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This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.

Sperm quality decreases over time, so bull semen may need to be preserved after field collection. However, the effect of handling such semen samples from commercial farms and placing them in very short–term storage has not been elucidated. Therefore, ejaculate from 25 bulls from 1 dairy and 14 beef cattle farms were collected under farm conditions and evaluated for semen quality during the first two hours after collection. Two commercial extenders (AndroMed® and BIOXcell®) and two different storage temperatures (5 °C and room temperature) were used to evaluate the influence on semen quality and sperm kinetics in ejaculates grouped into three evaluation times, based on time since collection (Time 1: n = 7; Time 2: 75–105 min, n = 11; and Time 3: 105–120 min, n = 7). Classical semen parameters, sperm motion kinetics by CASA and colony-forming units were assessed. The differences between both extenders in curvilinear and straight–line velocities (VCL and VSL) for the different time groups (Time 2 and Time 3) were statistically significant for p < 0.05. AndroMed® showed lower VSL, straightness and linearity in sperm compared to BIOXcell® (p < 0.05). In conclusion, AndroMed® induced more curvilinear movement, while BIOXcell® stimulated straighter motility.

Traditional breeding techniques, applied incrementally over thousands of years, have yielded huge benefits in the characteristics of agricultural animals. This is a result of significant, measurable changes to the genomes of those animal species and breeds. Genome editing techniques may now be applied to achieve targeted DNA sequence alterations, with the potential to affect traits of interest to production of agricultural animals in just one generation. New opportunities arise to improve characteristics difficult to achieve or not amenable to traditional breeding, including disease resistance, and traits that can improve animal welfare, reduce environmental impact, or mitigate impacts of climate change. Countries and supranational institutions are in the process of defining regulatory approaches for genome edited animals and can benefit from sharing approaches and experiences to institute progressive policies in which regulatory oversight is scaled to the particular level of risk involved. To facilitate information sharing and discussion on animal biotechnology, an international community of researchers, developers, breeders, regulators, and communicators recently held a series of seven virtual workshop sessions on applications of biotechnology for animal agriculture, food and environmental safety assessment, regulatory approaches, and market and consumer acceptance. In this report, we summarize the topics presented in the workshop sessions, as well as discussions coming out of the breakout sessions. This is framed within the context of past and recent scientific and regulatory developments. This is a pivotal moment for determination of regulatory approaches and establishment of trust across the innovation through-chain, from researchers, developers, regulators, breeders, farmers through to consumers.

Las técnicas de reproducción asistida (TRA) son una herramienta clave en la conservación de especies, así como en el aumento de la productividad y rentabilidad de los animales de granja mediante un mayor control de la función reproductiva. Sin embargo, en el caso de los pequeños rumiantes, tales como cérvidos y ovinos, las técnicas más desarrolladas han sido únicamente la inseminación artificial y la transferencia de embriones, dejando a un lado otras técnicas como la producción in vitro de embriones (PIV) debido al bajo rendimiento de la misma. El escaso desarrollo de la PIV muestra la necesidad de controlar o al menos conocer los factores limitantes de esta técnica. El primer paso durante PIV es la recolección de ovocitos de alta calidad y competencia para el desarrollo embrionario. Para especies silvestres, como el ciervo ibérico, la recogida de muestras representa un problema ya que el sacrificio de los animales suele realizarse lejos de los laboratorios, implicando tiempos de transporte prolongados hasta la recolección y procesado de los ovocitos. Esto puede influir negativamente en la capacidad de desarrollo de los ovocitos inmaduros y, por lo tanto, en su calidad. Del mismo modo, la recolección de muestras durante la temporada de verano, cuando las temperaturas son altas, da como resultado un aumento de la temperatura corporal que puede disminuir la calidad de los ovocitos y la competencia del embrión. Dichos factores pueden afectar la eficiencia de la técnica de producción de embriones in vitro por lo que conservar la calidad de los ovocitos podría mejorar el número de embriones obtenidos y aumentar la rentabilidad de la técnica para rumiantes. Los trabajos llevados a cabo en la presente Tesis Doctoral tienen como objetivo comprender los factores por los que la calidad de los ovocitos obtenidos se ve afectada, así como mejorar la preservación de la calidad de los mismos hasta que se procesan los ovarios con el fin último de aumentar el rendimiento de la PIV en pequeños rumiantes. En algunos experimentos, la especie ovina fue utilizada como modelo de pequeño rumiante por la disponibilidad de muestras. En el primer capítulo de la Tesis se estudiaron los eventos celulares y moleculares relacionados con la competencia de los ovocitos a lo largo del tiempo tras del sacrificio del animal, con el fin de comprender cómo puede verse afectada la calidad de los ovocitos, y por ende, la competencia del embrión. Se estudió el efecto del tiempo de almacenamiento de los ovarios (3, 5, 7, 9, 11 y 13 h) y el medio en el que fueron transportados (TCM199 y solución salina) sobre la calidad de los ovocitos y su competencia de desarrollo. Para ello, distintos parámetros fueron evaluados: viabilidad, fragmentación del ADN, estado oxidativo mediante la evaluación del contenido de glutatión (GSH) y especies reactivas de oxígeno (ROS), actividad caspasa-3, potencial y distribución de la membrana mitocondrial, y abundancia relativa de trascritos de ARNm. Tras la maduración in vitro (MIV), también se evaluaron la viabilidad y calidad de las células del cumulus la competencia meiótica y el porcentaje de fertilización, de embriones y la calidad de los blastocistos. Los resultados mostraron que a partir de las 7 horas de almacenamiento, la calidad y la competencia del ovocito se ve afectada. El segundo capítulo de la presente Tesis se estudió la calidad del ovocito a lo largo de diferentes estaciones del año vinculando la calidad de los mismos a un efecto de la temperatura. Así, los ovocitos recolectados en invierno mostraron una mayor competencia de desarrollo que los ovocitos recogidos en verano y otoño, pudiendo deberse al efecto de las altas temperaturas. Para conocer el efecto de las temperaturas sobre la calidad del ovocito, se llevó a cabo un estudio de estrés por calor. Para ello, se incubaron los ovarios en solución salina a distintas temperaturas: 30ºC, 38,5ºC, 40ºC o 41ºC. Tras el estrés por calor, las temperaturas más altas 40ºC y 41ºC afectaron a la calidad y competencia del ovocito. El tercer capítulo de la Tesis se centró en la suplementación de melatonina a los medios de transporte de los ovarios, con el fin de prevenir o incluso revertir el daño producido por tiempos prolongados de transporte y así mejorar la competencia del ovocito. Para ello, se evaluó el efecto de diferentes concentraciones de melatonina (10-11, 10-9, 10-7, 10-5 y 10-3 M) sobre la competencia del ovocito y el desarrollo y la calidad de los blastocistos. Los resultados revelaron una respuesta dependiente de la dosis de melatonina utilizada, donde 10-9 M fue el tratamiento más efectivo en términos de calidad de ovocitos y rendimiento de blastocistos bajo condiciones de estrés. En conclusión, la presente Tesis aporta nueva información sobre los mecanismos por los que se ve afectada la calidad de los ovocitos, especialmente cuando son inevitables tiempos de transporte de ovarios prolongados o temperaturas extremas. Además, también permite comprender cómo la suplementación con melatonina en los medios de transporte de los ovarios preserva la calidad de los ovocitos hasta que se procesan los ovarios, lo que podría promover el uso de tecnologías reproductivas en pequeños rumiantes.

El oviducto proporciona el microambiente óptimo para el desarrollo embrionario temprano, periodo en el que acontecen en el embrión procesos críticos como la reprogramación epigenética... Fil: Barrera, Antonio Daniel. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina. Fil: García, Elina Vanesa. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina. Fil: Gómez, Paula. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina.

La PCR es una técnica ampliamente utilizada por su alta sensibilidad y reproducibilidad. Una de las variantes más reconocidas es la PCR en tiempo real que combina simultáneamente la amplificación y la detección, correlacionando el producto de cada ciclo con una señal de intensidad de fluorescencia lo que posibilita además su cuantificación... Fil: Gómez, Paula. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina. Fil: García, Elina Vanesa. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina. Fil: Furnus, Cecilia. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina. Fil: Barrera, Antonio Daniel. Universidad Católica de Salta. Facultad de Ciencias Agrarias y Veterinarias; Argentina.

In Nellore beef cattle, studies addressing genetic correlations between ultrasound marbling content and other economically important traits are still incipient. Therefore, this work aimed to estimate heritability and genetic correlations between ultrasound marbling content in the longissimus dorsi muscle (MARB) and growth, reproductive, feed efficiency, and carcass-related traits in a Nellore beef cattle population from Brazil. Phenotypic records of 614,395 Nellore animals were used and included adjusted weight at 210 (W210) and 450 (W450) days of age, adult cow weight (AW), early heifer pregnancy (EH), stayability (STAY), adjusted scrotal circumference at 365 days of age (SC365), ribeye area (REA), subcutaneous backfat thickness (BF), rump fat thickness (RF), and marbling (MARB). The genetic parameters for all traits but EH and STAY were estimated considering a linear animal model, whereas for those two nonlinear traits, a threshold animal model was used. The direct and correlated response to selection for MARB versus the other traits, and the relative efficiency of selection, were also calculated. The heritability estimate for MARB was 0.31 and for the other conventional evaluated traits was low to moderate, with values ranging from 0.14 to 0.41. The genetic correlations between MARB and growth, reproductive, feed efficiency, and carcass-related trait were very low, with values close to zero, with similar correlated responses. The MARB displayed adequate genetic variability to respond to selection and crossbreeding programs looking forward to higher meat quality and differential market standards for the Nellore beef. The selection for growth, reproductive, feed efficiency, and carcass-related traits would not affect MARB in Nellore beef cattle and vice versa. Therefore, this trait should be included as a selection criterion in the Nellore breeding program.

