Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle

Hojjat Asadollahpour Nanaei; Mostafa Dehghani Qanatqestani; Ali Esmailizadeh

doi:10.1016/j.ygeno.2019.06.002

Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle

Genomics. 2020 Jan;112(1):880-885. doi: 10.1016/j.ygeno.2019.06.002. Epub 2019 Jun 3.

Authors

Hojjat Asadollahpour Nanaei¹, Mostafa Dehghani Qanatqestani¹, Ali Esmailizadeh²

Affiliations

¹ Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
² Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran. Electronic address: aliesmaili@uk.ac.ir.

PMID: 31170439
DOI: 10.1016/j.ygeno.2019.06.002

Abstract

Milk production and composition are the most economically important traits affecting profitability in dairy cattle. In this study, we aimed at detecting signatures of positive selection in Kenana, known as one of the high milk production African indigenous zebu cattle, using next-generation sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F_ST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi). Further analysis showed that several candidate genes such as CSN3, IGFBP-2, RORA, ABCG2, B4GALT1 and GHR are positively selected for milk production traits in Kenana cattle. The candidate genes and enriched pathways identified in this study may provide a basis for future genome-wide association studies and investigations into genomic targets of selection in dairy cattle.

Keywords: African cattle; Kenana; Milk production traits; Signatures of positive selection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Africa
Animals
Cattle / genetics*
High-Throughput Nucleotide Sequencing
Milk*
Polymorphism, Single Nucleotide
Selection, Genetic
Whole Genome Sequencing