Estudo de associação genômica para habilidade de permanência no rebanho na raça Nelore, considerando diferentes idades
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2018-12-19
Autores
Silva, Diogo Osmar
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Universidade Estadual Paulista (Unesp)
Resumo
A habilidade de permanência no rebanho (HPR) é medida tardiamente na vida do animal. Com isso, quando esta característica é usada como critério de seleção, o intervalo de geração, definido como a média de idade dos pais ao nascimento da progênie, tende a aumentar, provocando a diminuição do ganho genético. A mensuração das fêmeas em uma idade mais precoce seria uma forma de contornar este problema. Neste sentido, um melhor entendimento das regiões genômicas envolvidas na expressão desta característica em diferentes idades/partos é necessário. O objetivo com o presente estudo foi, então, identificar regiões genômicas associadas à HPR medida em diferentes partos de fêmeas da raça Nelore. Considerando apenas fêmeas com idade ao primeiro parto de até 40 meses, os fenótipos para HPR foram gerados observando se cada fêmea teve oportunidade de permanecer no rebanho do segundo ao oitavo parto, de maneira que cada vaca poderia ter até sete observações para HPR. Ao final, o banco de dados possuía 195.452, 161.261, 130.236, 103.043, 79.844, 62.663 e 47.045 fêmeas com fenótipos para o segundo, terceiro, quarto, quinto, sexto, sétimo e oitavo parto, respectivamente. Do total de animais no banco de dados, 3.849 (2.720 fêmeas e 1.129 touros) apresentavam informações genotípicas de 472.640 marcadores do tipo SNPs (Illumina BovineHD BeadChip). Ao todo, foram realizadas sete análises uni-características, considerando modelos thresholds com função de ligação probit. A metodologia do single-step GBLUP foi utilizada para estimar componentes de variância para HPR em cada parto bem como para a realização de estudos de associação genômica, nos quais considerou-se, na identificação das regiões de maior efeito, a variância explicada por janelas de 100 SNPs consecutivos. As estimativas de herdabilidade variaram de 0,15 (terceiro parto) a 0,18 (oitavo parto) e as correlações de Pearson entre os valores genéticos genômicos preditos variaram de 0,52 (entre o segundo e o oitavo parto) a 0,93 (entre o sétimo e o oitavo parto). Em média, as dez janelas com maior importância no estudo de associação explicaram 15,41% da variância genética aditiva, variando entre 13,08% e 17,67% de acordo com o parto avaliado. As janelas selecionadas estavam localizadas em 18 cromossomos (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 25 e 28). A região entre 42 Mb e 49 Mb do cromossomo 6 foi identificada para o segundo, terceiro, quarto, quinto e sétimo parto. Esta é uma região de QTL com efeito pleiotrópico, a qual já havia sido associada com outras características como: facilidade de parto, probabilidade de natimorto, consumo alimentar residual e produção de leite e gordura. Várias regiões foram identificadas em comum entre partos adjacentes, como no cromossomo 1, 2, 4, 11, 18 e 19. No geral, a análise funcional das regiões identificadas indicou que a expressão da HPR nos primeiros partos sofre maior influência de fatores reprodutivos, enquanto que, nos últimos partos, fatores adaptativos e relacionados ao metabolismo, principalmente de carboidratos e lipídeos, bem como fatores ligados à saúde do animal, passam a ter maior importância para esta característica. Os resultados apresentados podem favorecer a definição de estratégias eficientes de seleção para HPR na raça Nelore, uma vez que foram geradas informações importantes sobre o controle genético desta característica ao longo da vida produtiva dos animais.
