptin concentrations (P = 0.03) than heifers from other groups. The response to the puberty induction protocol was similar (P = 0.90) among treatments. Regarding sire effects (genetic effects), there was an effect (P = 0.03) on the percentage of heifers pubertal by 18 mo of age and a tendency (P = 0.07) of sire effect in response to the puberty induction protocol. Compensatory growth appears to be an effective managerial approach to decrease feeding costs and stimulate puberty in Nellore heifers. Department of Nutrition and Animal Production College of Veterinary and Animal Science University of São Paulo, Duque de Caxias North Avenue, n 225 Department of Animal Science Federal University of Amazonas, Macurany Avenue, Jacareacanga Department of Animal Science Texas A&M University, 2471 TAMU Department of Animal Science College of Agriculture “Luiz de Queiroz” University of São Paulo, Pádua Dias Avenue, n 11, PO Box 09 College of Veterinary Medicine São Paulo State University (UNESP) College of Veterinary Medicine São Paulo State University (UNESP)

Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Made available in DSpace on 2022-04-28T19:41:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Context: Livestock feed costs have a higher impact on the profitability of beef production systems and are directly related to feed efficiency. However, these traits are hard and have high costs to measure, reducing the availability of phenotypic records and reliability of genetic evaluations. Thus, the use of genomic information can increase the robustness of genetic studies that address them. Aims: The aim of the present study was to estimate genetic parameters for feed efficiency, growth, reproductive and carcass traits in Nelore cattle and the correlated response among them, using genomic information. Methods: Residual feed intake (RFI), dry-matter intake, feed conversion ratio, feed efficiency (FE), residual average daily gain (RG), residual feed intake and average daily gain (RIG), birthweight, weight at 120, 240, 365 and 450 days of age, scrotal circumference at 365 and 450 days of age, rib-eye area, backfat thickness and rump fat thickness were evaluated. The genetic parameters were estimated using the single-step genomic best linear unbiased prediction approach. Key results: The FE-related traits showed low to moderate heritability ranging from 0.07 to 0.23. Feed efficiency-related traits showed low genetic correlations with reproductive (-0.24 to 0.27), carcass (-0.17 to 0.27) and growth (-0.19 to 0.24) traits, except for growth with dry-matter intake (0.32-0.56) and weight at 365 days of age with FE (-0.40). Conclusions: The selection to improve growth, reproductive and carcass traits would not change RFI, RG and RIG. The choice of the most adequate selection criterion depends on the production system, that is, RFI might be used for low-input beef cattle systems, and RIG would be used for more intensive and without-any-dietary-restrictions beef cattle systems. Implications: The estimates of heritability and genetic correlations suggest that genetic selection for feed efficiency using RFI, RG and RIG in Nellore cattle leads to higher genetic gain than does that using FE and feed conversion ratio without affecting other profitability traits. Department of Animal Science Federal University of Goiás (UFG) Embrapa Rice and Beans Department of Animal Science São Paulo State University (UNESP) Cobb-Vantress Inc. 72761 National Association of Breeders and Researchers (ANCP) Department of Veterinary Medicine Faculty of Animal Science and Food Engineering University of Sao Paulo Embrapa Cerrados, Planaltina Department of Animal Science São Paulo State University (UNESP)

