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Characterized by the incomplete development of the germinal epithelium of the seminiferous tubules, Testicular hypoplasia (TH) leads to decreased sperm concentration, increased morphological changes in sperm and azoospermia. Economic losses resulting from the disposal of affected bulls reduce the efficiency of meat production systems. A genome‐wide association study and functional analysis were performed to identify genomic windows and the underlying positional candidate genes associated with TH in Nellore cattle. Phenotypic and pedigree data from 207,195 animals and genotypes (461,057 single nucleotide polymorphism, SNP) from 17,326 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. A possible correlated response on TH resulting from the selection for scrotal circumference was evaluated by using a two‐trait analysis. Thus, estimated breeding values were calculated by fitting a linear‐threshold animal model in a Bayesian approach. The SNP effects were estimated using the weighted single‐step genomic BLUP method. Twelve non‐overlapping windows of 20 adjacent SNP that explained more than 1% of the additive genetic variance were selected for candidate gene annotation. Functional and gene prioritization analysis of the candidate genes identified genes (KHDRBS3, GPX5, STAR, ERLIN2), which might play an important role in the expression of TH due to their known roles in the spermatogenesis process, synthesis of steroids and lipid metabolism. [ABSTRACT FROM AUTHOR]

There is a great worldwide demand for cheese made with buffalo milk, due to its flavour and nutritional properties. In this context, there is a need for increasing the efficiency of buffalo milk production (including lactation persistence), which can be achieved through genomic selection. The most used methods for the genetic evaluation of longitudinal data, such as milk‐related traits, are based on random regression models (RRM). The choice of the best covariance functions and polynomial order for modelling the random effects is an important step to properly fit RRM. To our best knowledge, there are no studies evaluating the impact of the order and covariance function (Legendre polynomials—LEG and B‐splines—BSP) used to fit RRM for genomic prediction of breeding values in dairy buffaloes. Therefore, the main objectives of this study were to estimate variance components and evaluate the performance of LEG and BSP functions of different orders on the predictive ability of genomic breeding values for the first three lactations of milk yield (MY1, MY2, and MY3) and lactation persistence (LP1, LP2, and LP3) of Brazilian Murrah. Twenty‐two models for each lactation were contrasted based on goodness of fit, genetic parameter estimates, and predictive ability. Overall, the models of higher orders of LEG or BSP had a better performance based on the deviance information criterion (DIC). The daily heritability estimates ranged from 0.01 to 0.30 for MY1, 0.08 to 0.42 for MY2, and from 0.05 to 0.47 for MY3. For lactation persistence (LP), the heritability estimates ranged from 0.09 to 0.32 for LP1, from 0.15 to 0.33 for LP2, and from 0.06 to 0.32 for LP3. In general, the curves plotted for variance components and heritability estimates based on BSP models presented lower oscillation along the lactation trajectory. Similar predictive ability was observed among the models. Considering a balance between the complexity of the model, goodness of fit, and credibility of the results, RRM using quadratic B‐splines functions based on four or five segments to model the systematic, additive genetic, and permanent environment curves provide better fit with no significant differences between genetic variances estimates, heritabilities, and predictive ability for the genomic evaluation of dairy buffaloes. [ABSTRACT FROM AUTHOR]

Heat stress causes extensive losses in the dairy sector, due to negative effects on milk production and reproduction. Cows have evolved a series of protective mechanisms, (physiological, biochemical, behavioural) to cope with the thermostressing environments, which have allowed the preservation of productive and reproductive potential of specific animals during summer; these animals are considered thermotolerant and could be used to design programs of selective breeding. These programs, targeting the generations of a population of heat‐resistant animals, would increase the frequency of the desired phenotypes, tackling the financial losses on one hand and reducing the carbon footprints of the dairy sector on the other. The development of genomics techniques has enabled genome wide variant calling, to detect SNPs associated with the desired phenotypes. In this study, we used a comparative genomics approach to detect genetic variation associated with thermotolerance and to design molecular markers for characterizing the animals as tolerant/sensitive. A total of 40 cows from each group were split in four sequencing pools and a whole‐genome sequencing approach was used. Results and conclusion: Genome‐wide genetic variation between groups was characterized and enrichment analysis revealed specific pathways which participate in the adaptive mechanisms of thermotolerance, implicated into systemic and cellular responses, including the immune system functionality, Heat Stress and Unfolded Protein Response. The markers made a promising set of results, as specific SNPs in five genes encoding for Heat Shock Proteins were significantly associated with thermotolerance. [ABSTRACT FROM AUTHOR]

Dietary l-arginine (ARG) supplementation has been studied as a nutritional strategy to improve reproductive performance of pregnant sows, since arginine is a conditionally essential amino acid. However, reports addressing the molecular mechanisms that mediate supplementation effects on embryos and fetuses development are still scarce. Therefore, we aimed to evaluate the effects of 1.0% ARG supplementation of commercial pregnant gilts on genes and proteins from energy metabolism and antioxidant defense pathways in embryos and fetuses. We also analyzed the global transcriptome profile of 25- and 35-day-old conceptuses. At Day 25, we observed a lower abundance of phospho-AMP-activated protein kinase (phospho-AMPK) protein and downregulation of oxidative phosphorylation system genes in ARG embryos. On the other hand, ARG fetuses showed greater expression of MLST8 and lower expression of MTOR genes, in addition to lower abundance of phospho-AMPK and phospho-mammalian target of rapamycin (phospho-mTOR) proteins. Transcriptome analysis at Day 35 did not present differentially expressed genes. For the antioxidant defense pathway, no differences were found between CON and ARG conceptuses, only trends. In general, supplementation of gilts with 1.0% ARG during early gestation affects energy sensitive pathways in 25- and 35-day conceptuses; however, no effects of supplementation were found on the antioxidative defense pathway in 25-day embryos., (© 2020 Wiley Periodicals LLC.)