Antimicrobial resistance is an important threat to public health worldwide, being one of the main death causes in 2050. Moreover, global health is currently underpinned by the “One Health” concept, whereby livestock is strictly related to human and environmental health. However, in the case of the meat rabbit industry, antibiotic additives are still added to prevent gastrointestinal diseases. Current food and consumer awareness require the implementation of sustainable production systems, where robustness and resilience are increasingly important. Hence, the aim of this study was to evaluate the effect of antibiotic feed supplementation on microbiota, and productive performance during the rabbit growing period in a robust genetic line. For this purpose, a total of 432 weaned rabbits were randomly housed, cecum samples were taken on the weaning day and at the end of the growing period (28 and 61 days of age, respectively), and 16S rRNA sequencing analysis was performed. Results showed a higher microbiota complexity at the end of growing in both experimental groups. Firmicutes represented the dominant phylum of the cecal community, followed by Bacteroidota in both groups. Moreover, Victivallis and Escherichia-Shigella genera were only identified in the experimental group without antibiotic supplementation at the end of the growing period. In conclusion, antibiotic feed supplementation had no effect on microbiota composition and productive performance in the robust genetic line reared. These results evidence the importance of the development of rabbit robust genetic lines as an alternative tool to antibiotic administration in epizootic enteropathy control.

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.

Submitted by Rodrigo Zeni dos Santos (rodrigo.zeni@unesp.br) on 2022-08-09T20:20:17Z No. of bitstreams: 1 Dissertação_Zeni_vs6.pdf: 2835746 bytes, checksum: 6832e7ce3e33e4b2b1de875b24aec13e (MD5) Rejected by Lucilene Cordeiro da Silva Messias null (lubiblio@bauru.unesp.br), reason: Favor refazer a submissão seguindo as orientações abaixo: 1 - Inserir a cópia da ata de defesa após a ficha catalográfica, pois é um elemento obrigatório Agradecemos a compreensão. on 2022-08-10T11:33:08Z (GMT) Submitted by Rodrigo Zeni dos Santos (rodrigo.zeni@unesp.br) on 2022-08-11T13:07:28Z No. of bitstreams: 1 Dissertação_Zeni_vs6.pdf: 2908902 bytes, checksum: 7a9439b226624a6c63936161e2814957 (MD5) Approved for entry into archive by Lucilene Cordeiro da Silva Messias null (lubiblio@bauru.unesp.br) on 2022-08-11T13:33:55Z (GMT) No. of bitstreams: 1 santos_rz_me_bauru.pdf: 2908902 bytes, checksum: 7a9439b226624a6c63936161e2814957 (MD5) Made available in DSpace on 2022-08-11T13:33:55Z (GMT). No. of bitstreams: 1 santos_rz_me_bauru.pdf: 2908902 bytes, checksum: 7a9439b226624a6c63936161e2814957 (MD5) Previous issue date: 2022-07-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Os genomas dos organismos eucariotos estão repletos de sequências de DNA repetitivos. Dentre eles, os DNAs satélites (satDNAs) constituídos em arranjos de sequências repetidas em tandem. Historicamente, técnicas distintas foram utilizadas para o isolamento e caracterização destes satDNAs, porém o advento de tecnologias de Sequenciamento de Nova Geração (NGS), possibilitou a utilização de reads curtos, que juntos a ferramentas bioinformáticas, foi decisivo para estudos que permitiram a caracterização de coleções de satDNAs (satelitomas) de uma espécie. O primeiro satelitoma caracterizado em peixes foi realizado na espécie Psalidodon paranae, com a utilização da pipeline RepeatExplorer1 e revelou uma quantidade significativa deste tipo de sequência no genoma deste organismo, incluindo várias famílias presentes no cromossomo B desta espécie. Com isso, o objetivo inicial do estudo foi utilizar de uma nova pipeline, o TAREAN, para uma reavaliação do satelitoma da espécie P. paranae e uma comparação entre diferentes pipelines usadas para a caracterização destas sequências, o que resultou em 56 novas famílias caracterizadas para esta espécie. Com o sequenciamento de seis novas bibliotecas de reads curtos de P. paranae, três indivíduos contendo cromossomo B e três indivíduos não contendo, foram apresentados dados de abundância de todo este satelitoma, com enfoque em satélites presentes no cromossomo B. Os resultados evidenciaram um satélite caracterizado por TAREAN mais abundantes que o ApaSat02, que até o atual trabalho era o segundo mais abundante da espécie, novos quatro DNAs satélites mais abundantes que o ApaSat03, além de novos satélites muito presentes nos cromossomos B da espécie, apresentando essa pipeline como um grande auxílio para a expansão dos satelitomas anteriormente caracterizados. Além disso, uma análise mais detalhada em reads longos possibilitou a estudo de como cada DNA satélite do catálogo é estruturado ao longo do genoma de Psalidodon paranae, apresentando seu tamanho médio e o valor máximo atingindo de cada arrays destes DNAs satélites, auxiliando na explicação destes possuírem ou não uma sinais a nível cromossômico e nos apontando futuros candidatos a aplicação da técnica de FISH. The genomes of eukaryotic organisms have a large number of repetitive DNA 99 sequences. Among them, the satellite DNAs (satDNAs) constitute arrays of tandem 100 repeated sequences. Historically, different techniques were used for the 101 characterization of satDNAs, the advent of Next Generation Sequencing (NGS) 102 technologies enabled the use of short reads, with bioinformatics tools, was decisive 103 for studies that allowed the characterization collections of satDNAs (satellitomes)in 104 a specie. The first fish satellitome characterized was for the species Psalidodon 105 paranae, characterized using the pipeline RepeatExplorer1 and revealed a 106 significant amount of this type of sequence in the genome of this organism, 107 including several families present in the B chromosome of this species. Thus, the 108 initial objective of this study was using a new pipeline, TAREAN, to expand the 109 satellite of the Psalidodon paranae and a comparison between different pipelines 110 used for the characterization of these sequences, which resulted in 56 new families 111 characterized for this species. We perform the sequencing of six new libraries of 112 short reads of P. paranae, three individuals containing B chromosome and three 113 individuals not containing, abundance of all this satelitome were calculated, 114 focusing on satellites present in the B chromosome. Resulting in a satellite 115 characterized by TAREAN more abundant than ApaSat02, until the current work the 116 second most abundant of this species, in addition to four others more abundant 117 than ApaSat03, and new satellites very present in the B chromosomes of the 118 species, contributing for the expansion of previously characterized satellites. In 119 addition, a detailed analysis of long reads was performed and presented the 120 average size and the maximum value reached for each array of these satellite DNAs 121 of the Psalidodon paranae species, helping to explain the chromosomal signaling of 122 these satellite DNAs. 88887.483888/2020-00