Several models for predicting dry matter intake (DMI) of replacement dairy heifers have been developed, however, only a few have been evaluated using data from heifers of different breeds raised under tropical conditions. Thus, the objective of this study was to evaluate the DMI equations for dairy heifers managed under tropical conditions. A total of 230 treatment means from 61 studies using dairy heifers (n = 1513 heifers, average body weight = 246 kg) were used. The animals were grouped into two groups based on their genetics: (1) Bos taurus (Holstein, Jersey, Brown Swiss, and Holstein × Jersey) and (2) crossbred (Bos taurus × Bos indicus). Seven previously published DMI equations (HH, HHJ, QUI, STA, 2001 NRC, OFLin, and OFNLin) for heifers were evaluated using mean bias, slope bias, mean squared prediction errors (MSPE) and its decomposition, and other model evaluation statistics. For Bos taurus heifers, our results indicated that OFNLin and HHJ had lower mean bias (0.13 and 0.16 kg/d, respectively) than other models. There was no significant slope or mean bias for HHJ and OFNLin (p &gt, 0.05), indicating agreement between the observed and predicted DMI values. All other models had a significant mean bias (p &lt, 0.05), whereas the QUI model also presented a significant slope bias (p &lt, 0.02). For crossbred heifers, the STA equation was the only one that did not present mean and slope bias significance (p &gt, 0.05). All other DMI models had significant mean bias when evaluated using crossbred data (p &lt, 0.04), and QUI, OFLin, and OFNLin also presented significant slope bias (p &lt, 0.01). Based on our results, predictions from OFNLin and HHJ best represented the observed DMI of Bos taurus heifers (MSPE ≤ 1.25 kg2/d2, mean bias ≤ 0.16 kg/d), whereas STA was the best model for crossbred heifers (MSPE = 1.25 kg2/d2, mean bias = 0.09 kg/d). These findings indicate that not all available models are adequate for estimating the DMI of dairy heifers managed under a tropical climate, with HHJ and OFNLin for Bos taurus and STA for crossbreds being the most suitable models for DMI prediction. There is evidence that models from Bos taurus heifers could be used to estimate the DMI of heifers under tropical conditions. For heifer ration formulation is necessary to consider that DMI is influenced by breed, diet, management, and climate. Future work should also include animal genetic and environmental variables for the prediction of DMI in dairy heifers.

BackgroundHumplessBos tauruscattle are one of the earliest domestic cattle in Africa, followed by the arrival of humpedBos indicuscattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids betweenBos taurusandBos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds.MethodsData for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 EuropeanBos taurus, 4Bos indicus,and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’sFstatistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations.ResultsThe first two principal components differentiatedBos indicusfrom EuropeanBos taurus, and AfricanBos taurusfrom other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure AfricanBos taurusor admixtures of AfricanBos taurusandBos indicus.The African zebu breeds had highest proportions ofBos indicusancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% AfricanBos taurus, ranged from 42 to 70% or 23 to 61%Bos indicusancestry. The AfricanBos tauruspopulations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor.Neestimates based onr2andr2adjshowed a decline inNefrom a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs.ConclusionAfrican indigenous cattle breeds have a large genetic diversity and are either pure AfricanBos taurusor admixtures of AfricanBos taurusandBos indicus.This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies havedemonstrated that breeding European taurine cattle such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon.We conducted a cross-sectional study of 2346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negativesamples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchicalclustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations.

