Genome-wide association study for milk production traits in Valle del Belice sheep

Abstract

Over the last years, high-throughput technologies have provided the opportunity to explore the genomes of livestock species to identify regions influencing traits of economic interest. Genome wide association studies (GWAS) have been widely used to disentangle the genetic variation in complex phenotypes, such as milk production traits in sheep. The study presented here investigated the possible association of genome-wide SNPs and breeding values for milk production traits in the Valle del Belice sheep. The studied population consisted of a total of 481 ewes belonging to 9 half-sib families with available records for milk yield (MY), protein and fat percentage (P% and F%, respectively). All animals were genotyped for 54,241 SNPs, using the Illumina OvineSNP50K Genotyping BeadChip. During quality control, SNPs with minor allele frequency (MAF)<5%, call rate <95% and out of Hardy Weinberg Equilibrium (HWE) p<.001, were excluded from the analysis. In addition, sheep that missed more than 5% of genotypes were also removed. Finally, after quality control, 39,110 SNPs and 469 individuals were available for the GWAS. Univariate animal models were used to estimate variance components and breeding values for MY, P% and F%. The genome-wide association using mixed model and regression- genomic control approach as implemented in GenABEL was used. P-values of 5105 were considered as significant associations. Heritability estimates for MY, P% and F% was 0.21, 0.34, and 0.39 respectively. In total, nine significant SNPs on six different Ovis aries chromosomes (Oar) (Oar1: rs402356478; Oar2: rs406142196 and rs426814658; Oar3: rs399070200; Oar10: rs406329083 and rs405825255; Oar20: rs398454547; Oar24: rs405426757 and rs412849969) associated with MY, P% and F% were identified. All significant detected SNPs were within or close to known ovine genes. In particular, one SNP associated with P% was found within the alphalactalbumin (LALBA) gene on OAR3, which is a functional and positional candidate underlying this association, and one SNP associated with MY was found near the cyclic AMPresponsive element-binding protein (CREB1) on OAR2, a gene associated to genesis and secretion of milk, development of mammary glands and circadian rhythms. Genomic regions found to be significantly associated with milk production traits in this study will further contribute to the identification of the genes regulating those traits in dairy sheep.