As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits. Therefore, the main objectives of this study were to: (1) estimate genomic-based genetic parameters; (2) define animal biotypes utilizing PCA; and (3) utilize GWAS to link the biotypes to candidate genes and quantitative trait loci (QTL). The phenotypic dataset included 2583 phenotypic records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,309 animals with 35,651 single nucleotide polymorphisms (SNPs). Eight principal components (PCs), accounting for a total of 99.7% of the population variation, were defined for three growth, eight conventional carcass, 10 pork quality and 18 novel carcass traits. The eight biotypes defined from the PCs were found to be related to growth rate, maturity, meat quality and body structure, which were then related to candidate genes. Of the 175 candidate genes found, six of them [LDHA (SSC1), PIK3C3 (SSC6), PRKAG3 (SSC15), VRTN (SSC7), DLST (SSC7) and PAPPA (SSC1)] related to four PCs were found to be associated with previously defined QTL, linking the biotypes with biological processes involved with muscle growth, fat deposition, glycogen levels and skeletal development. Further functional analyses helped to make connections between biotypes, relating them through common KEGG pathways and gene ontology (GO) terms. These findings contribute to a better understanding of the genetic relationships between growth, carcass and meat quality traits in Duroc pigs, enabling breeders to better understand the biological mechanisms underlying the phenotypic expression of these traits., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)

Globalization and habitat destruction pose a significant threat to wildlife felids. Even though conservation banks for genetic materials have been created, the sperm cryopreservation with minimal cell damage is still a great challenge. Thus, this study aimed to compare the effects of two commercial extenders with different concentrations of alternative cryoprotectants on thawed sperm quality of domestic cats. Five adult cats were anaesthetized (using a combination of 40 μg/kg medetomidine associated to 5 mg/kg ketamine), and the semen was collected by electroejaculation (electrical stimulation of 2-3 V). Semen samples were evaluated for sperm characteristics (kinetics, morphology, membrane integrity and morphometry). Subsequently, they were sorted into two aliquots and centrifuged. The aliquots were added to a commercial extender containing 3% glycerol and 2% methylformamide (extender I) or 2% glycerol and 3% methylformamide (extender II), frozen, thawed (37°C/30 s) and reevaluated. Comparatively, the sperm kinetics and membrane integrity of fresh semen were higher (p < .002) than frozen samples in extender I and II. Total and progressive motility were lowest in the thawed samples. However, the subjective analysis indicated high sperm motility, since the kinetics evaluation was impaired by the low cell number in the thawed samples. There were no differences in sperm morphology between the groups. In the sperm morphometric analysis, a significant difference (p = .04) was identified in the length of the intermediate piece in extender II samples compared with fresh and extender I. Thus, it can be concluded that although the concentrations tested did not maintain the kinetic parameters and membrane integrity of spermatozoa after thawing, the extender with a lower concentration of glycerol was less toxic for maintaining the midpiece length., (© 2024 Wiley-VCH GmbH. Published by John Wiley & Sons Ltd.)

Commercial pooled semen from boars of maternal and terminal genetic lines was analysed over two consecutive years, as part of an external quality control program. Semen doses were prepared for two total sperm counts (2.0 × 109/75 ml [n = 578] and 1.5 × 109/34 ml [n = 643]). Semen doses were evaluated for motility, morphology and bacterial contamination at days 1 and 4 after collection. Additionally, temperature during transport was tracked and correlated to sperm motility. Sperm motility and morphology were significantly affected by genetic line, but not by total sperm per doses. Total motility (TM) was affected (p <.05) by season. Progressive motility (PM) was lower (p <.05) in some winter months, and higher (p <.05) in summer for maternal‐line doses. Normal sperm morphology was higher (p <.05) in some months of late fall and winter, with an apparent decrease in some summer months. In general, motility was significantly higher on day 1 than on day 4, and was also affected (p <.05) by temperature, especially for terminal‐line doses. Semen doses exposed to >15°C had higher (p <.05) TM, VSL (straight‐line velocity) and linearity than doses exposed to <15°C. Progressive motility and straightness increased (p <.05) proportionally with temperature. At day 1, motility, average path velocity (VAP) and VSL increased (p <.05) with temperature, and was higher than the corresponding group at day 4, except for VSL. Sperm motility and kinematics at day 4 were similar between temperature groups, except for doses exposed to >20°C that had higher (p <.05) VAP and VSL than doses exposed to <12°C. Microbiology evaluation revealed that less than 8.2% (15/184) of the semen doses had bacterial growth. Sphingobacterium lactis was the most prevalent bacterium identified. In conclusion, genetic line strongly influences sperm motility, while total sperm count does not have an impact. Transient reduced temperatures during shipping do not impair sperm quality after 4 days of storage. Seasonal and temperature effects on sperm motility of pooled boar semen are not overcome by pre‐production ejaculate selection and semen pooling. [ABSTRACT FROM AUTHOR]

Coat color is one of the important economic traits in sheep and it can be used for breed identification and characterization as well. The aim of the present study was to perform genome wide association study (GWAS) and pathway analysis based on gene set enrichment analysis for identifying the loci associated with coat color in Lori-Bakhtiari sheep breed. The GWAS was carried out using PLINK v. 1.90. The gene enrichment analysis was performed by goseq R package in R v.3.6.1 with the aim of identifying functional clusters and biological pathways of the genes in selected candidate regions and finally, for bioinformatics analysis we used online databases and softwares of GO, Metacyc, KEEG, Reactome and panther. In this study significant SNP markers were identified on chromosomes 1, 2, 6, 9, 10, and 16 that overlapped with EDNRB, PDGFRA, TCF25, and TYRPI genes. According to pathway analysis, four GO pathways were associated with the coat color trait (P<0.05). Among these pathways, regulation of protein tyrosine kinase activity', regulation of protein kinase A signaling and activation of protein kinase activity biological pathways, were previously reported to have an important role on the melanocyte development and coat pigmentation. Considering that the genomic regions identified in the current study have been confirmed to be associated with coat color in sheep and other species in previous reports, as well as the identification of some novel putative regions, the identified candidate genes in our study could be further studied and eventually used in genetic selection for coat color in sheep. [ABSTRACT FROM AUTHOR]