Resumen Introducción. Existe escasa información sobre ganado puro con certificado genealógico en Costa Rica. Es necesario conocer el estado de esta población para dirigir esfuerzos en la mejora productiva del ganado cebú. Objetivo. Actualizar la base de datos de la Asociación de Criadores de Ganado Cebú de Costa Rica (ASOCEBÚ), caracterizar dicha población y analizar el uso de los machos de la raza Brahman gris en el país. Materiales y métodos. Se realizó un inventario en 121 ganaderías para actualizar la base de datos de la Asociación al año 2018. La información se clasificó por raza, sexo, edad, total de animales, criadores, región socio-económica, provincia y cantón. Se determinó la frecuencia de uso de reproductores Brahman gris. Resultados. Se contabilizaron 10 995 animales puros, distribuidos en seis razas (Brahman gris, Brahman rojo, Nelore, Gyr, Guzerat e Indubrasil). La raza Brahman gris predominó con un 74,5 % de la población y 76,8 % del total de criadores. La región Chorotega presentó la mayor población inscrita (49,5 %) y el mayor número de criadores (37,2 %). El 55,8 % de la población total provino de diez criadores, sin embargo, el mayor número de ganaderías correspondió a fincas con pocos animales. En la raza Brahman gris, el 60,8 % de la población provino de toros nacionales y el 39,2 % del extranjero. Conclusión. Los cebuinos puros registrados se distribuyen en todo el país. Se debe poner atención al manejo genético para minimizar la consanguidad. Se recomienda a los encargados de censos y encuestas, incluir la población de razas puras dentro de las evaluaciones. Abstract Introduction. There is not much information on pure cattle with a genealogical certificate in Costa Rica. It is necessary to know the status of this population to direct efforts towards the productive improvement of the Zebu cattle breeds. Objective. To update the database of the Costa Rican Cebu Cattle Breeders Association (ASOCEBÚ), characterize this population and analyze the use of males of the gray Brahman breed in the country. Materials and methods. An inventory was done in 121 herds to update the Association’s database to 2018. The information was sorted by breed, sex, age, total animals, breeders, socio-economic region, province, and canton. The frequency of use of gray Brahman breeders was determined. Results. A total of 10 995 pure animals were counted, distributed in six breeds (gray Brahman, red Brahman, Nelore, Gyr, Guzerat, and Indubrasil). The gray Brahman breed predominated with 74.5 % of the population and 76.8 % of the total of breeders. The Chorotega region had the highest registered population (49.5 %) and the highest number of breeders (37.2 %). 55.8 % of the total population came from ten breeders, however, the largest number of herds corresponds to farms with few animals. In the gray Brahman breed, 60.8 % of the population comes from domestic bulls, and 39.2 % from other countries. Conclusion. Registered pure zebu cattle are distributed throughout the whole country. Attention should be put to genetic management to minimize inbreeding. Census and survey managers are encouraged to include the purebred populations in their assessments.

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Made available in DSpace on 2021-06-26T02:54:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-07-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) This experiment was designed to evaluate the effects of lipid source and fatty acid (FA) profile on intake, performance, carcass characteristics, expression of enzymes, and sensorial analysis of Bos indicus animals offered a high-concentrate diet. On day 0, 96 noncastrated animals were blocked by initial body weight (400 +/- 19.3 kg), randomly allocated to 1 of 24 pens (4 animals/ pen), and pens were randomly assigned to receive: 1) control: basal diet composed of whole cottonseed and corn germ as lipid substrates (CONT; n = 6), 2) calcium salts of fatty acids (CSFA) of soybean: CSFA of soybean oil as replacement for whole cottonseed and corn germ (calcium salts of soybean oil [CSSO]; n = 6), 3) CSFA-Blend: CSFA of palm, cottonseed, and soybean oil as replacement for whole cottonseed and corn germ (calcium salts of vegetable oils [CSVO]; n = 6), and 4) Mix: basal diet containing whole cottonseed, corn germ, and CSVO (MIXT; n = 6). Experiment lasted 108 d and performance, ultrasound measurements, as well as carcass characteristics were evaluated. Additionally, meat FA profile, expression of enzymes involved in lipid metabolism, and sensorial analysis were evaluated. No treatment effects were observed on performance variables, ultrasound, and carcass traits (P >= 0.22), whereas animals receiving CONT had a greater intake of C10:0, C16:0, C16:1 trans-9, C18:1 cis-9, C18:2, C18:3, total FA, monounsatured FA (MUFA), and polyunsaturated FA (PUFA) vs. CSSO and MIXT (P < 0.05). Conversely, intake ratios of saturated FA (SFA):MUFA and SFA:PUFA were all reduced for CONT vs. other treatments. Meat obtained from CONT animals had greater colorimetric (L*, a*, and b*) values vs. MIXT (P < 0.01). On meat FA profile, CONT increased C18:0 vs. supplementation with calcium salts (P < 0.02) and supplementation with CSSO yielded greater meat concentrations of C18:1 trans-10 and C18:2 CLA intermediates (P < 0.01). Expression of SREBP-1, SCD, and LPL was downregulated for CSSO (P < 0.05). For sensorial analysis, regular flavor was greater (P = 0.01) for CSSO vs. other treatments, but also greater aroma (P = 0.05) vs. CONT and CSVO. In summary, addition of different lipid sources with varying FA profiles into high-concentrate diets did not affect performance and carcass characteristics of B. indicus animals, but supplementation with calcium salts of soybean oil inhibited the mRNA expression of enzymes involved in lipid metabolism, whereas flavor and aroma were positively affected by this lipid source. Univ Estadual Paulista, Fac Med Vet & Zootecnia, BR-18618000 Botucatu, SP, Brazil EMPAER, BR-78049903 Cuiaba, MT, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Tecnol, BR-17900000 Dracena, SP, Brazil Univ Sao Paulo, Fac Med Vet & Zootecnia, BR-13635900 Pirassununga, SP, Brazil Nutricorp, BR-13601000 Araras, SP, Brazil Nutribeef Consultoria, BR-18610630 Botucatu, SP, Brazil Univ Estadual Paulista, Fac Med Vet & Zootecnia, BR-18618000 Botucatu, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Tecnol, BR-17900000 Dracena, SP, Brazil FAPESP: 2017/01126-9