Submitted by Leonardo Moura Giglio (leonardo.moura@unesp.br) on 2022-08-15T18:10:25Z No. of bitstreams: 1 Dissertacao - Leonardo Moura Giglio - final ata e ficha.pdf: 2057593 bytes, checksum: 2323dc25ea2c642f6572549b0129b124 (MD5) Approved for entry into archive by Lucilene Cordeiro da Silva Messias null (lubiblio@bauru.unesp.br) on 2022-08-16T11:34:09Z (GMT) No. of bitstreams: 1 giglio_lm_me_bauru.pdf: 2057593 bytes, checksum: 2323dc25ea2c642f6572549b0129b124 (MD5) Made available in DSpace on 2022-08-16T11:34:09Z (GMT). No. of bitstreams: 1 giglio_lm_me_bauru.pdf: 2057593 bytes, checksum: 2323dc25ea2c642f6572549b0129b124 (MD5) Previous issue date: 2022-07-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) O genoma dos organismos eucariotos apresenta uma porção repetitiva bastante expressiva, com a classe dos DNAs satélites podendo representar grande parte do DNA nuclear e, também, contribuir para a diferença do tamanho dos genomas entre diferentes espécies. Considera-se que os DNAs satélites surgem a partir de duplicações de novo de sequências preexistentes no genoma das espécies, se disseminam, e posteriormente expandem seus arranjos, a forma em que se organizam. Esses arranjos passam por processos de homogeneização e posterior fixação de sua composição, sob o regime da evolução em concerto. Esses mecanismos evolutivos podem agir independentemente nas diferentes espécies, inclusive, agir independentemente nos diferentes arranjos dentro de um mesmo genoma, o que normalmente resulta em DNAs satélites gênero ou espécie específicos. Porém, hoje temos conhecimento de alguns casos de satélites que se mantiveram conservados em diferentes espécies distribuídas por táxons maiores, como toda uma ordem, apresentando inclusive transcrição, o que vai contra as predições da evolução em concerto em um contexto de ausência de função. Outro modelo de evolução de DNAs satélites é o da hipótese library , que prediz que grupos proximamente relacionados compartilham uma porção do conteúdo ancestral de DNAs satélites, apresentando normalmente diferenças quantitativas relativas a sua abundância no genoma. No presente estudo utilizamos a subordem dos peixes Characoidei, da ordem dos Characiformes, altamente diversa e com origem antiga, e portanto considerada ideal para verificar a existência de satélites compartilhados pelo grupo, testar a hipótese library, e analisar a ação da evolução em concerto nos satélites destas espécies. Para isto, utilizamos bibliotecas genômicas de 15 espécies de diferentes famílias da ordem dos Characiformes e realizamos análises bioinformáticas com a aplicação do TAREAN, uma ferramenta que utiliza um algoritmo de agrupamento de reads para realizar o isolamento dos DNAs satélites das espécies, além de ferramentas de montagem de novo, alinhamento e mapeamento de cópias para realizar a comparação destes satélites entre as espécies. Encontramos sete DNAs satélites presentes nas quatro superfamílias de peixes Characoidei analisadas, demonstrando o compartilhamento de satélites super conservados por toda uma subordem, o que contraria as predições da evolução em concerto, e também corroboram com a hipótese library de evolução dos DNAs satélties. The eukaryotic genomes present a very expressive repetitive portion, with the satellite DNAs class representing a great part of the nuclear DNA and, also, contributing to the differences observed in the species genome sizes. Its assumed that the satellite DNAs originate by de novo duplications in preexistent sequences in the genome, are scattered to different locations and, subsequently, expand their arrays, the way they are organized. These arrays goes through composition homogenization and fixation steps, under the concerted evolution regime. These evolutive mechanisms can act independently in each species, or even act differently in arrays of different genomic locations, and that usually results in genus- or species-specific sallite DNAs. However, today we know of some cases of satellites that have remained conserved in different species distributed over larger taxa, such as an entire order, even presenting transcription, which goes against the predictions of concerted evolution in a context of absent function. Another model of satellite DNA evolution is the library hypothesis, which predicts that closely related groups share a portion of the ancestral content of satellite DNAs, typically showing quantitative differences relative to their abundance in the genome. In the present study, we used the suborder of Characoidei fishes, from the order Characiformes, highly diverse and with ancient origin, and therefore considered ideal to verify the existence of satellites shared by the group, test the library hypothesis, and analyze the action of the concerted evolution in the satellites of these species. For this, we used genomic libraries of 15 species from different families of the Characiformes order and performed bioinformatic analyses with the application of TAREAN, a tool that uses a read clustering algorithm to isolate the species satellite DNAs, as well as de novo assembly, alignment, and copy mapping tools to compare these satellites between species. We found seven satellite DNAs present in the four analyzed Characoidei fish superfamilies, demonstrating the sharing of super conserved satellites across an entire suborder, which contradicts the predictions of concerted evolution, and also corroborates with the library hypothesis of satellite DNA evolution. CAPES: 88887.483868/2020-00

Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

Development of new methods for early diagnosis of pregnancy can be important to increase the reproductive efficiency and profitability of dairy herds. The bovine conceptus secretes IFN-τ that stimulates the transcription of several genes in circulating immune cells and extrauterine tissues. The aims of this study were to evaluate the mRNA abundance for pregnancy predictability of a classic gene stimulated by IFN-τ (ISG15) and a novel potential pregnancy marker (LGALS3BP) in peripheral blood mononuclear cells (PBMC), total blood leukocytes (TBL) or milk leukocytes (TML), and cervical cells (CC) on d 20 after timed artificial insemination (TAI) in dairy cattle. Eighteen Holstein females (12 cows and 6 heifers) were submitted to an estrous synchronization protocol for TAI (d 0). On d 20 post-TAI, blood samples were collected from coccygeal vessels for isolation of PBMC and in Tempus Blood RNA tubes (Applied Biosystems) for TBL. Samples of CC were collected using a cytological brush, and the TML were isolated from milk samples collected before routine milking. Pregnancy diagnosis was performed on d 30 post-TAI using transrectal ultrasonography, and females were classified as pregnant (n = 8) or nonpregnant (n = 10). Total RNA was extracted and mRNA abundance of target genes (ISG15 and LGALS3BP) was quantified by reverse-transcription quantitative PCR and normalized in relation to reference genes. Data were analyzed by ANOVA using the MIXED procedure of SAS (SAS Institute Inc.). The mRNA abundance of ISG15 was greater in pregnant than in nonpregnant animals for PBMC, TBL, and CC. No difference was detected for TML based on pregnancy status. For LGALS3BP mRNA abundance, no difference was detected between pregnant and nonpregnant animals for PBMC, TBL, and TML, but a tendency for greater abundance in pregnant animals was observed for CC. The fold change for ISG15 in each pregnant cow related to the mean of nonpregnant animals was 2.73 ± 0.31, 3.40 ± 2.17, 1.64 ± 0.29, and 0.005 ± 0.002 for PBMC, CC, TBL, and TML, respectively. The fold change for LGALS3BP in each pregnant cow related to the mean of nonpregnant animals was 0.97 ± 0.38, 1.77 ± 0.39, 0.20 ± 0.08, and 0.70 ± 0.11 for PBMC, CC, TBL, and TML, respectively. The receiver operating characteristic curve analysis indicated that ISG15 abundance predicted pregnancy in PBMC (area under curve, AUC = 0.92) and CC (AUC = 0.77) but not in TBL (AUC = 0.72) or TML (AUC = 0.52). In conclusion, mRNA abundance for ISG15 in PBMC was the best predictor for pregnancy at d 20 post-TAI, whereas TBL and TML were not good predictors of pregnancy on d 20 post-TAI. The mRNA abundance of LGALS3BP was not associated with pregnancy status in any type of cell evaluated.

