Genetic diversity of Jiangsu native chicken breeds assessed with the mitochondrial DNA D-loop region

Abstract

1. The objective of this study was to determine the origin and evolution of chickens from 5 native breeds that are traditionally raised in Jiangsu Province. 2. To address this question, the complete mitochondrial DNA D-loop sequence of 149 chickens from 5 native breeds of Jiangsu Province was analysed. 3. Sequence read lengths of the native breeds were 1231 to 1232 bp, with a single-base deletion from the 859 bp site in the 1231 bp haplotype. A total of 33 variable sites that defined 19 haplotypes were identified. The average haplotype diversity and nucleotide diversity were 0.862 ± 0.017 and 0.00591 ± 0.00135. 4. Phylogenetic analysis showed that genetic structure of the mtDNA haplotypes of Jiangsu chickens are distributed across 5 clades (haplogroups): Clades A, B, C, D, and E. However, most of the individuals characterised in this study belonged to clades A and B. 5. The results of this study indicate that Jiangsu chicken populations have relatively low nucleotide and haplotype diversity and likely share 5 common maternal lineages.

Diversity Analysis of Chinese Tibetan Naqu Yak (Bos grunniens) Populations Using mtDNA

“…Additionally, this value was much larger than the number of polymorphisms found in the mtDNA ND6 gene (Hai et al, 2014). This observation is consistent with the hypothesis that the D-loop region contains the most polymorphisms in the mitochondrial DNA (Tsai and St John, 2016;Gao et al, 2017). Second, in comparison with previous studies, the haplotype diversity (Hi) of the 4 Naqu yak populations (0.9420 to 0.9770) was higher than the diversities among the eight different known Tibetan populations (0.827 to 0.927; Song et al, 2014), the Tianzhu white yak (Gansu, China), and the Jiulong yak (Sichuan, China) but was lower than the diversity of the Maiwa yak (Sichuan, China; Lai et al, 2005).…”

“…Recently, mitochondrial DNA polymorphisms have been widely used to estimate the gene flow and phylogenetic relationships of maternal lineages in domestic animals (e.g., Nguluma et al, 2017;Jia et al, 2017;Deng et al, 2017;Almarzook et al, 2017) and wild animals (e.g., Elsner et al, 2017;Khaire et al, 2017). The domestic yak (Bos grunniens) is a large and commercially important animal living in the Qinghai-Tibetan Plateau of China with a high-altitude climate (Guangxin et al, 2016).…”

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

“…Although, this is a small study including only two breeds, it Other mitochondrial markers such as D-loop (control region) have also been used by various investigators to explore diversity among different native chicken breeds across the world. Higher number of polymorphic sites defining more number of haplotypes were reported in Samar Philippines native chickens (17 and 5) [17], Hungarian native chickens (17 and 11) [18], Egyptian native chickens (28 and 18) [19], native chicken breeds of Jiangsu (33 and 19) [20], and chicken breeds of Korea (84 and 31) [21]. These studies showed high genetic diversity with higher haplotype and nucleotide diversity in Samar Philippines native chickens (0.92 and 0.0056) [22], Hungarian native chickens (0.626 and 0.0049) [18], Egyptian native chickens (0.81 and 0.0045) [19], native chicken breeds of Jiangsu (0.862 and 0.00591) [20], and chicken breeds of Korea (0.604 and 0.007) [21].…”

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

“…The majority of studies have estimated genetic variability in Chinese indigenous chickens using microsatellites [ 45 , 46 ] or mtDNA [ 47 , 48 ], but genome-wide SNPs have seldomly been used. We estimated the genetic diversity in three chicken populations using SNP markers.…”