Stayability (STAY) is a trait measured late in the animal's life. Thus, when this trait is used as selection criteria, the generation interval, defined as the parents average age at the progeny birth, tends to increase, causing a decrease in the genetic gain. Measuring females at an earlier age could be a way to circumvent this problem. In this sense, a better understanding of genomic regions involved in the expression of this trait at different ages/calving is necessary. The objective of the present study was to identify genomic regions associated with STAY measured in different calving of Nelore females. Considering only females that had their first calving up to 40 months of age, the phenotypes for STAY were generated by observing whether each female had the opportunity to remain in the herd from the second to the eighth calving, in such a way that each cow could have up to seven records. The final dataset had 195,452, 161,261, 130,236, 103,043, 79,844, 62,663 and 47,045 females with phenotypes for the second, third, fourth, fifth, sixth, seventh and eighth calving, respectively. In total, 3,849 (2,720 females and 1,129 bulls) animals from the whole dataset used in the analyses had genotypic information of 472,640 SNPs (Illumina BovineHD BeadChip) markers. In total, seven single-trait analyzes were performed considering threshold animal models with probit link function. The single-step GBLUP methodology was used to estimate variance components for STAY at each calving as well as to perform genomic association studies, in which the variance explained by windows of 100 consecutive SNPs was used to identify genomic regions with major effect on the trait. The heritabilities ranged from 0.15 (third calving) to 0.18 (eighth calving) and the Pearson correlations between genomic estimated breeding values ranged from 0.52 (between second and eighth calving) to 0.93 (between seventh and the eighth calving). On average, the ten most important windows explained 15.41% of the genetic additive variance, varying between 13.08% and 17.67%. The selected windows were located on 18 chromosomes (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 25, and 28). The region between 42 Mb and 49 Mb of the chromosome 6 was identified for the second, third, fourth, fifth and seventh calving. This is a QTL region with pleiotropic effect that has been associated with calving ease, stillbirth, residual feed intake and milk and fat production. Several regions were identified in common with adjacent calvings, as those in chromosomes 1, 2, 4, 11, 18 e 19. In general, the functional analyses suggested that the expression of STAY in the first calving is more influenced by reproductive factors, whereas, in the last calving, adaptive and metabolic factors, especially carbohydrates and lipids, as well as factors related to animal health, have become more important for STAY. The results presented here may contribute to the definition of efficient selection strategies for STAY in Nelore, since important information on the genetic control of this trait throughout the productive life of the animals has been generated.
Stayability (STAY) is a trait measured late in the animal's life. Thus, when this trait is used as selection criteria, the generation interval, defined as the parents average age at the progeny birth, tends to increase, causing a decrease in the genetic gain. Measuring females at an earlier age could be a way to circumvent this problem. In this sense, a better understanding of genomic regions involved in the expression of this trait at different ages/calving is necessary. The objective of the present study was to identify genomic regions associated with STAY measured in different calving of Nelore females. Considering only females that had their first calving up to 40 months of age, the phenotypes for STAY were generated by observing whether each female had the opportunity to remain in the herd from the second to the eighth calving, in such a way that each cow could have up to seven records. The final dataset had 195,452, 161,261, 130,236, 103,043, 79,844, 62,663 and 47,045 females with phenotypes for the second, third, fourth, fifth, sixth, seventh and eighth calving, respectively. In total, 3,849 (2,720 females and 1,129 bulls) animals from the whole dataset used in the analyses had genotypic information of 472,640 SNPs (Illumina BovineHD BeadChip) markers. In total, seven single-trait analyzes were performed considering threshold animal models with probit link function. The single-step GBLUP methodology was used to estimate variance components for STAY at each calving as well as to perform genomic association studies, in which the variance explained by windows of 100 consecutive SNPs was used to identify genomic regions with major effect on the trait. The heritabilities ranged from 0.15 (third calving) to 0.18 (eighth calving) and the Pearson correlations between genomic estimated breeding values ranged from 0.52 (between second and eighth calving) to 0.93 (between seventh and the eighth calving). On average, the ten most important windows explained 15.41% of the genetic additive variance, varying between 13.08% and 17.67%. The selected windows were located on 18 chromosomes (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 25, and 28). The region between 42 Mb and 49 Mb of the chromosome 6 was identified for the second, third, fourth, fifth and seventh calving. This is a QTL region with pleiotropic effect that has been associated with calving ease, stillbirth, residual feed intake and milk and fat production. Several regions were identified in common with adjacent calvings, as those in chromosomes 1, 2, 4, 11, 18 e 19. In general, the functional analyses suggested that the expression of STAY in the first calving is more influenced by reproductive factors, whereas, in the last calving, adaptive and metabolic factors, especially carbohydrates and lipids, as well as factors related to animal health, have become more important for STAY. The results presented here may contribute to the definition of efficient selection strategies for STAY in Nelore, since important information on the genetic control of this trait throughout the productive life of the animals has been generated.
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Palavras-chave
Características reprodutivas, Single-step, Raça zebuína, Reproductive traits, Single-step, Zebu breed