Femoral head separation (FHS) is characterized by the detachment of growth plate (GP) and articular cartilage, occurring in tibia and femur. However, the molecular mechanisms involved with this condition are not completely understood. Therefore, genes and biological processes (BP) involved with FHS were identified in 21-day-old broilers through RNA sequencing of the femoral GP. 13,487 genes were expressed in the chicken femoral head transcriptome of normal and FHS-affected broilers. From those, 34 were differentially expressed (DE; FDR =0.05) between groups, where all of them were downregulated in FHS-affected broilers. The main BP were enriched in receptor signaling pathways, ossification, bone mineralization and formation, skeletal morphogenesis, and vascularization. RNA-Seq datasets comparison of normal and FHS-affected broilers with 21, 35 and 42 days of age has shown three shared DE genes (FBN2, C1QTNF8, and XYLT1) in GP among ages. Twelve genes were exclusively DE at 21 days, where 10 have already been characterized (SHISA3, FNDC1, ANGPTL7, LEPR, ENSGALG00000049529, OXTR, ENSGALG00000045154, COL16A1, RASD2, BOC, GDF10, and THSD7B). Twelve SNPs were associated with FHS (p < 0.0001). Out of those, 5 were novel and 7 were existing variants located in 7 genes (RARS, TFPI2, TTI1, MAP4K3, LINK54, and AREL1). We have shown that genes related to chondrogenesis and bone differentiation were downregulated in the GP of FHS-affected young broilers. Therefore, these findings evince that candidate genes pointed out in our study are probably related to the onset of FHS in broilers. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Agriculture & Nature / Kahramanmaraş Sütçü İmam Üniversitesi Tarım & Doğa Dergisi is the property of Kahramanmaras Sutcu Imam Universitesi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Litter size is an important economic trait in the goat industry. Previous studies on the bone morphogenetic protein 15 (BMP15) gene detected some single-nucleotide polymorphisms (SNPs) such as c.963A > G that were associated with an increase in ovulation rate and litter size. The aim of this study was to conduct a meta-analysis on the effect of this polymorphism on litter size. We gathered and pooled data from five eligible published studies. To investigate the effect of c.963A > G on litter size, we utilized four different genetic models assuming dominant (GG + GA vs. AA), recessive (GG vs. GA + AA), additive (GG vs. AA) and co-dominant (GG + AA vs. GA) model of inheritance. Data were analyzed under random-effects models based on the I2 value. Furthermore, sensitivity analysis was carried out to validate the stability of results. The results showed that the c.963A > G polymorphism is associated with litter size when applying a dominant model (standardized mean difference (SMD) is 0.815, 95 % CI [0.170, 1.461], P value = 0.013) and also with an additive model (SMD = 0.755, 95 % CI [0.111, 1.400], P value = 0.022). However, the effect of c.963A > G polymorphism was not significant under recessive (SMD = 0.186, 95 % CI [ - 0.195, 4.259], P value = 0.339) and co-dominant (SMD = - 0.119, 95 % CI [ - 0.525, 0.288], P value = 0.568) models. Sensitivity analysis demonstrated that dropping studies with wide confidence intervals affects overall results under the assumption of an additive model. The meta-analysis results revealed that the AA genotype could be positively connected with litter size in goats. [ABSTRACT FROM AUTHOR]

Background: India, a major livestock region of the Asian countries is rich in animal genetic resources having special qualities of hardy nature, resistance to many diseases and adopted to adverse climatic conditions. The cattle MHC, Bovine Lymphocyte Antigen DRB3 (BoLA-DRB3) is considered to be a major gene linked with disease resistance traits of Indian cattle. Methods: The present study was carried out to sequence the BoLA-DRB3.2 alleles in Deoni and Ongole breeds of Indian cattle. PCR RFLP analysis of the BoLA-DRB3.2 alleles in Deoni (n=51) and Ongole (n=60) cattle using three different restriction enzymes RsaI, BstYI and HaeIII to find out the possible restriction pattern. Based on the combined allelic patterns, each sample was further analyzed by PCR-SBT technique to detect the SNP variations present in BoLA-DRB3.2 alleles. Result: The PCR RFLP analysis revealed that the highest frequent alleles are *6 (0.216) and *15 (0.225) in Deoni and Ongole breeds of cattle, respectively. The second-highest frequency was observed for BoLA alleles *11 and *6 which were present at a frequency of 0.167 and 0.200 in Deoni and Ongole breeds of cattle, respectively. To get the complete picture of polymorphic pattern of BoLADRB3.2 allele direct sequencing was carried out for each plymorphic pattern. The interesting feature noticed in the Ongole breed was that at position 91 and 133 of the sequence, it had both A and G nucleotides in contrast to Bos taurus breed, which had only TT nucleotides. The sequence analysis of BoLA-DRB3 exon 2 between two breeds revealed that there are numerous variations in exon 2, whatever variation, that lead to different mobility shift and band pattern in gels. Deoni and Ongole breeds of cattle had similar variations at positions 94, 134, 211, 235 and 258noticed due to the unique nature of native breeds. [ABSTRACT FROM AUTHOR]

In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (F PED ) and genomic data based on runs of homozygosity (ROH) in the genome (F ROH ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (F PED10 ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised., (© 2023 John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.)

Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value—which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models—especially those using XGBoost—in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds. [ABSTRACT FROM AUTHOR]

This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores within the tree ensemble non-linear structure. Data from Nellore cattle were used, including records of animals born between 1984 and 2015 and raised in commercial herds located in different regions of Brazil. The estimated breeding values (EBV) were computed and used as the response variable in the genomic analyses. After quality control, the remaining number of animals and SNPs considered were 3,174 and 360,130, respectively. Five independent RF analyses were carried out, considering different initialization seeds. The importance score of each SNP was averaged across the independent RF analyses to rank the markers according to their predictive relevance. A total of 117 SNPs associated with AFC were identified, which spanned 10 autosomes (2, 3, 5, 10, 11, 17, 18, 21, 24, and 25). In total, 23 non-overlapping genomic regions embedded 262 candidate genes for AFC. Enrichment analysis and previous evidence in the literature revealed that many candidate genes annotated close to the lead SNPs have key roles in fertility, including embryo pre-implantation and development, embryonic viability, male germinal cell maturation, and pheromone recognition. Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening candidate regions associated with complex traits. Complementary analyses revealed that many SNPs top-ranked in the RF-based GWAS did not present a strong marginal linear effect but are potentially involved in epistatic hotspots between genomic regions in different autosomes, remarkably in the BTAs 3, 5, 11, and 21. The reported results are expected to enhance the understanding of genetic mechanisms involved in the biological regulation of AFC in this cattle breed. [ABSTRACT FROM AUTHOR]