255 p. Zelulen patroi epigenetikoak haien fisiologia zehazten du, eta organismo baten garapenean zehar zelula bakoitzak duen patroi espezifikoak haren diferentziazioa bideratzen du, organismo osoaren garapen egokia bat koordinatuz. Hala ere, inguruneak eta bizi estiloak eragin kaltegarriak eragin ditzake norbanakoengan, zelulen fisiologia zehazten duen patroi epigenetikoan eraginez. Biomedikuntzak egun duen erronka handienetariko bat inguruneak edota kanpo faktoreek eragindako aldaketa epigenetikoek sortu ditzaketen osasun arazoen edo gaixotasunen atzean dauden mekanismo molekularrak ulertzea da. Bestalde, aldaketa fisiologiko horiek eragiten dituzten marka epigenetikoak denboran zehar mantendu daitezkeela ikusi da. Beraz, kanpo faktore horiekin kontaktu zuzena izan duten bizidunek eragin nabarmenak pairatzeaz gain, denbora zehar mantentzen dituzte memoria zelularra baimentzen duten mekanismoen bidez, eta horrez gain, eragin horien belaunaldiz belaunaldiko herentzia bat ere eman daitekeela ziurtatzen dituzten zantzuak geroz eta ugariagoak dira.Aurrekari horiek kontuan hartuta, doktore-tesi honen helburu nagusia morfinak eragin ditzakeen aldaketa epigenetiko nagusiak identifikatu, eta horiek zelulen edota organismo bizidun konplexuen fisiologian eragin ditzakeen aldaketak aztertzea izan da. Aldaketa fisiologiko horiek eragiten dituzten mekanismo epigenetiko ezberdinak badaude ere, kasu honetan DNAren metilazioan zentratu gara, eta Bigarren Belaunaldiko Sekuentziazio teknikak erabili ditugu metiloma aztertzeko helburuarekin. Ikerketa lan honek, besteak beste, memoria epigenetikoaren atzean dauden mekanismoak aztertzeko aukera eskaini digu. Morfinak asaldurak sortzen ditu birprogramazio epigenetikoan funtsezko prozesua den X kromosomaren inaktibazioan, eta gainera, asaldura horiek mantentzeko eta heredatzeko potentzialtasuna dutenez, morfinak eragindako zelularteko memoriaren azpian dauden mekanismo epigenetikoak ikertu ditugu. Horrez gain, birprogramazioaren helburu nagusia den eta zelula amen bereizgarria den pluripotentzia indartua geratzen dela frogatu dugu morfinaren presentzian, horretarako ezinbestekoak diren zenbait prozesu molekular bultzatuz; transkripzio faktore garrantzitsuen adierazpena doiketa, genomaren estatus epigenetikoa murrizketa, eta X kromosoma egoera aktiboaren mantenua. Horrek, morfinaren erabilpenak zelulen fisiologian izan ditzakeen ondorioetan are gehiago sakontzeko aukera eskaini digu, aurrerapauso interesgarriak gauzatuz enbrioiaren garapen-prozesuaren ezagutzan.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior DNA repetitivo compõe uma porção substancial do genoma eucariótico e é importante para sua estabilidade, evolução, regulação e arquitetura. Formigas cultivadoras de fungos (subtribo Attina, clados Paleoattina e Neoattina) mostram altas taxas de rearranjos estruturais em seus genomas, com contrações e expansões gênicas, que foram necessárias para o estabelecimento de seu estilo de vida baseado em sociedades agrícolas. Processos que levaram a diversificação genômica em Attina também podem ter atuado sobre sequências repetitivas, destacando a importância do estudo do DNA repetitivo nesse grupo. Consistente com essa hipótese, dados citogenéticos em Attina mostram que sequências repetitivas heterocromáticas são ricas em GC, o que é um traço incomum em Formicidae. Assim, essa tese focou no estudo do DNA repetitivo em Attina a partir de uma abordagem citogenética molecular. Considerando que a maior parte dos estudos disponíveis envolvendo sequências repetitivas para Attina bem como para Formicidae, estão disponíveis para genes rDNA, no capítulo I dados sobre mapeamento de genes rDNA em formigas foram compilados e resultados inéditos de 13 espécies neotropicais são apresentados. Os dados mostraram que um único sítio de rDNA intracromossômico é a característica mais frequente e provavelmente ancestral em formigas, e que a localização cromossômica de clusters rDNA influencia na restrição/dispersão desses genes no cariótipo. No capítulo II, caracterizamos as espécies de Neoattina Cyphomyrmex transversus, Sericomyrmex maravalhas e Mycetomoellerius relictus, através de citogenética clássica, molecular e bandamentos. Cyphomyrmex transversus e S. maravalhas mostram cariótipos inéditos em seus respectivos gêneros. As três espécies apresentam heterocromatina rica em GC, o que reforça a hipótese de origem comum dessa heterocromatina em Attina. Dados obtidos associados a estudos prévios sugerem que um único sítio de rDNA intracromossômico é plesiomórfico em Attina e que inversões parecem ser importantes para mudar a posição desses genes no cariótipo. No capítulo III, foi produzido uma sonda C 0 t-DNA (sequências altamente e moderadamente repetitivas) de M. relictus que foi hibridizada nos cariótipos de espécies de Paleoattina e Neoattina. Os resultados indicam pelo menos cinco eventos evolutivos que levaram à diferenciação da heterocromatina rica em GC em Attina desde seu provável surgimento no ancestral da subtribo. Adicionalmente, mapeamos as sequências repetitivas (GA) 15 e (TTAGG) 6 em espécies dos dois clados que mostraram resultados mais homogêneos localizadas na eucromatina e telômeros, respectivamente. No capítulo IV, o cariótipo da formiga cortadeira Atta cephalotes foi caracterizado por citogenética clássica, bandamentos cromossômicos e mapeamento físico de diferentes sequências repetitivas (teloméricas, microssatélites e genes rDNA 18S). Atta cephalotes mostrou um cariótipo conservado em relação as demais espécies de Atta, e os possíveis fatores que influenciam essa conservação cromossômica no gênero são discutidos. Os primeiros insights sobre a diversidade e organização cromossômica de vários DNAs repetitivos são apresentados em formigas cortadeiras, úteis para estudos futuros comparativos. Os marcadores citogenéticos utilizados nesta tese em diferentes espécies de Attina indicam padrões distintos de diversificação para o DNA repetitivo localizado na heterocromatina, enquanto o DNA repetitivo da eucromatina e telômeros parece ser mais conservado na subtribo. Palavras-Chave: Formigas. Heterocromatina. Microssatélites. DNA. Telômero. Repetitive DNA constitutes a substantial portion of the eukaryotic genome and are important for its stability, evolution, regulation, and architecture. Fungus farming ants (Attina subtribe, Paleoattina and Neoattina clades) show high rates of structural rearrangements in their genomes, with gene contractions and expansions, which were necessary for the establishment of their lifestyle based on agriculture. Processes that led to genomic diversification in Attina may also have acted on repetitive sequences, highlighting the importance of studying repetitive DNA in this group. Consistent with this hypothesis, cytogenetic data in Attina show that repetitive heterochromatic sequences are rich in GC, which is an uncommon trait in Formicidae. Thus, this thesis focused on the study of repetitive DNA in Attina from a molecular cytogenetic approach. Considering that most of studies involvig repetitive sequences available for Attina as well as Formicidae are available on rDNA genes, in chapter I data on mapping rDNA genes in ants were compiled and unpublished results from 13 Neotropical species are presented. The data showed that a single intrachromosomal rDNA site is the most frequent and probably ancestral feature in ants, and that the chromosomal location of rDNA clusters influences the restriction/dispersion of these genes in the karyotype. In chapter II, we characterized the Neoattina species Cyphomyrmex transversus, Sericomyrmex maravalhas and Mycetomoellerius relictus, through classical and molecular cytogenetics, and chromosomal banding. Cyphomryemx transversus and S. maravalhas show new karyotypes in their respective genera. The three species present GC-rich heterochromatin, which reinforces the hypothesis of a common origin of this heterochromatin in Attina. Data obtained in association with previous studies suggest that a single intrachromosomal rDNA site is plesiomorphic in Attina and that inversions seem to be important to change the position of these genes in the karyotype. In chapter III, a C 0 t-DNA probe (highly and moderately repetitive sequences) from M. relictus was produced and hybridized in the karyotypes of species from Neoattina and Paleoattina clades. The results indicate at least five evolutionary events that led to the differentiation of GC-rich heterochromatin into Attina since its probable emergence in the subtribe's ancestor. Additionally, the repetitive sequences (GA) 15 and (TTAGG) 6 were mapped in species of the two clades that showed more homogeneous results located in euchromatin and telomeres, respectively. In chapter IV, the karyotype of the leaf-cutting ant Atta cephalotes was characterized by classical cytogenetics, chromosomal banding and physical mapping of different repetitive sequences (telomeric, microsatellites and 18S rDNA genes). Atta cephalotes showed a conserved karyotype in relation to other Atta species, and the possible factors that influence this chromosomal conservation in the genus are discussed. The first insights into the chromosomal diversity and organization of the various repetitive DNAs are presented in leaf- cutting ants, useful for future comparative studies. The cytogenetic markers used in this thesis in different Attina species indicate distinct patterns of diversification for the repetitive DNA located in heterochromatin while the repetitive DNA of euchromatin and telomeres seems to be more conserved in the subtribe. Keywords: Ants. Heterochromatin. Microsatelites. DNA. Telomeres.

Resumo: Este estudo analisou a estrutura populacional de ovinos deslanados do núcleo de conservação do estado do Ceará, Brasil. Os parâmetros populacionais foram estimados com base nos dados genealógicos de indivíduos das raças Santa Inês (SI), Somalis (SO) e Morada Nova (MN), nascidos entre os anos de 2001 e 2014. Os parâmetros estimados foram: número de gerações completas equivalentes (GCE), intervalo entre gerações (IEG), número de fundadores (Nf), número efetivo de fundadores (fe), número efetivo de ancestrais (fa), coeficiente de endogamia (F) e índice de contribuição genética (ICG). O GCE médio foi de 1,82, 2,78 e 1,52 para SI, SO e MN, respectivamente. O IEG foi próximo entre as raças, 3,67 anos em média. O Nf para SI, SO e MN foi igual a 225, 194 e 153, respectivamente. As razões fe/fa foram distantes de 1 nas três populações, o que indica ocorrência de gargalo genético, principalmente para SO. Os coeficientes médios de endogamia foram de 1,81%, 0,78% e 0,78% para SI, SO e MN, respectivamente. O ICG foi de 3,32, 5,38 e 2,87 para SI, SO e MN, respectivamente. Os parâmetros populacionais estimados apontam que parte da genética original desses rebanhos foi perdida, principalmente na população da raça Somalis. [Population structure analysis in sheep without wool in the conservation nucleu]. Abstracts: This study evaluated the population structure of sheep without wool from the conservation nucleus in Ceará State, Brazil. Population parameters were estimated on genealogical records of Santa Ines (SI), Somali (SO,) and Morada Nova (MN) breeds, that were born between 2001 and 2014. The following estimates were obtained: number of complete generation equivalents (GCE), generation intervals (IEG), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), inbreeding coefficient (F), and genetic contribution index (ICG). Average GCE was 1.82, 2.78, and 1.52 for SI, SO, and MN respectively. Mean IEG was similar between breeds, 3.67 years. The Nf was 225, 194, and 153 for SI, SO, and MN respectively. The fe/fa ratios were different to 1, which is an indication of genetic bottleneck, mainly for SO. The average inbreeding coefficients were 1.81%, 0.78%, and 0.78% for SI, SO, and MN respectively. The ICG was 3.32, 5.38, and 2.87 for SI, SO, and MN respectively. Estimated population parameters indicate that part of the genetics of these breeds was lost, mainly in Somalis. Made available in DSpace on 2020-02-17T18:13:33Z (GMT). No. of bitstreams: 1 cnpc2020Analisedaestrutura.pdf: 705746 bytes, checksum: 41b3c667bd43340725e8c1ed751a757c (MD5) Previous issue date: 2020

International audience; AbstractSex determination is one of the major developmental events in higher metazoans, where complex molecular mechanisms define two physiologically and behaviorally distinct organisms still genetically compatible. In honey bees, the sex determination cascade is initiated by the allelic composition of complementary sex determiner (csd) gene: males develop from hemi or homozygous embryos, whereas females develop from heterozygous embryos. In females, different alleles of csd lead to the formation of female-specific variants of feminizer (fem) and doublesex (dsx). In males, male-specific variants of fem and dsx are formed by default. In this paper, we investigated the genes of sex determination in the stingless bees Melipona quadrifasciata, Scaptotrigona postica, and Frieseomelitta varia. Our results revealed that the architecture of fem and dsx transcripts is highly conserved among the three stingless bee species, and also with honey bees.

