Inspection of real and imputed genotypes reveled 76 SNPs associated to rear udder height in Holstein cattle

Authors

  • Mirvana Gonzalez Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Rafael Villa Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Carlos Villa Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Victor Gonzalez Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Martin Montano Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Gerardo Medina Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
  • Pad Mahadevan Department of Biology, University of Tampa, Tampa, FL, USA

Keywords:

Genotypes; QTLs; association; SNPs

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.

Adv. Vet. Anim. Res., 7(2): 234-241, June 2020

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Published

2020-06-12

How to Cite

Gonzalez, M., Villa, R., Villa, C., Gonzalez, V., Montano, M., Medina, G., & Mahadevan, P. (2020). Inspection of real and imputed genotypes reveled 76 SNPs associated to rear udder height in Holstein cattle. Journal of Advanced Veterinary and Animal Research, 7(2), 234–241. Retrieved from https://www.banglajol.info/index.php/JAVAR/article/view/47517

Issue

Vol. 7 No. 2 (2020)

Section

Original Articles

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