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species‐specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species‐specific changes in many pregnancy‐related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance. [ABSTRACT FROM AUTHOR]

It is well known that Dorper (DP) is a full-bodied, fast-growing and high dressing percentage breed, while the production performance of Small-tailed Han sheep (STH) is not so excellent, in contrast to DP. Therefore, in this study, a comparative transcriptomic analysis of liver and muscle tissues from DP and STH breeds was carried out to find differentially expressed genes (DEGs) that affect their growth and meat quality traits. The results showed that the total number of DEGs was 2,188 in the two tissues. There were 950, 160 up-regulated and 1,007, 71 down-regulated genes in the liver and muscle, respectively. Several DEGs such as TGFB1 , TGFB3 , FABP3 , LPL may be associated with growth and development in DP. Also, several GO terms were found to be associated with muscle growth and development, such as developmental growth (GO:0048589), and myofibril (GO:0030016). Further validation of eight genes (6 up-regulated, and 2 down-regulated) was performed using quantitative RT-PCR. These findings will provide valuable information for studying growth and development as well as meat quality traits in sheep. [ABSTRACT FROM AUTHOR]

Copyright of Taurus is the property of Revista Taurus and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves are poorly characterized in cattle. Here, we selected 13 genes from the literature which have previously been shown to have strong evidence for an association with fertility in Brahman cattle (Bos taurus indicus) or closely related breeds. We examine the expression variation of the 13 genes that are associated with cattle fertility using RNA-seq, CAGE-seq, and ISO-seq data from 11 different tissue samples from an adult Brahman cow and a Brahman fetus. Tissues examined include blood, liver, lung, kidney, muscle, spleen, ovary, and uterus from the cow and liver and lung from the fetus. The analysis revealed several novel isoforms, including seven from SERPINA7. The use of three expression characterization methodologies (5′ cap selected ISO-seq, CAGE-seq, and RNA-seq) allowed the identification of isoforms that varied in their length of 5′ and 3′ untranslated regions, variation otherwise undetectable (collapsed as degraded RNA) in generic isoform identification pipelines. The combinations of different sequencing technologies allowed us to overcome the limitations of relatively low sequence depth in the ISO-seq data. The lower sequence depth of the ISO-seq data was also reflected in the lack of observed expression of some genes that were observed in the CAGE-seq and RNA-seq data from the same tissue. We identified allele specific expression that was tissue-specific in AR , IGF1 , SOX9 , STAT3 , and TAF9B. Finally, we characterized an exon of TAF9B as partially nested within the neighboring gene phosphoglycerate kinase 1. As this study only examined two animals, even more transcriptional variation may be present in a genetically diverse population. This analysis reveals the large amount of transcriptional variation within mammalian fertility genes and illuminates the fact that the transcriptional landscape cannot be fully characterized using a single technology alone. [ABSTRACT FROM AUTHOR]

It has been proven that the random regression model has a great advantage over the repeatability model in longitudinal data analysis. At present, the random regression model has been used as a standard analysis method in longitudinal data analysis. The aim of this study was to estimate the variance components and heritability of semen traits over the reproductive lifetime of boars. The study data, including 124,941 records from 3,366 boars, were collected from seven boar AI centers in South China between 2010 and 2019. To evaluate alternative models, we compared different polynomial orders of fixed, additive, and permanent environment effects in total 216 models using Bayesian Information Criterions. The result indicated that the best model always has higher-order polynomials of permanent environment effect and lower-order polynomials of fixed effect and additive effect regression. In Landrace boars, the heritabilities ranged from 0.18 to 0.28, 0.06 to 0.43, 0.03 to 0.14, and 0.05 to 0.24 for semen volume, sperm motility, sperm concentration, and abnormal sperm percentage, respectively. In Large White boars, the heritabilities ranged from 0.20 to 0.26, 0.07 to 0.15, 0.10 to 0.23, and 0.06 to 0.34 for semen volume, sperm motility, sperm concentration, and abnormal sperm percentage, respectively. [ABSTRACT FROM AUTHOR]

Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin-regulated networks underlying maize root development, we have characterized auxinresponsive transcription across two time points (30 and 120 min) and four regions of the primary root: the meristematic zone, elongation zone, cortex and stele. Hundreds of auxinregulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin-regulated genes are region unique and are predominantly observed in differentiated tissues compared with the root meristem. Auxin gene regulatory networks were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin-Response Factor subnetworks were generated to identify target genes that exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop. [ABSTRACT FROM AUTHOR]

White‐lipped peccary (Tayassu pecari) is a neotropical mammal that plays a fundamental role in maintaining the integrity of tropical forest systems. However, due to hunting and deforestation the species is currently classified as vulnerable. As there are reports of difficulties in captive reproduction, it was proposed to use assisted reproduction techniques for later reintroduction into their natural habitat. Therefore, the objective was to describe the physical, chemical, morphological and functional characteristics of its semen. Sixteen adult male, white‐lipped peccary, aged between three and seven years old, distributed in three groups, were used in this study. After physical and chemical retainment, semen was collected by electroejaculation from 16 individuals. It was evaluated by computer analysis (CASA). The mean values recorded were as follows: volume 0.5 ± 0.6 ml, pH 7.2 ± 0.3, sperm concentration 967.2 ± 947.3 × 106 spermatozoon/ml and total motility of 75.4 ± 16.2. The average sperm reactive to the hypo‐osmotic test was 85.3% ± 21.0%, and 62.4% ± 43.9% of the cells presented intact membranes in the structural integrity test. Additionally, the semen showed milky consistency (80%), yellowish colour (40%) and sui generis odour (100%). The sperm parameters of the white‐lipped peccary are within the desirable standards, allowing them to be considered as potentially fertile for the development of assisted reproduction techniques that may contribute to the conservation of the species. [ABSTRACT FROM AUTHOR]

