Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel

High-throughput cow genotyping has opened new
perspectives for genome-wide association studies
(GWAS). Directly recorded phenotypes and several records
per animal could be used. In this study, a GWAS
on lactation curve traits of 337 Italian Simmental cows
genotyped with the Illumina (San Diego, CA) lowdensity
BeadChip (7K) was carried out. Scores of the
first 2 principal components extracted from test-day
records (7 for each lactation) for milk yield, fat and
protein percentages, and somatic cell score were used as
phenotypes. The first component described the average
level of the lactation curve, whereas the second summarized
its shape. Data were analyzed with a mixed
linear model that included fixed effects of herd, calving
month, calving year, parity, SNP genotype, and random
effects of animal and permanent environment. All
statistically significant markers (Bonferroni corrected)
were associated with the average level component
(2 for milk yield, 9 for fat percentage, 6 for protein
percentages, and 1 for somatic cell score). No markers
were found to be associated with the lactation curve
shape. Gene discovery was performed using windows
of variable size, according to the linkage disequilibrium
level of the specific genomic region. Several suggestive
candidate genes were identified, some of which already
reported to be associated with dairy traits, such as
DGAT1. Others were involved in lipid metabolism, in
protein synthesis, in the immune response, in cellular
processes, and in early development. The large number
of genes flagged in the present study suggests interesting
perspectives for the use of low-density genotyped
females for GWAS, also for novel phenotypes that are
not currently considered as breeding goals.