Data from: Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle

Seasonal shedding of winter hair at the start of summer is well-studied in
wild and domesticated populations. However, the genetic influences on this
trait and their interactions are poorly understood. We use data from
13,364 cattle with 36,899 repeated phenotypes to investigate the
relationship between hair shedding and environmental variables, single
nucleotide polymorphisms, and their interactions to understand
quantitative differences in seasonal shedding. Using de-regressed
estimated breeding values from a repeated records model in a genome-wide
association analysis (GWAA) and meta-analysis of year-specific GWAA gave
remarkably similar results. These GWAA identified hundreds of variants
associated with seasonal hair shedding. There were especially strong
associations on chromosomes 5 and 23. Genotype-by-environment interaction
GWAA identified 1,040 day-length-by-genotype interaction associations and
17 apparent temperature-by-genotype interaction associations with hair
shedding, highlighting the importance of day length on hair shedding.
Accurate genomic predictions of hair shedding were created for the entire
dataset, Angus, Hereford, Brangus, and multi-breed datasets. Loci related
to metabolism and light-sensing have a large influence on seasonal hair
shedding. This is one of the largest genetic analyses of a phenological
trait and provides insight for both agriculture production and basic
science.