Copyright of Agronomía Colombiana is the property of Universidad Nacional de Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Properly quantifying environmental heat stress (HS) is still a major challenge in livestock breeding programs, especially as adverse climatic events become more common. The definition of critical periods and climatic variables to be used as the environmental gradient is a key step for genetically evaluating heat tolerance (HTol). Therefore, the main objectives of this study were to define the best critical periods and environmental variables (ENV) to evaluate HT and estimate variance components for HT in Large White pigs. The traits included in this study were ultrasound backfat thickness (BFT), ultrasound muscle depth (MDP), piglet weaning weight (WW), off-test weight (OTW), interval between farrowing (IBF), total number of piglets born (TNB), number of piglets born alive (NBA), number of piglets born dead (NBD), number of piglets weaned (WN), and weaning to estrus interval (IWE). Seven climatic variables based on public weather station data were compared based on three criteria, including the following: (1) strongest G×E estimate as measured by the slope term, (2) ENV yielding the highest theoretical accuracy of the genomic estimated breeding values (GEBV), and (3) variable yielding the highest distribution of GEBV per ENV. Relative humidity (for BFT, MDP, NBD, WN, and WW) and maximum temperature (for OTW, TNB, NBA, IBF, and IWE) are the recommended ENV based on the analyzed criteria. The acute HS (average of 30 days before the measurement date) is the critical period recommended for OTW, BFT, and MDP in the studied population. For WN, WW, IBF, and IWE, a period ranging from 34 days prior to farrowing up to weaning is recommended. For TNB, NBA, and NBD, the critical period from 20 days prior to breeding up to 30 days into gestation is recommended. The genetic correlation values indicate that the traits were largely (WN, WW, IBF, and IWE), moderately (OTW, TNB, and NBA), or weakly (MDP, BFT, and NBD) affected by G×E interactions. This study provides relevant recommendations of critical periods and climatic gradients for several traits in order to evaluate HS in Large White pigs. These observations demonstrate that HT in Large White pigs is heritable, and genetic progress can be achieved through genetic and genomic selection. [ABSTRACT FROM AUTHOR]

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage. [ABSTRACT FROM AUTHOR]

The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy–Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia. [ABSTRACT FROM AUTHOR]

The purpose of this paper was to analyse the aetiology and methods of diagnosing reproductive disorders in male dromedary camels. Male camel infertility manifests as one of three conditions: post‐coital infertility (IG), inability to copulate (IC) and lack of sexual desire (LSD). IG is mainly a testicular disorder that is linked to a deteriorated seminogram, arrested spermatogenesis, Sertoli cell‐only syndrome and testicular degeneration. For IG diagnosis, semen analysis, testicular biopsy and fine‐needle aspiration are gold standards. Testicular ultrasonography was generally inefficient. High serum FSH was found in IG camels with oligo‐ and azoospermia, implying primary spermatogenesis defects. The testis‐expressed protein (TEX101) and the epididymis‐expressed protein (ECM1) are reliable biomarkers for distinguishing between obstructive and non‐obstructive azoospermia. IC manifests in two forms: phimosis (PHI) and erectile dysfunction (ED). PHI is frequently linked to preputial and penile pathologies, as well as leucocytosis, neutrophilia and elevated nitric oxide metabolites. The majority of camels with ED have normal genital organs, and the condition is associated with an increase in cardiac troponin I. LSD is a rare disorder brought on by hormonal imbalances, high temperatures, stress and debilitating diseases. In conclusion, IG diagnosis necessitates semen analysis, testicular biopsy or fine‐needle aspiration, and FSH testing, whereas IC diagnosis requires preputial and penile examinations. Diagnostic aids include serum and seminal biomarkers. [ABSTRACT FROM AUTHOR]

A study was conducted to evaluate the effect of cyclic or chronic heat stress (HS) on the incidence and severity of white striping (WS) and histopathological changes in breast muscle of broiler chickens. One hundred eighty 1-day-old male chickens were randomly assigned to three research groups: control (standard temperature throughout the experiment), cyclic HS (32 ºC between 0800 and 2000 h from day 21 until the end of the experiment), and chronic HS (32 ºC from day 21 onwards). Cyclic and chronic HS groups showed a significant (P < 0.05) decrease in body weight gain and feed intake and poor feed conversion ratio in grower, finisher, and overall period. Serum biochemical profile was not different among the groups except globulin and P which were significantly higher (P < 0.05 and P < 0.001, respectively), in cyclic and chronic HS groups. Overall, WS incidence was numerically higher in control birds followed by chronic HS and cyclic HS birds, respectively. The chronic HS group had a lower incidence of mild (score 1) and a higher incidence of severe (score 2) WS lesions compared to control and cyclic HS groups. Histopathological analysis revealed that broilers subjected to chronic HS showed increased severity of myodegenerative changes, perivenular CD3 + cell infiltration, and lipidosis compared to control group. However, control and cyclic HS groups were not different in terms of histopathological lesions. In conclusion, this study confirms that cyclic or chronic HS may adversely affect the growth performance and that chronic HS may increase the severity of WS in broiler chickens. [ABSTRACT FROM AUTHOR]

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The aim of this study was to evaluate an effect of betaine and creatine monohydrate supplementation on chemical composition, meat quality, and oxidative stability of pork in pigs genotyped on mutation in RYR1 gene. Totally, sixty pigs - crosses of Lx(HAxPN) were involved in the experiment. Pigs were divided to one homozygous (NN) - control (C1), and three heterozygous (Nn) groups, each group including 15 animals. One group of Nn pigs was the control (C2) and two Nn groups were experimental. Control groups received a standard diet without supplement. Experimental groups were fed the same composition as controls but with supplement of betaine - BET (1.25 g/kg of feed) or creatine monohydrate - CMH (2.0 g/kg of feed) for thirty days prior to slaughter. Pigs C2 had worse meat quality, especially pH45, colour L* and drip loss (P<0.05), than homozygous C1 pigs. Dietary supplementation with betaine increased initial pH and decreased drip loss in Nn group (P<0.05) compared to C2 group. Supplementary CMH also increased pH45 and had a tendency to lowering the drip loss (P=0.058). Both feed additives substantially improved oxidative stability of pork, especially after 120 min incubation (P<0.01), compared to control C2 pigs. [ABSTRACT FROM AUTHOR]

