Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences

Abstract

Chinese indigenous chicken breeds are geographically widespread, and a total of 116 indigenous chicken breeds are listed as Chinese national genetic resources. However, these indigenous chicken breeds are facing serious challenges as declining population and germplasm degeneration because lots of commercial chicken breeds had been introduced. In this study, the genetic variations of eleven Chinese indigenous chicken breeds of Sichuan province and three commercial chicken breeds were investigated based on the partial mitochondrial DNA D-loop of 487bp in length. 147 individuals from 14 breeds were examined and 34 haplotypes were observed. Genetic diversity analysis showed that the highest haplotype diversity level was found in Dahen Chicken (DH) population, while the Arbor Acres Chicken (WF) and Roman layer (RM) showed lower genetic diversity levels. The long-term artificial selection may lead to reduced nucleotide diversity. Genetic population differentiation analysis indicated that most of the variation (80.80%) was attributed to variations among breeds. Phylogenetic analysis revealed that these individuals were divided into four distinct genetic clades, including cluster A, B, C and D. Eighteen haplotypes were classified as cluster A, eight haplotypes were classified as cluster B, five haplotypes were classified as cluster C and three haplotypes were classified as cluster D. There was no breed-specific clade. Our study firstly identified the population's genetic structure of Chinese indigenous chickens and the most important commercial breeds in Sichuan province, though the genetic diversity of indigenous breeds did not suffer obvious decrease, but could be helpful for efficient artificial breeding selection and genetic resources conservation.

Potential mitochondrial diversity role in the productivity of three lines of Japanese quails

“…This analysis revealed considerable genetic diversity in the white line quails, which is known to have been reared for egg production. However, long-term artificial selection programs may lead to reduced nucleotide diversity (Yu et al 2019). This finding implies that the current selection programs for egg production have not conducted over long time.…”

“…These mitochondrial sequences are inherited maternally and evolve five to ten times faster than nuclear genetic markers as it appears in multiple copies in the cells and the mitochondrial gene content is strongly conserved across generations (Di Lorenzo et al 2015). Due to this largest variation and highest mutation rate, mtDNA has been regarded as an appropriate marker to study the genetic biodiversity (Yu et al 2019). Moreover, mtDNA has become a useful marker for the study of genetic variability and population structure in livestock (Muchadeyi et al 2008).…”