Submitted by Beatriz Batista Trigo (beatrizbtrigo@hotmail.com) on 2022-03-31T18:52:38Z No. of bitstreams: 1 Tese-Beatriz_Batista_Trigo.pdf: 9927755 bytes, checksum: 3eaffa71b2346bc9a92980cbdda5477b (MD5) Rejected by Ederson Vasconcelos Pereira (edersonpereira@fmva.unesp.br), reason: Prezada Doutoranda Beatriz Batista Trigo: Solicito que realize as seguintes correções em sua tese: * SUMÁRIO: Atente-se para o modelo da página 19 da Normalização - Títulos dos Capítulos - Letra maiúscula. * TESE: - Incluir seções em todos os títulos ( páginas 25,26,50,51 e 63 da tese) - Vide páginas 27 e 28 da Normalização. - Inserir o Resumo/Abstract nos 2 capítulos conforme modelo da página 19 da normalização; * Títulos nas páginas 65,69 e 76; - Fonte 14; Maiúscula; Negrito; Centralizado; ( vide página 22 da Normalização) Solicito que , após as correções, submeta novamente. Atenciosamente Ederson Vasconcelos Pereira Repositório Institucional UNESP - FMVA on 2022-04-08T21:07:48Z (GMT) Submitted by Beatriz Batista Trigo (beatrizbtrigo@hotmail.com) on 2022-04-09T18:42:42Z No. of bitstreams: 1 Tese-Beatriz_Batista_Trigo.pdf: 9995879 bytes, checksum: 3085f2736ad2840f18177d9a151ba3b1 (MD5) Approved for entry into archive by Ederson Vasconcelos Pereira (edersonpereira@fmva.unesp.br) on 2022-04-13T13:03:44Z (GMT) No. of bitstreams: 1 trigo_bb_dr_araca_int.pdf: 9988281 bytes, checksum: 5f27ca1d8108ae27a26f3932485b052b (MD5) Made available in DSpace on 2022-04-13T13:03:44Z (GMT). No. of bitstreams: 1 trigo_bb_dr_araca_int.pdf: 9988281 bytes, checksum: 5f27ca1d8108ae27a26f3932485b052b (MD5) Previous issue date: 2022-02-22 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) O gado zebuíno da raça Nelore (Bos indicus) é conhecido por sua fácil adaptação nos ambientes de climas tropicais e subtropicais. Uma das características fenotípicas relacionadas à essa adaptação e principalmente à tolerância à radiação ultra-violeta é o padrão de coloração da pele e da pelagem apresentado pela raça. Outras raças zebuínas também apresentam padrão de pelagem semelhante ao Nelore. Dada a potencial contribuição da variação na pelagem destes animais na adaptação dos mesmos nos climas tropicais e sub-tropicais, objetivou-se mapear variantes genéticas candidatas estruturais ou funcionais que estivessem associadas ao escurecimento da pelagem nos zebuínos. Realizando análise de associação genômica ampla (genome-wide association study – GWAS) e posterior análise de dados de sequenciamento completo foi possível encontrar uma complexa variante estrutural nas proximidades do gene da proteína sinalizadora agouti (agouti signaling protein -ASIP) a qual foi denominada de ASIP-SV1, sendo fortemente correlacionada ao escurecimento da pelagem em regiões específicas no corpo dos bovinos das raças Nelore e Brahman. A variante estrutural ASIP-SV1 também foi predita como sendo de origem B. indicus, para confirmar tal predição foram analisadas sequencias da região da variante estrutural de animais zebuínos e não-zebuínos para elucidar a segregação desta variante. Nas análises realizadas 45,3% dos zebuínos analisados apresentaram a variante estrutural enquanto que dos taurinos somente 6.3% continham a variante no gene ASIP sendo que esses taurinos eram de raças conhecidas por apresentarem introgressão zebuína em seu genoma. Concluiu-se que a variante ASIP-SV1 causa o escurecimento na pigmentação da pelagem em regiões específicas do corpo destes animais causando um aumento na produção de eumelanina, a variante se mostrou robusta e sugeriu-se que, em conjunto a outros genes, essa variação possa contribuir com a adaptação dos bovinos aos climas tropicais e sub-tropicais. Indicine Nellore cattle (Bos indicus) had as main characteristic their adaptation in tropical and subtropical climate. The pigmentation of skin and coat color are both phenotype characteristics related to its climate adaptation and heat tolerance. Several indicine breeds also had the same coat color pattern as shown by Nellore cattle. Given the potential contribution of coat color variation on their adaptation in tropical and subtropical environments the aim of the study was to map candidate genetic structure or functional variants associated with darkness of hair coat in zebu cattle. Using genome-wide association study (GWAS) and latter analysis of whole-genome sequence it was possible to identity a complex structural variant in vicinity of agouti signaling protein (ASIP) gene named as ASIP-SV1, being strongly correlated to darkness of hair coat in specific body regions of Nellore and Brahman cattle. ASIP-SV1 was also predicted to be B. indicus origin. To confirm this prediction, it was analyzed sequences from ASIP-SV1 region from indicine and non-indicine cattle to elucidate this variant segregation. It was possible to identify 45.3% from zebu animals analyzed showing ASIP-SV1 while only 6.3% from taurine animals analyzed had this structural variant. The taurine cattle with ASIP-SV1 in ASIP gene is known to had zebu introgression on their genome. It was possible to conclude that ASIP-SV1 variant cause the darkness of hair coat on specifics regions of the body of these animals increasing eumelanin production, the variant shows to be robust and results suggest that ASIP-SV1, in a set of other genes, should play a role on cattle tropical and subtropical climate adaptation. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Código de Financiamento 001

Background There is a growing interest to decipher the genetic background of resilience and its possible improvement through selective breeding. The objective of the present study was to provide new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. Commercial Duroc pigs were challenged with an attenuated Aujeszky vaccine at 12 weeks of age. Two resilience indicators were used: deviation from the expected body weight at 16 weeks of age given the growth curve of non-vaccinated pigs (∆BW) and the increase in acute-phase protein haptoglobin at four days post-vaccination (∆HP). Genome-wide association analyses were carried out on 445 pigs, using genotypes at 41,165 single nucleotide polymorphisms (SNPs) and single-marker and Bayesian multiple-marker regression approaches. Results Genomic regions on pig chromosomes 2, 8, 9, 11 (∆BW) and 8, 9, 13 (∆HP) were found to be associated with the resilience indicators and explained high proportions of their genetic variance. The genomic regions that were associated explained 27 and 5% of the genetic variance of ∆BW and ∆HP, respectively. These genomic regions harbour promising candidate genes that are involved in pathways related to immune response, response to stress, or signal transduction (CD6, PTGDR2, IKZF1, RNASEL and MYD88), and growth (GRB10 and LCORL). Conclusions Our study identified novel genomic regions that are associated with two resilience indicators (∆BW and ∆HP) in pigs. These associated genomic regions harbour potential candidate genes involved in immune response and growth pathways, which emphasise the strong relationship between resilience and immune response.