Improving feed efficiency would increase profitability for producers. The objective of this study was to detect the expression levels of ME1 and CA1 and the polymorphisms of ME1 and CA1 associated with the feed conversion ratio (FCR) and residual feed intake (RFI) of Hu sheep by using qRT‐PCR, pooled DNA sequencing and KASPar assay. The qRT‐PCR results indicated that the expression levels of ME1 and CA1 were significantly higher in the liver tissues of low‐RFI sheep than in those of the high‐RFI sheep (p <.01). Association analysis demonstrated that the polymorphism ME1 g.453 C > T was significantly associated with FCR and RFI (p <.05). The polymorphism CA1 g.199 C > T had a significantly associated with FCR (p <.05) and no association with RFI (p >.05). Significant differences were observed between the combined genotypes and FCR and RFI at different measurement periods (p <.05). Thus, we propose the use of these two polymorphisms as new candidate molecular markers for improving feed efficiency in sheep populations. [ABSTRACT FROM AUTHOR]

The effect of essential oil (EO) supplementation on carcass characteristics of Japanese quails and interactions between ingredients and intestinal morphology were investigated in this study. A total of 250 quails were fed different diet: D1, basal diet (BD); D2, BD plus palmarosa oil (PO; 100 µg/kg diet); D3, BD plus lemon myrtle oil (LMO; 100 µg/kg diet); D4, BD plus α‐Tops (mixture of α‐terpineol, cineole and terpinene‐4‐ol; 100 µg/kg diet); and D5, BD plus cyclodextrin. Overall growth performance was determined at multiple time points during 35 days of experiment. Carcass characteristics (fatty acid, pH and colour), intestinal morphology and the expression levels of meat quality‐related genes including the insulin‐like growth factor (IGF‐1), myogenin and avian uncoupling protein (avUCP) were examined at the end of the trial. Additionally, intestinal microbiome of quails was studied by next‐generation sequencing‐based culture‐independent analysis. Although the inclusion of EOs into the diet had no effect on the growth performance of quails and the microbial profile, the significant changes in pH24 and colour (a*) of the quail's breast muscle (p <.05) in the group receiving PO were observed. Additionally, oleic acid content in the breast muscle was significantly higher in the EOs supplemented groups (p <.01). Quails fed the PO supplemented diet had higher villus and relatively rich in oleic acid. The expression levels of IGF‐1 and myogenin genes in quail's muscle were not affected, but the expression of avUCP gene was significantly lower in quails fed with LMO and α‐Tops (p <.05). The results demonstrated variable effects of these treatments on intestinal morphology. Taken together, dietary inclusion of EOs is found to be beneficial and hence can be recommended for improving the quality of poultry meat. [ABSTRACT FROM AUTHOR]

Stress factors during poultry production can evoke changes in gene transcription and protein synthesis in the hen oviduct and could affect the internal and external egg quality. Studies of relative gene expression require the identification of the most stable reference genes for the quantitative polymerase chain reaction (qPCR) to investigate the reproductive tissues' response in laying hens kept in different production systems. The objective of this study was to determine the most stable reference genes of the magnum tissues of laying hens housed in two different production systems. Hy‐Line Brown hens were reared under the same sanitary conditions until 15 weeks of age. Later on, they were transferred into two different production systems, conventional cage (CC) and cage free (CF), up to 82 weeks of age. At 50 and 60 weeks, a total of six hens from each production system were euthanized, and magnum samples were collected. The qPCR was used to determine the RNA transcription level of five reference genes, ACTB, 18S, GAPDH, MSX2 and HMBS. These genes were evaluated for transcript expression in magnum tissues by NormFinder, BestKeeper, geNorm and RefFinder software. The results indicated that the most stable gene in the CF housing system was HMBS in three of the algorithms and in the CC housing system was the 18S, and the best combination of reference genes was HMBS/GAPDH in CF and 18S/HMBS in CC. In conclusion, HMBS, 18S and GAPDH genes could be used together as reference genes for the normalization of the magnum tissues transcript expression of hens in CF and CC housing systems. [ABSTRACT FROM AUTHOR]

The semen movement and sperm head size patterns of boar ejaculates were analysed using computer‐assisted semen analysis (CASA)‐Mot and ‐Morph systems. The aim of the present study was to compare morphometric and kinematics variables from boars and to determine the relationship with sow fertility variables related to litter size. The females were from maternal crossing schemes such as the continuous 3‐generation cross between York (Y), Landrace (L), and Pietrain (P) hybrid sows and Pietrain boars. Semen samples were collected from 11 sexually mature boars from two sire lines. Samples were analysed using the ISAS®v1 system to evaluate eight kinematic variables of sperm velocity, progressiveness and undulations. Four morphometric parameters of sperm head size (length, width, area and perimeter) were analysed. Bayesian analysis revealed relevant differences in four kinematic variables (VSL, LIN, STR and WOB) between sire lines, with a probability of relevance (PR) of 0.79–0.91, and Pietrain boars were associated with higher progressive motility compared with Duroc x Pietrain boars. Moreover, there were relevant differences in all morphometric variables (PR = 0.82–0.85) between sire lines. The dam line Y‐L‐50 (½ Y × ½ L) had higher total born per litter and piglets born alive, and YLP‐75 (1/8 Y × 1/8 L × 3/4 P) was associated with higher values of litter weight at birth (highest posterior density region at 95% = 9.92, 16.41 kg). There are relevant differences in kinematic variables between the assessed sire lines and the differences in morphometric and litter size variables were also relevant. The York‐Landrace hybrid sows had higher total born per litter and piglets born alive, and there were relevant differences when compared with YLP‐50 (¼ York × ¼ Landrace × ½ Pietrain). Differences in kinematic and morphometric variables between sire and dam lines related to fertility need to be further studied. [ABSTRACT FROM AUTHOR]

Single- and group-housed pregnant sows were assessed during 8 weeks (4th and 8th to 14th) with regard to physiological, reproductive, welfare indicators and gene expression profiling. Compared to single-housed sows, group-housed sows had decreased non-return to estrus at 56 days after artificial insemination (AI) (83% vs 92%) and farrowing rate (78% vs 88%), respectively. Furthermore, group-housed sows showed a higher degree (p < 0.01) of advantageous physiological indicators, such as albumin (odds ratio [OR] = 4.4), alkaline phosphatase (OR = 1.5), bactericidal (OR = 3.2) and complement (OR = 24.3), and disadvantageous for alanine amino transferase (OR = 0.5), bilirubin (OR = 0.4), lysozyme (OR = 0.3) and C-reactive protein compared to single-housed. Eighty-seven genes related to immune response were underexpressed (log fold change ≤ 1.5; p < 0.05) during the 8th to 14th weeks in the group compared to single-housed sows, which in turn showed an immunomodulatory reduction on the expression of 43 genes during the 11th to 14th compared to the 4th week. Overall, the results were interpreted as indicative of greater comfort state of the group compared to single-housed sows. [ABSTRACT FROM AUTHOR]

