Determination of Potential Candidate Genes Associated with Milk Lactose in Egyptian Buffalo.

Abstract

The aim of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with lactose percentage (LP) and lactose yield (LY) in Egyptian buffalo. The phenotypic dataset included 60,318 monthly measures for LP and LY from 1481 animals. A total number of 114 animals with high and low deviated performance were selected for genotyping with Axiom Buffalo Genotyping 90K Array. Genome-wide analysis was performed using a single marker regression. The GWAS revealed 32 significant and seven suggestive SNPs for LP, however; only two suggestive SNPs were identified for LY. The identified genomic regions are overlapped with previously reported QTL in different cattle breeds. In addition, novel genomic loci were detected. The identified genomic regions harbored many candidate genes with biological roles associated with milk production traits, such as TPD52 and ZBTB10 on chromosome 15; AADAT and GALNTL6 on chromosome 3 and COL8A1 and PLOD2 on chromosome 1. Our findings provide the basis to uncover the key markers and candidate genes affecting lactose traits which facilitate the exploration of the genetic mechanisms that control lactose traits variation in Egyptian buffalo.

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

“…For buffalo, development of Axiom Buffalo Genotyping Array (90k SNPs) opens new opportunities to identify candidate genes associated with buffalo milk production traits and provides the possibility of predicting genomic breeding values for buffalo breeds in different countries. So far, 87 significant and 354 suggestive genomic regions were reported for milk production traits in Brazilian, Chinese, Egyptian, Iranian, Italian and Philippino buffalo (de Camargo et al ., 2015; El-Halawany et al ., 2017; Iamartino et al ., 2017; Mokhber, 2017; da Costa Barros et al ., 2018; Herrera et al ., 2018; Liu et al ., 2018; Abdel-Shafy et al ., 2020; Awad et al ., 2020; Lu et al ., 2020). Despite the fact that these loci were distributed on almost all chromosomes, none of these SNPs were overlapped between studies indicating the complexity of milk production traits and the modest effect of such SNPs (Abdel-Shafy et al ., 2020).…”

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

“…Whole-genome analyses [ 116 ] have also shown that this gene family plays a role in the regulation of lactation in sheep. On OAR22, CFAP46 or cilia and flagella associated protein 46, has been associated to lactose content [ 117 ] whereas RBM34 or RNA-binding protein 34 gene on OAR25 has role in nucleic acid binding and nucleotide binding, and it was found by GWAS study on cattle to be associated with milk yield [ 118 ].…”

Editorial: Buffalo Genetics and Genomics

“…Recently, it has been reported that incorporating biological information and pre-selected genetic markers can increase the accuracy of prediction (Hayes and Daetwyler, 2019). Detection of these loci can be achieved by GWASs, as it has been previously reported for milk production traits in different buffalo breeds (de Camargo et al, 2015;El-Halawany et al, 2017;Iamartino et al, 2017;Mokhber, 2017;da Costa Barros et al, 2018;Liu et al, 2018;Herrera et al, 2018;Lu et al, 2020;Abdel-Shafy et al, 2020b;Awad et al, 2020). However, none of the detected regions was overlapped among different populations and/or validated.…”