Genetic diversity and population structure of indigenous chicken breeds in South China

Abstract

A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure. All microsatellites were found to be polymorphic. The number of alleles per locus ranged from 5 to 36, with an average of 12.10 AE 7.00 (SE). All breeds, except White Recessive Rock, had high allelic polymorphism (>0.5). Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds. Potential introgression from the commercial breeds into the indigenous chickens was also detected. The population structure of these indigenous chicken breeds could be explained by their geographical distribution, which suggested the presence of independent history of breed formation. Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

“…Interestingly, a three-way sub-clustering pattern is consistent in PCA, ADMIXTURE, and NJ phylogenetic tree and amazingly mirrors the geographical distributions of the YFCs. The 10 YFC populations divide into northern, central and southern clusters, agreeing with the trends earlier proposed by microsatellite-based studies of chickens from these regions of China [1,11,12]. This sub-structuring may be reflective of some extent of differential exchange of genetic materials in neighboring locations, breeding histories, or natural and artificial selection drivers as described in several chicken populations [16,26].…”

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

“…Interestingly, a three-way sub-clustering pattern is consistent in PCA, ADMIXTURE, and NJ phylogenetic tree and amazingly mirrors the geographical distributions of the YFCs. The 10 YFC populations divide into northern, central and southern clusters, agreeing with the trends earlier proposed by microsatellite-based studies of chickens from these regions of China [1,11,12]. This sub-structuring may be reflective of some extent of differential exchange of genetic materials in neighboring locations, breeding histories, or natural and artificial selection drivers as described in several chicken populations [16,34].…”

“…Different cultures and ethnicities around the globe have developed unique cuisines, into which chickens are incorporated in diverse ways. Chicken consumption is popular globally, with the preference for chicken meat eclipsing that of red meat [1,2]. Yellow-feathered chickens, otherwise known as "three-yellow chickens" because of their characteristic yellow beak, feathers, and feet [1], and herein abbreviated as YFCs, are a favorite choice for traditional broths and soups in Asian countries, particularly in Korea and southern China.…”

“…Previous research on YFCs primarily focused on understanding the chemical properties of meat and soups [2,[8][9][10], or their genetic diversity compared to commercial breeds using low-density markers [1,11,12]. Hardly any genome-wide investigations of the population structure and genetic basis of the unique YFC phenotypic traits have been conducted, a major drawback in rational improvement and conservation of these chickens.…”

Widespread introgression in Chinese indigenous chicken breeds from commercial broiler

“…In fact, analysis on microsatellites revealed that China's chicken resource structure changed after the introduction of a large number of foreign commercial chickens in the 1980s. According to this report, Huiyang Bearded chicken suffered from admixture and decreasing population size (Huang et al, 2016), and this is a common phenomenon in developing countries (Alqamashoui, Simianer, Kadim, & Weigend, 2014).…”