Se estudio una muestra de 500 animales adultos (335 hembras y 165 machos) de ganado porcino criollo de la Zona de Planificación 5 (Ecuador) con el objetivo de realizar un análisis biométrico como base para su caracterización racial. Se obtuvieron los estadísticos descriptivos de 16 variables zoométricas, el peso vivo y 18 índices zoométricos. Asimismo, se estimaron los coeficientes de correlación Pearson, así como se efectuó un análisis de varianza univariante con el sexo y provincia como factores de variación. Se realizo un análisis discriminante canónico utilizando solo hembras para conocer las relaciones existentes entre poblaciones, primero entre las cuatro poblaciones porcinas de la Zona de Planificación 5 de Ecuador y, posteriormente, entre doce poblaciones porcinas iberoamericanas: Bolívar (75), Guayas (109), Los Ríos (95) y Santa Elena (59) de Ecuador, criollo Cubano (50), Pelón mexicano (158), y Entrepelado (149), Lampino (77), Manchado de Jabugo (16), Portugués (20), Retinto (207) y Torbiscal (86) como variedades de la raza Ibérica (España). Se calcularon las distancias de Mahalanobis para estimar el grado de diferenciación entre dichas poblaciones. Los resultados obtenidos confirmaron que la población porcina de la Zona de Planificación 5 presento tendencia elipométrica, perfil fronto-nasal rectilíneo y proporciones corporales sublongilíneas. Asimismo, estos animales presentaron una tipología braquicéfala, con índice pelviano elevado y línea dorsolumbar con inclinación caudal ascendente. En conjunto, esta población presento un elevado grado de homogeneidad y armonía morfoestructural, resaltando la existencia de un escaso dimorfismo sexual a nivel general, el cual oscilo desde la ausencia de diferencias entre sexos en la población de Santa Elena hasta un dimorfismo sexual acusado en la población de Bolívar, mostrando un comportamiento intermedio en las otras poblaciones de Guayas y Los Ríos. El análisis morfométrico comparativo evidencio una clara diferenciación entre las poblaciones porcinas ecuatorianas analizadas, en especial del ganado de Los Ríos frente al resto de poblaciones, lo que apuntaría a la existencia de entes raciales diferentes, así como al posible efecto de los distintos factores ambientales predominantes en cada provincia. De la misma forma, las poblaciones porcinas ecuatorianas se agruparon en el conglomerado de razas criollas iberoamericanas en comparación con el conjunto de variedades ibéricas, confirmando la tendencia al agrupamiento del ganado porcino criollo de Bolívar, Guayas y Santa Elena y la segregación de la población de Los Ríos. Del mismo modo se analizaron 6 variables cualitativas, 4 de ellas de tipo faneróptico, así como otras 2 variables morfológicas, siguiendo la metodología expuesta por Sánchez e Iglesias (2009). Se calculo la proporción media y el error estándar de la proporción media, un análisis de varianza no paramétrico (test de Kruskal Wallis) considerando el sexo y la provincia como factores de variación, así como el test de Whitney-Mann como prueba de homogeneidad a posteriori. Los resultados obtenidos confirman el predominio de animales con de perfil fronto-nasal rectilíneo, orejas en teja, color de capa en negro, mucosas y pezuñas con pigmentación intensa, con presencia de pelo y ausencia de mamellas. Para la caracterización genética mediante marcadores microsatélites, se tomó una muestra de pelo en 90 animales elegidos al azar. Se analizaron los 25 microsatélites, recomendados por el comité de expertos de la FAO/ISAG (Food and Agriculture Organization of the United Nations/ International Society of Animal Genetics) para el estudio de la diversidad genética en la especie porcina. Los fragmentos obtenidos mediante la PCR se sometieron a una electroforesis en gel de poliacrilamida en un secuenciador automático capilar ABI 3130XL. El genotipado se analizó con los programas Genescan AnalysisR v 3.1.2 y GenotyperR 2.5. Asimismo, en un análisis de diferenciación, estructura y distancia genética se han utilizado además otras 24 poblaciones porcinas de la base de datos del Laboratorio de Genética Molecular Aplicada de Animal Breeding Consulting S.L. y del Consorcio BioPig http://biopig.jimdofree.com). Se calculo el número medio de alelos por locus (MNA), las frecuencias alélicas, las heterocigosis esperada (He) y observada (Ho) y el contenido de información polimórfica (PIC) con el programa MICROSATELLITE TOOLKIT software para Excel. Los valores de FIS (coeficiente de consanguinidad) se calcularon el programa informático GENETIX v. 4.05 y se realizó una prueba de equilibrio Hardy-Weinberg (HW) usando el programa GENEPOP v. 3.1c. El coeficiente de consanguinidad FIT, el coeficiente de diferenciación genética FST y FIS (coeficiente de endogamia de cada individuo en relación a la subpoblación a la que pertenece), fue calculado mediante el programa GENETIX; un Análisis Factorial de Correspondencia con el programa GENETIX; la distancia genética DA con el programa informático POPULATIONS y los valores de distancia obtenidos se realizó un dendograma Neighbor - Joining mediante el programa TREEVIEW. Los 25 marcadores fueron polimórficos y se han observado entre un mínimo de 6 alelos para los marcadores S0215, SW72 y SW951 y un máximo de 28 alelos para el locus CGA. El número medio de alelos es muy elevado (10,96), aunque el número efectivo de alelos (4,75) fue sensiblemente inferior. La heterocigosidad esperada promedio (He) y heterocigosidad observada promedio (Ho) fueron de 0,729 y 0,665, respectivamente. Por tanto, todas las variables consideradas indican que los porcinos criollos de la Zona de Planificación 5 mostraron una diversidad genética alta. El valor de FIS con un intervalo de confianza al 95% con 1000 remuestreos es de 0,089 (0,055-0,111), lo que indico que la población no mostro una desviación significativa del equilibrio Hardy-Weinberg, lo que se consideró favorable al no apreciar exceso de homocigotos ni heterocigotos. El panel de microsatélites empleado en la caracterización genética resulto idóneo como herramienta de apoyo en pruebas de exclusión de paternidad/maternidad, así como en la correcta adscripción de individuos a la población dentro de un eventual programa de cría oficial en esta raza. Aunque no se detectó diferenciación genética entre los cerdos muestreados en las diferentes provincias por lo que se podría gestionar como una sola población, los análisis de diversidad genética inter-racial determinaron la existencia de diferenciación genética entre las 25 poblaciones porcinas incluidas en el estudio es elevada. Además, las distancias genéticas DA indicaron la proximidad existente entre el ganado porcino criollo de la Zona de Planificación 5 y el criollo ecuatoriano de la Amazonia, diferenciándose ambas razas del resto de poblaciones analizadas, si bien se conformó un único agrupamiento para las razas criollas iberoamericanas. Finalmente, el compendio de información obtenida del estudio zoométrico, faneróptico, morfológico y genético confirma la identidad de la población de Ganado Porcino Criollo de la Zona de Planificación 5 de Ecuador, siendo necesario diseño e implementación de un programa de gestión genética adecuado a las necesidades técnicas demandadas en esta población. A sample of 500 adult animals (335 females and 165 males) of creole pigs from Planning Zone 5 (Ecuador) was studied in order to perform a biometric analysis as a basis for their breed characterization. Descriptive statistics were obtained in 16 zoometric variables, the live weight and 18 zoometric indices. Likewise, Pearson correlation coefficients were estimated, as well as a univariate analysis of variance with sex and province as variation factors. A canonical discriminant analysis was carried out using only females to know the existing relationships between populations, first among the four pig populations of Planning Zone 5 of Ecuador and, later, between twelve Ibero- American pig populations: Bolivar (75), Guayas (109), Los Rios (95) and Santa Elena (59) from Ecuador, Cuban Creole (50), Mexican Pelon (158), and Entrepelado (149), Lampino (77), Manchado de Jabugo (16), Portuguese (20), Retinto (207) and Torbiscal (86) as varieties of Iberian breed (Spain). Mahalanobis distances to estimate the degree of differentiation between these populations were calculated. The results obtained confirmed pig population of Planning Zone 5 has an elipometric trend, a rectilinear fronto-nasal profile and sublongilinear body proportions. Likewise, these animals presented a brachycephalic typology, with an elevated pelvic index and thoracolumbar line with ascending caudal inclination. As a whole, this population presented a high degree of morphostructural homogeneity and harmony, highlighting the existence of scarce sexual dimorphism at a general level, which ranged from absence of differences between sexes in Santa Elena pig population, to a pronounced sexual dimorphism in Bolivar pig population, showing an intermediate behavior in others pigs populations of Guayas and Los Rios. The comparative morphometric analysis showed a clear differentiation between Ecuadorian pig populations analyzed, especially in Los Rios pig population compared to the rest of the populations, which would point to the existence of different breed entities, as well as possible effect of different predominant environmental factors in each province. In the same way, Ecuadorian pig populations were grouped in the conglomerate of Ibero-American creole breeds in comparison with set of Iberian varieties, confirming the tendency towards grouping of creole pig population from Bolivar, Guayas and Santa Elena and the segregation of Los Rios population. In the same way, 6 qualitative variables were analyzed, 4 of them of phaneroptic type, as well as other 2 morphological variables. The mean proportion and the standard error of the mean proportion, a non-parametric analysis of variance (Kruskal Wallis test) considering gender and province as variation factors, as well as the Whitney-Mann test as a homogeneity test were calculated. The obtained results confirmed the predominance of animals with a rectilinear fronto-nasal profile, tiled ears, black coat color, mucous membranes and hooves with intense pigmentation, with the presence of hair and the absence of mammillas. A random sample of hair from 90 animals was taken for genetic characterization using microsatellite markers. A set of 25 microsatellites markers, as recommended by the FAO / ISAG (Food and Agriculture Organization of the United Nations / International Society of Animal Genetics) committee of experts for the study of genetic diversity in pig species, were analyzed. The fragments obtained by PCR were subjected to polyacrylamide gel electrophoresis in an ABI 3130XL capillary automatic sequencer. Genotyping was analyzed with Genescan AnalysisR v 3.1.2 and GenotyperR 2.5 programs. Likewise, in an analysis of differentiation, structure and genetic distance, another 24 pig populations from the database of the Laboratory of Applied Molecular Genetics of Animal Breeding Consulting S.L. and the BioPig Consortium (http://biopig.jimdofree.com). Mean number of alleles per locus (MNA), allelic frequencies, expected heterozygosity (He), observed heterozygosity (Ho) and polymorphic information content (PIC) with MICROSATELLITE TOOLKIT software for Excel were calculated. FIS (coefficient of inbreeding) values were calculated using the GENETIX v. 4.05 and a Hardy-Weinberg (HW) equilibrium test was performed using the GENEPOP v. 3.1c. The coefficient of inbreeding (FIT), coefficient of genetic differentiation (FST) and inbreeding coefficient of each individual in relation to the subpopulation to which it belongs (FIS), were calculated through the GENETIX program; A factorial analysis of correspondence with the GENETIX program was caltulated; DA genetic distances with the POPULATIONS software and distance values obtained, a Neighbor - Joining dendrogram was performed using the TREEVIEW program. The 25 markers were polymorphic and have been observed between a minimum of 6 alleles for S0215, SW72 and SW951 markers and a maximum of 28 alleles for CGA marker. The mean number of alleles was very high (10.96), although the effective number of alleles (4.75) was significantly lower. The average expected heterozygosity (He) and average observed heterozygosity (Ho) were 0.729 and 0.665, respectively. Therefore, all the variables considered indicate that Creole pigs from Planning Zone 5 showed a high genetic diversity. The FIS value with a 95% confidence interval with 1000 resampling was 0.089 (0.055-0.111), which indicated that the population did not show a significant deviation from the Hardy-Weinberg equilibrium, which was considered favorable as no excess neither homozygous nor heterozygous. The microsatellite panel used in the genetic characterization was ideal as a support tool in paternity/maternity exclusion tests, as well as in the correct assignment of individuals to the population within an eventual official breeding program in this breed. Although no genetic differentiation was detected between the pigs sampled in the different provinces, so it could be managed as a single population, the analysis of inter-racial genetic diversity determined that the existence of genetic differentiation between the 25 pig populations included in the study was high. In addition, the DA genetic distances indicated the proximitybetween the Creole pig cattle of Planning Zone 5 and the Ecuadorian Creole of Amazon, differentiating both breeds from the rest of the populations analyzed, although a single grouping was formed for the Ibero-American Creole breeds. Finally, the compendium of information obtained from the zoometric, phaneroptic, morphological and genetic study confirms the identity of the Criollo Pig Livestock population of Planning Zone 5 of Ecuador, requiring the design and implementation of a genetic management program appropriate to the needs techniques demanded in this population.