The aim of the present study was to evaluate the inclusion of narasin, salinomycin, or flavomycin for 140 d on ruminal fermentation parameters, apparent nutrient digestibility, and performance of Nellore cattle offered a forage-based diet. In experiment 1, 32 rumen-cannulated Bos indicus Nellore steers [initial body weight (BW) = 220 ± 12.6 kg] were assigned to individual pens in a randomized complete block design according to their initial shrunk BW. Within block, animals were randomly assigned to 1 of 4 treatments: (1) forage-based diet without feed additives (CON; n = 8), (2) CON diet plus 13 ppm of narasin (NAR; n = 8), (3) CON diet plus 20 ppm of salinomycin (SAL; n = 8), or (4) CON diet plus 3 ppm of flavomycin (FLA; n = 8). The experimental period lasted 140 d and was divided into 5 periods of 28 d each. The inclusion of feed additives did not impact (P ≥ 0.17) dry matter intake (DMI), nutrient intake, and apparent total tract digestibility of nutrients. Nonetheless, steers fed NAR had lower (P < 0.01) molar proportion of acetate compared with CON, SAL, and FLA steers, whereas ruminal acetate tended to be greater (P < 0.09) for SAL vs. CON and FLA, but did not differ (P = 0.68) between CON vs. FLA steers. Ruminal propionate was the highest (P < 0.01) for steers fed NAR and did not differ (P > 0.20) between CON, SAL, and FLA. Consequently, NAR steers had the lowest (P < 0.01) Ac:Pr ratio, whereas Ac:Pr did not differ (P > 0.18) among CON, SAL, and FLA. Total volatile fatty acids were greater (P < 0.04) for NAR and CON vs. SAL and FLA, but did not differ (P > 0.67) among NAR vs. CON and SAL vs. FLA. In experiment 2, 164 Nellore bulls (initial shrunk BW = 299 ± 2.5 kg) were assigned to feedlot pens for 140 d in a randomized complete block design. Within block (n = 10), animals were randomly assigned to the same treatments used in experiment 1. Average daily gain was greater (P < 0.01) in NAR vs. CON, SAL, and FLA bulls, and did not differ (P > 0.12) between CON, SAL, and FLA bulls. Bulls fed NAR had greater (P < 0.02) DMI (as kg/d or % BW) and final shrunk BW compared with CON, SAL, and FLA bulls, whereas DMI and final shrunk BW did not differ (P > 0.26) between CON, SAL, and FLA bulls. Feed efficiency, however, was not impacted (P = 0.51) by any feed additives used herein. Collectively, narasin was the only feed additive that benefited performance and ruminal fermentation of Nellore animals fed a forage-based diet.

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits. Made available in DSpace on 2020-10-10T09:14:31Z (GMT). No. of bitstreams: 1 AP-Allele-specific-2020.pdf: 1969866 bytes, checksum: 3b858fd65a6e059a02cd3b893d37b41c (MD5) Previous issue date: 2020 Na publicação: Adhemar Zerlotini. Article number: 10204.

Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

Background The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa. Results We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population. Conclusions Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.

Highlights • Bos indicus crossbred females had higher fecal eggs as calves than as yearlings. • More Bos indicus background had higher eggs per gram of feces through 1 year of age. • Cooperia and Haemonchus species predominated through 1 year of heifer age. • Ostertagia and Trichostrongylus species were detected mostly after 1 year of age. • Eggs per gram of feces correlated with few production traits of heifers., Gastrointestinal nematodes (GIN) do not detrimentally affect cattle to the extent of small ruminants. However, they are developing resistance to drugs used to treat them. Genetic strategies to control the nematodes and/or their detrimental effects could be a sustainable alternative to treatment with drugs. An essential first step in development of such a strategy is characterization of nematode populations in commonly used breed types of cattle in local conditions. Fecal egg counts (FEC) were obtained every two months on a cohort of 53 crossbred Nellore-Angus heifers grazing Central Texas pastures from an average heifer age of 3 months to approximately 2 years of age. For 10 of those 12 sets of samples, coprocultures were set up to characterize gastrointestinal nematode species present. Heifers were ½ Nellore ½ Angus (n = 18) or ¾ Angus ¼ Nellore (n = 35). They were born in the spring of 2014 to cows that were from 3–5 years old. They were maintained as a group throughout weaning, postweaning, exposure to bulls as yearlings, and as pregnant cows through the birth of their first calves. An interaction of breed group with sampling time (P < 0.0001) highlighted favorable FEC of ¼ Nellore heifers as compared to ½ Nellore in all but two sampling times. Fecal egg count means were, in general, higher for heifers of both groups in sampling times up to one year of age. Season effects on FEC may be important, but the effect of age may have obscured their detection. There were few significant correlation coefficients for FEC traits with a variety of production traits of these females. Average FEC residuals were positively correlated (r = 0.28 and 0.41; P < 0.05) with winter coat shedding score evaluated at approximately 17 and 24 months of age. Residual correlations of average FEC with calf weaning weight and incidence of shedding with calf age at weaning (r> 0.3) may be indicative of the increased susceptibility of females that lactate heavily or longer to internal parasite infection. Proportions of GIN genera by sampling day differed from χ2 expectation (P < 0.0001). Cooperia and Haemonchus species were detected in large proportions in sampling dates that corresponded to heifers less than one year of age. Ostertagia and Trichostrongylus species predominated in sampling dates after heifers reached one year of age.

Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle. Made available in DSpace on 2020-08-15T04:11:44Z (GMT). No. of bitstreams: 1 AP-Potential-biomarkers-2020.pdf: 6772400 bytes, checksum: b6d50a8237cd649b3e08ecc7fb04b44e (MD5) Previous issue date: 2020 Article 189. Na publicação: Luciana C. A. Regitano.

Highlights • Inverted T helper (CD4)/Cytotoxic T cell (CD8) ratio in Boran cattle. • Higher absolute numbers of circulating CD8 T cells in Boran cattle than EASZ, N'dama, Nelore and Holstein-Friesian. • Female cattle have significantly higher CD4/CD8 ratio than male cattle., The CD4+/CD8+ ratio is used as a marker of the immune regulation of T cell balance. When the ratio in peripheral blood is less than 1, this is considered an indication of immune suppression in an individual. Previous work on bovine Peripheral Blood Mononuclear Cells (PBMC) has consistently reported a ratio ≥1 as seen in other mammalian hosts, i.e. higher circulating CD4+ cell numbers than CD8+ cell numbers. However, a consistent inverted CD4+/CD8+ ratio (