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Prospecting genomic regions associated with milk production traits in Egyptian buffalo

Published online by Cambridge University Press:  13 November 2020

Hamdy Abdel-Shafy ,
Mohamed A. A. Awad ,
Hussein El-Regalaty ,
S. E.-D. El-Assal  and
Samy Abou-Bakr
Hamdy Abdel-Shafy*
Affiliation:
Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma street, 12613Giza, Egypt
Mohamed A. A. Awad
Affiliation:
Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma street, 12613Giza, Egypt
Hussein El-Regalaty
Affiliation:
Department of buffalo research, Animal Production Research Institute, Agricultural Research Center, Dokki, Giza, Egypt
S. E.-D. El-Assal
Affiliation:
Department of Genetics, Faculty of Agriculture, Cairo University, El-Gamma street, 12613Giza, Egypt
Samy Abou-Bakr
Affiliation:
Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma street, 12613Giza, Egypt
*
Author for correspondence: Hamdy Abdel-Shafy, Email: hamdyabdelshafy@agr.cu.edu.eg
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Abstract

The objectives of the current study were to detect putative genomic loci and to identify candidate genes associated with milk production traits in Egyptian buffalo. A total number of 161 479 daily milk yield (DMY) records and 60 318 monthly measures for fat and protein percentages (FP and PP, respectively), along with fat and protein yields (FY and PY, respectively) from 1670 animals were used. Genotyping was performed using Axiom® Buffalo Genotyping 90 K array. Genome-wide association study (GWAS) for each trait was performed using PLINK. After Bonferroni correction, 47 SNPs were associated with one or more milk production traits. These SNPs were distributed over 36 quantitative trait loci (QTL) and located on 20 buffalo chromosomes (BBU). For the 47 SNPs, one was overlapped for three traits (DMY, FY, and PY), six were associated with two traits (one for PP and PY and five for FY and PY) while the rest were associated with only one trait. Out of 36 identified QTL, eleven were overlapped with previously reported loci in buffalo and/or cattle populations. Some of these SNPs are placed within or close to potential candidate genes, for example: TPD52, ZBTB10, RALYL and SNX16 on BBU15, ADGRD1 on BBU17, ESRRG on BBU5 and GRIP1 on BBU4. This is the first reported study between genome-wide markers and milk components in Egyptian buffalo. Our findings provide useful information to explore the genetic mechanisms and relevant genes contributing to the variation in milk production traits. Further confirmation studies with larger population size are necessary to validate the findings and detect the causal genetic variants.

Keywords

Candidate genegenetic markersgenome-wide associationmilk quality
Type
Research Article
Information
Journal of Dairy Research , Volume 87 , Issue 4 , November 2020 , pp. 389 - 396
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of Hannah Dairy Research Foundation

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