Background: Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated with high accuracy. The objectives of this study were to use a large pig dataset from seven intensely selected lines to assess the benefits of using WGS for genomic prediction compared to using commercial marker arrays and to identify scenarios in which WGS provides the largest advantage. Methods: We sequenced 6931 individuals from seven commercial pig lines with different numerical sizes. Genotypes of 32.8 million variants were imputed for 396,100 individuals (17,224 to 104,661 per line). We used BayesR to perform genomic prediction for eight complex traits. Genomic predictions were performed using either data from a standard marker array or variants preselected from WGS based on association tests. Results: The accuracies of genomic predictions based on preselected WGS variants were not robust across traits and lines and the improvements in prediction accuracy that we achieved so far with WGS compared to standard marker arrays were generally small. The most favourable results for WGS were obtained when the largest training sets were available and standard marker arrays were augmented with preselected variants with statistically significant associations to the trait. With this method and training sets of around 80k individuals, the accuracy of within-line genomic predictions was on average improved by 0.025. With multi-line training sets, improvements of 0.04 compared to marker arrays could be expected. Conclusions: Our results showed that WGS has limited potential to improve the accuracy of genomic predictions compared to marker arrays in intensely selected pig lines. Thus, although we expect that larger improvements in accuracy from the use of WGS are possible with a combination of larger training sets and optimised pipelines for generating and analysing such datasets, the use of WGS in the current implementations of genomic prediction should be carefully evaluated against the cost of large-scale WGS data on a case-by-case basis. The authors acknowledge the financial support from the BBSRC ISPG to The Roslin Institute (BBS/E/D/30002275), from Genus plc, Innovate UK (grant 102271), and from grant numbers BB/N004736/1, BB/N015339/1, BB/ L020467/1, and BB/M009254/1. MJ acknowledges financial support from the Swedish Research Council for Sustainable Development Formas Dnr 2016‑ 01386. For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) licence to any author accepted manuscript version arising from this submission.

Multitrait models can increase the accuracy of breeding value prediction and reduce bias due to selection by using traits measured before and after it has occurred. However, as the number of traits grows, a similar trend is expected for the number of parameters to be estimated, which directly affects the computing power and the amount of data required. The aim of the present study was to apply reduced rank (principal components model-PCM) and factor analytical models (FAM), to estimate (co)variance components for nineteen traits, jointly evaluated in a single analysis in Campolina horses. A total of 18 morphometric traits (MT) and one gait visual score (GtS), along with genealogical records of 48,806 horses, were analysed under a restricted maximum likelihood framework. Nine PCM, nine FAM and one standard multitrait model (MTM) were fitted to the data and compared to find the best suitable model. Based on Bayesian information criterion, the best model was the FAM option, considering five common factors (FAM5). After performing an intraclass analysis, none of MT were genetically negatively correlated, whereas GtS was negatively related to all MT, except for the genetic correlations among GtS and BLL, and between GtS and BLLBL (0.01 and 0.10 respectively). From all MT, two traits were derived computing ratios involving other traits, those had negative correlations with others MT, but all favourable for selection. Similar patterns were observed between the genetic parameters obtained from MTM and FAM5 respectively. The heritability estimates ranged from 0.09 (head width) to 0.47 (height at withers). Our results indicated that FAM was efficient to reduce the multitrait analysis dimensionality, and therefore, traits can be combined based on the first three eigenvectors from the additive genetic (co)variance matrix. In addition, there was sufficient genetic variation for selection, benefiting its potential implementation in a breeding program.

Made available in DSpace on 2022-05-01T16:02:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty-four young bulls were sampled to assess the beef FA profile by considering 14 phenotypes and including differentially expressed genes (DEG), co-expressed (COE), and differentially co-expressed genes (DCO) analyses. All samples (n = 44) were used for COE analysis, whereas 30 samples with extreme phenotypes for the beef FA profile were used for DEG and DCO. A total of 912 DEG were identified, and the polyunsaturated (n = 563) and unsaturated ω-3 (n = 346) FA sums groups were the most frequently observed. The COE analyses identified three modules, of which the blue module (n = 1776) was correlated with eight of 14 FA phenotypes. Also, 759 DCO genes were listed, and the oleic acid (n = 358) and monounsaturated fatty acids sum (n = 120) were the most frequent. Furthermore, 243 and 13, 319 and seven, and 173 and 12 gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were enriched respectively for the DEG, COE, and DCO analyses. Combining the results, we highlight the unexplored GIPC2, ASB5, and PPP5C genes in cattle. Besides LIPE and INSIG2 genes in COE modules, the ACSL3, ECI1, DECR2, FITM1, and SDHB genes were signaled in at least two analyses. These findings contribute to understand the genetic mechanisms underlying the beef FA profile in Nellore beef cattle finished in feedlot. School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (UNESP) School of Veterinary Medicine and Animal Science (FMVZ) University of São Paulo (USP) Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture & Food School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (UNESP) School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (UNESP) School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (UNESP)

The delivery of nucleic acids to cells is considered a crucial step for the success of genetic modifications aimed at therapeutic purposes or production of genetically modified animals. In this context, nanotechnology is one of the most promising fields of science, with the potential to solve several existing problems. Nanostructures have desirable characteristics to be used as carriers, such as nanometric size, large surface area, cell internalization capacity, prolonged and controlled release, among others. Genetically modified animals can contribute to the production of biopharmaceuticals, through the expression of high-associated-value molecules. The production of these animals, also known as biofactories, further enhances Brazilian agribusiness, since it allows adding value to the final product, and favors the integration between the agricultural market and the pharmaceutical sector. However, there is a growing concern about the safety and possible harmful effects of nanostructures, since data on the safe use of these materials are still insufficient. The objective of this review was to address aspects of the use of nanostructures, mainly carbon nanotubes as nucleic acid carriers, aiming at the production of genetically modified animals, with the certainty that progress in this field of knowledge depends on more information on the mechanisms of interaction between nanostructures, cells and embryos, as well as on its toxicity. Made available in DSpace on 2022-05-10T16:12:42Z (GMT). No. of bitstreams: 1 Challenges-use-nanostructures.pdf: 603206 bytes, checksum: 533820a862c7319ede6a9cab4fb3fa87 (MD5) Previous issue date: 2022

Aconteceu, de novo! Ano passado, quando tive a experiência exotérica de entrevistar um boi, desafiei o bom senso, reportando isso neste mesmo espaço e expondo-me a uma justificável desconfiança sobre minha sanidade mental.

