Population Structure and Genetic Diversity of Seven Chinese Indigenous Chicken Populations in Guizhou Province

AbstractGuangxi chickens play an important role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chicken from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was small, MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes have received strong selection in local breeds, these also provided novel breeding visual and data basis for future breeding.

Download Full-text

Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.20.0189 ◽

2020 ◽

Vol 33 (11) ◽

pp. 1732-1740

Author(s):

Muhammad Abdur Rashid ◽

Prabuddha Manjula ◽

Shakila Faruque ◽

A. K. Fazlul Haque Bhuiyan ◽

Dongwon Seo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Population Variation ◽

Fixation Index ◽

Indigenous Chicken ◽

Diversity Measures ◽

Red Jungle Fowl

Objective: The objectives of this study were to investigate the genetic diversity, population structure and relatedness among the five chicken populations of Bangladesh using microsatellite markers.Methods: A total of 161 individuals representing 5 chicken populations (non-descript Deshi [ND], naked neck [NN], hilly [HI], Aseel [AS], and red jungle fowl [JF]) were included in this study to investigate genetic diversity measures, population structure, genetic distance and phylogenetic relationships. Genotyping was performed using 16 selected polymorphic microsatellite markers distributed across 10 chromosomes.Results: The average observed and expected heterozygosity, mean number of alleles and polymorphic information content were found to be 0.67±0.01, 0.70±0.01, 10.7 and 0.748, respectively in the studied populations. The estimated overall fixation index across the loci (F), heterozygote deficiency within (FIS) and among (FIT) chicken populations were 0.04±0.02, 0.05 and 0.16, respectively. Analysis of molecular variance analysis revealed 88.07% of the total genetic diversity was accounted for within population variation and the rest 11.93% was incurred with population differentiation (FST). The highest pairwise genetic distance (0.154) was found between ND and AS while the lowest distance was between JF and AS (0.084). Structure analysis depicted that the studied samples can be categorized into four distinct types or varieties (ΔK = 3.74) such as ND, NN, and HI where AS and JF clustered together as an admixed population. The Neighbor-Joining phylogenetic tree and discriminant analysis of principal component also showed close relatedness among three chicken varieties namely AS, HI, and JF.Conclusion: The results reflected that indigenous chicken of Bangladesh still possess rich genetic diversity but weak differentiation among the studied populations. This finding provides some important insight on genetic diversity measures that could support the designing and implementing of future breeding plans for indigenous chickens of Bangladesh.

Download Full-text