Abstract
Objective:This paper presents the obtained result of a study that realizes to associate a set of real and imputed single nucleotide polymorphisms (SNP) genotypes to the rear udder height in Holstein cows.Materials and methods:Forty-six Holstein cows from an arid zone of Mexico were phenotyped and genotyped for this study. Blood samples were used for DNA extraction, genotyping was performed with the Illumina BovineLD Bead chip which interrogates 6,912 SNPs genome-wide, and imputation was performed using the Findhap software. After QC filters, a total of 22,251 high quality and informative SNPs were inspected.Results:The results showed the detection of 76 significant SNPs throughout the complete genome. Significant SNPs fall inside 111 Quantitative Loci Traits related to protein percentage, milk yield, and fat, among others, in chromosomes 1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 19, 20, 21, 23, 26, 27, and 29. Similarly, results confirm that a genotype imputation is a convenient option for genome-wide covering when selecting economic traits with low-density real SNP panels.Conclusion:This study contributes to establishing a low-cost and profitable strategy for applying genomic selection in developing countries.
Highlights
Humans have applied a strong selection pressure on cattle favoring health and economically important traits
Results confirm that a genotype imputation is a convenient option for genome-wide covering when selecting economic traits with low-density real single nucleotide polymorphisms (SNP) panels
35 significant SNPs were found to fall inside genes, while the rest fall outside genes but within an average distance of 323 kb around of annotated genes
Summary
Humans have applied a strong selection pressure on cattle favoring health and economically important traits. A genome-wide association of single nucleotide polymorphisms (SNPs) to genotypes and phenotypes have become a very powerful approach to identify genetic variants associated with the production, conformation, health, and reproduction characteristics [1,2,3,4]. In the northwest of Mexico, production and health animal in arid and semi-arid zones are closely related to several conformation and physiological traits. Previous studies in Holstein cows from arid zones in Mexico have demonstrated that implementing cooling management systems improves physiological status and lactation performance during summer heat [5,6]. Recent studies in Holstein cows from the same arid zones have been focused on associating genes and genetic variations to health and production traits [7,8]. Salomon-Torres et al [7,9] reported 34 Copy Number Variants overlapping with quantitative loci traits (QTLs) associated with an extensive group of traits, including disease susceptibilities, such as clinical mastitis and dystocia, milk fat, body length, meat color, milk protein, and height
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