Assessing the association of single nucleotide polymorphisms in thyroglobulin gene with age of puberty in bulls

Exploring evidence of positive selection signatures in cattle breeds selected for different traits

Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N'Dama cattle breeds using Tajima's D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N'Dama (West Africa-Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37 million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N'Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N'Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N'Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.

Environment-Dependent Genotype-Phenotype Associations in Avian Breeding Time

Understanding how genes shape phenotypes is essential to assess the evolutionary potential of a trait. Identifying the genes underlying quantitative behavioral or life-history traits has, however, proven to be a major challenge. The majority of these traits are phenotypically plastic and different parts of the genome can be involved in shaping the trait under different environmental conditions. These variable genotype-phenotype associations could be one explanation for the limited success of genome-wide association studies in such traits. We here use avian seasonal timing of breeding, a trait that is highly plastic in response to spring temperature, to explore effects of such genotype-by-environment interactions in genome-wide association studies. We genotyped 2045 great tit females for 384081 single nucleotide polymorphisms (SNPs) and recorded their egg-laying dates in the wild. When testing for associations between SNPs and egg-laying dates, no SNP reached genome-wide significance. We then explored whether SNP effects were modified by annual spring temperature by formally testing for an interaction between SNP effect and temperature. The models including the SNP^∗temperature interaction performed consistently better although no SNP reached genome-wide significance. Our results suggest that the effects of genes shaping seasonal timing depended on annual spring temperature. Such environment-dependent effects are expected for any phenotypically plastic trait. Taking these effects into account will thus improve the success of detecting genes involved in phenotypically plastic traits, thereby leading to a better understanding of their evolutionary potential.