Exploring genetic diversity and population structure of Myanmar indigenous chickens using double digest restriction site-associated DNA sequencing

Abstract

This study used double-digest restriction site-associated DNA sequencing to investigate the genetic diversity and population structure of eight populations of Myanmar indigenous chickens (MICs). We conducted genetic diversity and population structure analyses of indigenous chickens from Myanmar and other Asian countries and commercial chickens. A total of 20 261 autosomal SNPs were used. The expected heterozygosity of the eight populations of MICs ranged from 0.259 ± 0.175 (MYN_FCN) to 0.282 ± 0.152 (MYN_YGN), and the observed heterozygosity ranged from 0.245 ± 0.187 (MYN_FCN) to 0.265 ± 0.164 (MYN_YGN). The population structure analyses suggested that MICs possessed a genetic cluster that is limited in many chicken populations in this study. In addition, three distinct groups were found among Myanmar and Asian populations. We then identified differentially selected regions (DSRs) among these groups to understand their differences: 48 DSRs between Myanmar fighting chickens and MICs, 54 DSRs between Myanmar fighting chickens and a group of Myanmar and Asian indigenous chickens, and 48 DSRs between MICs and a group of Myanmar and Asian indigenous chickens. Gene Ontology enrichment analysis revealed certain significant genes in those group-pairs. The results revealed genetic differences between Myanmar and other Asian chickens.

Keywords: Myanmar indigenous chickens; differentially selected regions; gene ontology analysis; genetic diversity; population structure.