Genome-wide association study for stayability in Nelore cattle, considering different ages

Author(s)

Diogo Osmar Silva

• Document type: Master's Dissertation
• Press: Jaboticabal. 2019-01-21.
• Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
• Defense date: 2018-12-19
• Advisor: Lucia Galvão de Albuquerque

Abstract

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. (AU)

• FAPESP's process: 17/24272-0 - Genomic association study for stayability in Nellore cattle, in differents CALVINS
• Grantee: Diogo Osmar Silva
• Support Opportunities: Scholarships in Brazil - Master