Fatty acid composition is an important aspect of meat quality in ruminants. Improving the beneficial fatty acid level in cashmere goat meat is important to its economic value. To investigate microRNAs (miRNAs) and mRNAs that regulate or coregulate polyunsaturated fatty acid (PUFA) synthesis and metabolism in the Inner Mongolia cashmere goat, we used longissimus dorsi muscle (WLM) and biceps femoris muscle (WBM) for transcript-level sequencing. RT-qPCR was used to evaluate the expression of mRNAs and miRNAs associated with PUFA synthesis and metabolism. The total PUFA content in the WBM was significantly higher than that in the WLM (P < 0.05). Our study is the first to systematically report miRNAs in cashmere goat meat. At the mRNA level, 20,375 genes were identified. ACSL1 , CD36 and TECRL were at the center of a gene regulatory network and contributed significantly to the accumulation and metabolic regulation of fatty acids. At the miRNA level, 426 known miRNAs and 30 novel miRNAs were identified. KEGG analysis revealed that the miRNA target genes were involved mainly in the PPAR signaling pathway. The mRNA-miRNA coregulation analysis showed that ACSL1 was negatively targeted by nine miRNAs: chi-miR-10a-5p, chi-miR-10b-5p, chi-miR-130b-5p, chi-miR-15a-5p_R-1, chi-miR-15b-5p, chi-miR-16a-5p, chi-miR-16b-5p, chi-miR-181c-5p_R+1, and chi-miR-26b-5p. Finally, we speculated that the simultaneous silencing of ACSL1 by one or more of these nine miRNAs through PPAR signaling led to low ACSL1 expression in the WLM and, ultimately to high PUFA content in the WBM. Our study helps elucidate the metabolic regulation of fatty acids in Inner Mongolia cashmere goats. [ABSTRACT FROM AUTHOR]

Background: Meat from Jeju native pigs (JNPs) is highly popular among Korean consumers; however, the production efficiency is limited due to the low adult body weight. In contrast, the Berkshire breed, which has a genetic background closely related to Asian native pigs, gains weight more efficiently. Objectives: This study focused on the differential expression of genes related to muscle growth in postnatal myogenesis between Berkshire and JNPs, specifically the myogenic regulatory factor (MRF) genes (MyoD, Pax7, Myf5, Myf6 and MyBPH). The MRF family is primarily involved in the proliferation and development of muscle. Methods: Qualitative reverse transcription‐polymerase chain reaction and western blot analyses revealed that expression of MyoD and Pax7 was significantly higher in Berkshire pigs than in JNPs. In addition, co‐expression of MyoD and Pax7 was observed in myotubes formed in cultured C2C12 cells. ToppCluster was used to elucidate the relationship between biological processes of the MRFs and muscle‐related signalling pathways. Results: MyoD and Pax7 are factors essential for the activation of satellite cell during myogenesis. However, the mRNA and protein levels of MyBPH (which is responsible for meat quality, e.g. water content, colour and tenderness) are significantly higher in both 1‐day‐old piglets and adult JNPs than in Berkshire pigs. Conclusions: This study provides a genetic understanding of myogenesis in the postnatal and adult stages of Berkshire pigs and JNPs. Moreover, these results will help identify marker genes related to muscle mass, growth performance and meat quality in indigenous Korean pig breeds. [ABSTRACT FROM AUTHOR]

Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis. [ABSTRACT FROM AUTHOR]

The administration of fish oils is known to cause changes in several reproductive parameters of domestic animals. The ingestion of polyunsaturated fatty acids (PUFAs) of the omega‐3 family, such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), has been described and correlated with changes in the semen quality, testosterone levels and male fertility. Nevertheless, few studies monitored and registered effects after ceasing supplementation. In the present study, we monitored the Doppler velocimetric and ultrasonographic parameters of nine dogs' testis for 90 days (D90) checking the effect of salmon oil supplementation, and monitoring continued for 60 days more, after ceasing supplementation (D150). Ultrasonographic evaluations comprised determining the Doppler velocimetric parameters, testicular and epididymal volume, and testicular echotexture. Peak systolic velocity (PSV) as well as final diastolic velocity (EDV) in the supratesticular arteries (STA), and marginal artery (MA) increased during the period of treatment and kept that level up to D150. There was no difference between the fish‐oil supplementation period and the unsupplemented one regarding the testicular and epididymal volume and echogenicity and heterogeneity characteristics. A negative correlation was found between heterogeneity of testis and sperm production (r = −.41, p =.008). Doppler velocimetry indices were affected by the supplementation, leading to an increase in testicular blood flow. [ABSTRACT FROM AUTHOR]

The present experiment investigated the impact of administrations of lactic fermented turmeric, black pepper or a mixture of both into diets on the hematological parameters and intestinal ecology and morphology of broilers. Three hundred and ninety two broilers were spread to T0 (control), T1 (feed administrated with 1% lactic fermented turmeric), T2 (feed administrated with 1% lactic fermented black pepper) and T3 (feed administrated with 1% lactic fermented turmeric and 1% lactic fermented black pepper). Blood sampling was conducted at days 21 and 35, while intestinal sampling was at day 35. At day 21, erythrocyte counts were greater (P ≤ 0.05) for T1 compared to that for T2 and T3. Broilers in T1 had deceased (P ≤ 0.05) serum total triglyceride compared to that of T0 and T3. The concentration of globulin was reduced (P ≤ 0.05) in T3 than that in T0 and T1. At day 35, serum triglyceride level was more elevated (P ≤ 0.05) in T0 compared to that in T2 and T3 groups. Serum cholesterol as well as low-density lipoprotein levels were lower (P ≤ 0.05) in T3 than that in T0. Compared to other broilers, total protein and globulin concentrations were lower (P ≤ 0.05) in T3. A bigger (P ≤ 0.05) ratio of albumin to globulin (A/G) was seen in T3 compared to that in T1 and T2. Creatinine was greater (P ≤ 0.05) in T1 than in others. The titer of antibody toward vaccine of Newcastle disease was elevated (P ≤ 0.05) in T1 and T2 than in T0. The LAB counts were enhanced (P ≤ 0.05) in ileum of T1 and T2 than that in T0. Compared to T0, the villi height of jejunum was elevated (P ≤ 0.05) in treated broilers. In conclusion, administration of fermented turmeric powder improved erythrocyte counts, antibody titer toward Newcastle disease vaccine, LAB population and jejunal villi height of broilers. [ABSTRACT FROM AUTHOR]

Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature–humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected. Its magnitude was more substantial for loin depth and carcass growth, but all the traits studied showed a different impact of heat stress and different magnitude of genotype by environment interaction. For backfat depth, heritability was larger under comfortable conditions (no heat stress), as compared to heat stress conditions. Genetic correlations between extreme values of environmental conditions were lower (∼0.5 to negative) for growth and loin depth. Based on the solutions obtained from the model, sires were ranked on their breeding value for general performance and tolerance to heat stress. Antagonism between overall performance and tolerance to heat stress was moderate. Still, the models tested can provide valuable information to identify genetic material that is resilient and can perform equally when environmental conditions change. Overall, the results obtained from this study suggest the existence of genotype by environment interaction for carcass traits, as a possible genetic contributor to heat tolerance in swine. [ABSTRACT FROM AUTHOR]

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 <.05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int‐1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE‐related traits. [ABSTRACT FROM AUTHOR]

The missense mutation Asp298Asn in the melanocortin 4 receptor (MC4R) is associated with daily gain or fatness in pigs (Sus scrofa domesticus). However, to the best of our knowledge, no study has directly compared the effects of the polymorphism between different feeding levels, even though diet plays a vital role in the swine industry. To explore possible differences, data from 439 mostly commercial hybrids fattened ad libitum and 119 commercial hybrids fattened with restricted feed ration were collected. The recorded traits were average daily gain (ADG), feed conversion ratio (FCR), carcass weight (CW), dressing percentage (DP), lean meat content (LM), backfat thickness (BFT), lean cuts weight, and meat quality parameters such as pH, temperature, drip loss, and CIELAB colour space. The general linear model revealed that the overall effect of MC4R was not statistically significant, but significant differences (p < 0.05) were found in ADG, FCR, CW, DP, LM, and BFT. In the ad libitum category, the AA genotype (298Asn/298Asn) tended to be the most favourable for growth-related traits, with the lowest LM, which is consistent with previous findings. In the restricted category, on the other hand, GA heterozygotes (298Asp/298Asn) achieved the best performance in terms of growth, whereas AA homozygotes showed the worst performance. Therefore, these results raise the possibility of an interaction between MC4R and the feeding level., (© 2022 John Wiley & Sons Ltd.)

A study was conducted to assess the effect of feeding different crude protein (CP) levels with isocaloric metabolizable energy (ME) diets on growth performance, carcass traits, and myostatin (MSTN) gene expression of Aseel chicken during 0 to 16 weeks of age. A total of two hundred and ten day-old Aseel chickens were randomly allotted to seven dietary treatment groups. Each group had thirty chicks distributed into three replicates of ten chicks in each. Experimental diets were formulated to have varying levels of CP, viz. 18.5, 19.0, 19.5, 20.0, 20.5, 21.0, and 21.5%, with isocaloric energy of 2800 kcal ME/kg diets of mash feed fed to birds in a completely randomized design. Different CP levels had a significant effect (P < 0.05) on the body weight gain (BWG) of Aseel chicken. At the end of 16 weeks of age, the group fed 21% CP gained 223.53 g more than the lowest CP (18.5%)-fed group. The different CP levels did not significantly (P > 0.05) influenced the feed intake of all treatment groups, but numerically highest feed intake was observed in the lowest CP (18.5%)-fed group. However, significant differences in feed efficiency (FE) appeared from the 13th week only with the 21.0% CP-fed group showing the best FE until the 16th week (3.86 to 4.06). The maximum dressing % (70.61) was observed by the 21% CP-fed group. The CP 21% diet down-regulated the MSTN gene expression in breast muscle tissue to 0.07 folds when compared to the diet of CP 20%. The best economical coordinates for maximum performance for Aseel chicken appeared to be CP of 21% and ME of 2800 kcal/kg to achieve the best FE of 3.86 at the earliest age of 13 weeks. In conclusion, 21% CP in an isocaloric diet of 2800 kcal ME/kg, in Aseel chickens, would be optimum to improve the growth performance at maximum in terms of BWG and FE up to 16 weeks of age., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

In Brazil, water buffaloes have been used to produce milk for mozzarella cheese production. Consequently, the main selection criterion applied for the buffalo genetic improvement is the estimated mozzarella yield as a function of milk, fat and protein production. However, given the importance of reproductive traits in production systems, this study aimed to use techniques for identifying genomic regions that affect the age at first calving (AFC) and first calving interval (FCI) in buffalo cows and to select candidate genes for the identification of QTL and gene expression studies. The single‐step GBLUP method was used for the identification of genomic regions. Windows of 1 Mb containing single‐nucleotide polymorphisms were constructed and the 10 windows that explained the greatest proportion of genetic variance were considered candidate regions for each trait. Genes present into the selected windows were identified using the UOA_WB_1 assembly as the reference, and their ontology was defined with the Panther tool. Candidate regions for both traits were identified on BBU 3, 12, 21 and 22; for AFC, candidates were detected on BBU 6, 7, 8, 9 and 15 and for first calving interval on BBU 4, 14 and 19. This study identified regions with great contribution to the additive genetic variance of age at first calving and first calving interval in the population of buffalo cows studied. The ROCK2, PMVK, ADCY2, MAP2K6, BMP10 and GFPT1 genes are main candidates for reproductive traits in water dairy buffaloes, and these results may have future applications in animal breeding programs or in gene expression studies of the species. [ABSTRACT FROM AUTHOR]