Submitted by Gabriela David (gabriela.david@unesp.br) on 2022-03-03T18:27:08Z No. of bitstreams: 1 dissertação_gabriela david.pdf: 1563300 bytes, checksum: b08e52bc4941451f43bfeb9d62732560 (MD5) Approved for entry into archive by Laudicélia Martins Arantes (lm.arantes@unesp.br) on 2022-03-03T22:20:31Z (GMT) No. of bitstreams: 1 david_g_me_jabo.pdf: 1611732 bytes, checksum: 2c8276993f941a4133fe21e28508017c (MD5) Made available in DSpace on 2022-03-03T22:20:31Z (GMT). No. of bitstreams: 1 david_g_me_jabo.pdf: 1611732 bytes, checksum: 2c8276993f941a4133fe21e28508017c (MD5) Previous issue date: 2021-12-20 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) O Brasil está entre os principais produtores de carne. Animais taurinos são utilizados puros ou em cruzamentos em busca de maior produtividade e qualidade da carne e da carcaça. Entretanto, animais taurinos são mais suscetíveis à infestação por carrapatos. O Rhipicephalus microplus transmite os agentes patogênicos Anaplasma marginale, Babesia bigemina e Babesia bovis, que constituem a Tristeza Parasitária Bovina (TPB). Animais taurinos também são mais vulneráveis às infecções. Assim, além dos prejuízos causados, carrapato e babesiose bovina representam um entrave na intensificação da bovinocultura de corte. O presente estudo avaliou as características de níveis de infestação por R. microplus (Icar), por meio da contagem de carrapatos, infecção por B. bigemina (Ibig) e infecção B. bovis (Ibov), determinados por meio da técnica de Reação em Cadeia da Polimerase em Tempo Real (qPCR). Essas características são economicamente importantes e complexas e há dificuldade em selecionar animais resistentes pelo método BLUP tradicional. Foram estimados parâmetros genéticos e foi conduzido um estudo de associação genômica ampla (GWAS) para proporcionar maior entendimento da base genética dessas características, com o objetivo de auxiliar a seleção de animais resistentes. Foram realizadas análises para Icar (624 animais, n= 1246), Ibig (786 animais, n=1312) e Ibov (677 animais, n=980) utilizando 770 fêmeas genotipadas com painel de aproximadamente 150.000 marcadores do tipo SNP. Os componentes de variância foram obtidos por inferência bayesiana em um modelo tri-característica. A estimativa de herdabilidade para Icar foi de baixa magnitude (0,17), sugerindo que a seleção pelo fenótipo de contagem dos carrapatos trará respostas a longo prazo. Para Ibig e Ibov as estimativas foram próximas de zero, indicando maior influência ambiental. As repetibilidades de Icar (0,24), Ibig (0,12) e Ibov (0,12) também foram de baixa magnitude, evidenciando que as variações nos níveis de infestação e infecção podem ser atribuídas principalmente a fatores ambientais. As estimativas de correlações genética e fenotípica entre o Icar e níveis de infecção sugerem que não há relação entre níveis de infestação e infecção e a seleção para uma característica não afetaria significativamente a seleção para a outra, visto que, todas foram próximas de zero. A correlação genética entre Ibig e Ibov foi alta e negativa (-0,69). A correlação fenotípica também foi negativa (-0,10) e embora tenha apresentado valor de baixa magnitude, fortaleceu a associação inversa entre as características. Para o estudo de GWAS, foi empregado o método WssGBLUP, utilizando análises univariadas e realizando três iterações, as variâncias das soluções dos SNPs foram usadas como ponderadores. As 15 janelas com maior variação explicaram 30,84%, 54,30% e 47,63% da variância genética de Icar, Ibig e Ibov, respectivamente. Após análise funcional, diversos genes candidatos foram identificados nas 15 janelas de cada característica, contribuindo para a detecção de regiões promissoras para futuros estudos visando identificar genes diretamente envolvidos na resistência dos animais. Brazil is among the main beef producers. Taurine animals are used pure or in crossbreeding in search of greater productivity and quality of meat and carcass. However, Bos taurus taurus animals are more susceptible to tick infestation. Rhipicephalus microplus transmits the pathogens Anaplasma marginale, Babesia bigemina, and Babesia bovis, which constitute Bovine Parasiti Sadness (BPS). Taurine animals are also more vulnerable to infections. Thus, in addition to the damage caused, ticks and bovine babesiosis represent an obstacle in the intensification of beef cattle breeding. The present study evaluated the characteristics of Rhipicephalus microplus infestation level (IT), determined by tick counts, and infection levels by B. bigemina (Ibig) and Babesia bovis (Ibov), determined using the Real-Time Polymerase Chain Reaction (qPCR) technique. These traits are economically important and complex, and there is difficulty in selecting more resistant animals by the traditional method. Genetic parameters were estimated and a genome-wide association study (GWAS) was conducted to provide a further understanding of the genetic basis of these traits to aid in the selection of resistant animals. Analyses were performed for IT (624 animals, n= 1246), Ibig (786 animals, n=1312), and Ibov (677 animals, n=980) using 770 females genotyped with a panel of approximately 150,000 SNP markers. Variance components were obtained by Bayesian inference in a tri-characteristic model. The heritability estimate for IT was of low magnitude (0.17), suggesting that selection by phenotype will bring long-term responses. For Ibig and Ibov the estimates were close to zero, indicating greater environmental influence. The repeatabilities for IT (0.24), Ibig (0.12), and Ibov (0.12) were also of low magnitude, showing that the variations in the levels of infestation and infection can be attributed mainly to environmental factors. The correlation estimates between infestation and infection levels suggest that there is no relationship between them, and selection for one trait would not significantly affect selection for the other, since they were all close to zero. The genetic correlation between Ibig and Ibov was high and negative (-0.69), the phenotypic correlation was also negative (-0.10) and although it presented a low magnitude value, it strengthened the inverse association between the characteristics. For the GWAS, the WssGBLUP method was employed, using univariate analysis and performing three iterations, the variances of the SNP solutions were used as weights. The 15 windows with the highest variance explained 30.84%, 54.30%, and 47.63% of the genetic variance of IT, Ibig, and Ibov, respectively. After functional analysis, several candidate genes were identified in the 15 windows of each trait. Thus, contributing to the detection of promising regions for future studies aiming to identify genes directly involved in the resistance of animals. 88887.529051/2020-00 88887.373883/2019-00

ilustraciones, fotografías, gráficas, tablas During the last century, many species have become endangered, and conservation through captive breeding programs has become crucial for their survival. One of the primary considerations for the design of reintroduction programs is the preservation of genetic variability, which provides the raw material for adaptation. If management is based only on recorded pedigrees, information may be incomplete or inaccurate and may lead to an underestimation of relatedness. Incorrect management actions can alter the viability of reintroductions due to the loss of genetic diversity and genetic depression of the source population. In this Master thesis, we used a 17 microsatellite loci system to characterize the extent of the genetic variation of the biggest ex-situ population of the critically endangered Crocodylus intermedius in Colombia in charge of the Roberto Franco Tropical Biology Station (EBTRF) aiming at proposing management guidelines and at assessing past and future reintroductions. In Chapter 1 we compared genetic indexes of the Founder and Alive populations and we found that the living crocodiles maintain much of the founder diversity, high levels of heterozygosity, and a low overall inbreeding. In Chapter 2 we developed a powerful tool that combined information of relatedness, individual diversity, age, sex, size, and location of the living crocodiles that allowed us to build combinations of individuals to plan future breeding groups that maximize the population´s genetic diversity. We propose different reproductive nuclei, and we demonstrate that molecular data can be used to improve the management of the program, well beyond of what can be achieved with pedigree information alone. To provide insights on the genetic component of the released individuals and to suggest the improvement of crocodile’s reintroductions, in Chapter 3 we evaluated the genetic composition of four groups of crocodiles already reintroduced and of juveniles to be released. We propose that in the short term, reintroductions should only be carried out in places where it is certain that the populations have become completely extinct. In case the species is present before implementing reintroduction measures it is necessary to accurately assess its genetic profile and situation as well as to estimate population size. En el último siglo ha habido un aumento en el número de especies amenazadas y la conservación a través de programas de cría en cautiverio se ha vuelto crucial para su supervivencia. Una de las principales consideraciones para el diseño de programas de reproducción es la preservación de la variabilidad genética que proporciona la materia prima para la adaptación. Si el manejo se basa solo en los pedigrí registrados, la información puede estar incompleta o inexacta y puede llevar a una subestimación de las relaciones de parentesco. Las acciones de manejo incorrectas pueden alterar la viabilidad de las reintroducciones debido a la pérdida de diversidad y depresión genética de la población de origen. En esta tesis de Maestría, utilizamos un sistema de 17 loci de microsatélites para caracterizar la variación genética de la mayor población ex-situ del críticamente amenazado Crocodylus intermedius en Colombia a cargo de la Estación de Biología Tropical Roberto Franco (EBTRF) con el objetivo de proponer pautas de manejo y evaluar reintroducciones pasadas y futuras. En el Capítulo 1 comparamos los índices genéticos de las poblaciones Fundadora y Viva y encontramos que los cocodrilos vivos mantienen gran parte de la diversidad fundadora, altos niveles de heterocigosidad y una baja consanguinidad. En el Capítulo 2 desarrollamos una poderosa herramienta que combina información de parentesco, diversidad individual, edad, sexo, tamaño y ubicación de los cocodrilos vivos por medio de la cual construimos combinaciones de individuos para planificar futuros grupos reproductores que maximicen la diversidad genética de la población. Proponemos diferentes núcleos reproductivos y demostramos que los datos moleculares pueden ser utilizados para mejorar la gestión del programa mucho más allá de lo que se puede lograr solo con la información del pedigrí. Para proporcionar información sobre el componente genético de los individuos liberados y sugerir mejoras en las reintroducciones, en el Capítulo 3 evaluamos la composición genética de cuatro grupos de cocodrilos reintroducidos y de los juveniles que serán liberados. Proponemos que, a corto plazo, las reintroducciones solo se realicen en lugares donde se tenga la certeza de que las poblaciones se han extinguido por completo. En caso de que la especie esté presente, antes de implementar medidas de reintroducción, es necesario evaluar con precisión su perfil genético y su situación, así como estimar el tamaño de la población. (Texto tomado de la fuente) Maestría Magíster en Ciencias - Biología Genética de la conservación

Background Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Methods Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p –6 and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. Results We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN. Conclusions Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis.