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

• Published in: Journal of dairy science Vol. 98; no. 11; p. 8175
• Main Authors: Macciotta, N P P, Gaspa, G, Bomba, L, Vicario, D, Dimauro, C, Cellesi, M, Ajmone-Marsan, P
• Format: Journal Article
• Language: English
• Published: United States 01-11-2015
• Subjects: Animals; Cattle - genetics; Female; Genetic Association Studies; Genomics; Genotype; Italy; Lactation; Linear Models; Milk - secretion; Polymorphism, Single Nucleotide; Principal Component Analysis; Italy; low-density panel; lactation curve; principal component analysis; genome-wide association study
• ISSN: 1525-3198
• DOI: 10.3168/jds.2015-9500

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) low-density 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.