Whole-genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China
Whole-genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China
复制标题
全基因组SNP数据揭示了中国江西省本土鸡品种黑色羽毛的群体结构和选择特征
DOI：
10.1111/age.12827
复制
发表时间：
2019-07-15
期刊：
影响因子：
2.4
通讯作者：
Ren, J.
中科院分区：
文献类型：
--
作者：
Mao, H.;Wang, X.;Ren, J.
江西省有10个地方鸡种，是中国鸡遗传资源的重要组成部分。利用600K鸡微珠芯片SNP数据对江西7个鸡品种的群体遗传学进行了研究。为了从全基因组角度研究江西鸡的群体结构，本研究利用55K基因芯片对江西鸡7个品种的78个个体和余干黑、南城黑和万载黄3个未调查品种的63只鸡进行了基因分型。然后，我们探索了来自235个个体的17 101个SNP的合并数据，以推断10个品种的群体结构。结果表明，NC和YG是同一品种的两个区域群体，由于两个群体的个体聚在一起形成一个独立于其他品种的分支，在多维主成分分析中，它们总是聚在一起，表现出相同的祖先谱系组成模式。因此，NC和YG应该被认为是一个单一的品种，在国家支持的保护计划。此外，我们进行了基因组扫描，以寻找选择黑色羽毛的标志。两个对比组（三个黑色羽毛品种对六个非黑色羽毛品种）的Bayescan和HAPFlk分析一致地检测到25个假定的选择区域。9个色素沉着相关基因（DCT、SLC24A5、SLC30A4、MYO5A、CYP 19A1、NADK 2、SLC45A2、GNAQ和DCP 2）位于这些区域内，这些基因是鸡黑色羽毛的感兴趣的候选基因，并为进一步鉴定鸡黑色羽毛的致病突变提供了起点。
Ten indigenous chicken breeds were originally distributed in Jiangxi Province, China, and they define a critical component of Chinese chicken genetic resources. We have investigated the population genetics of seven Jiangxi chicken breeds using 600K chicken BeadChip SNP data. To provide a genome-wide perspective for the population structure of all 10 Jiangxi chicken breeds, we herein genotyped 78 additional individuals from the seven breeds and 63 chickens from three uninvestigated breeds-Yugan Black (YG), Nancheng Black (NC) and Wanzai Yellow using 55K chicken SNP arrays. We then explored merged data of 17 101 SNPs from 235 individuals to infer the population structure of the 10 breeds. We showed that NC and YG are two regional populations of the same breed, as individuals from the two populations clustered together to form a branch separate from the other breeds in the neighbor-joining tree, they always grouped together in multidimensional principal component analyses and they displayed an identical pattern of ancestral lineage composition. Hence, NC and YG should be considered a single breed in the state-supported conservation scheme. Moreover, we conducted a genome scan for signatures of selection for black plumage. bayescan and hapflk analyses of two contrasting groups (three black-feathered breeds vs. six non-black-feathered breeds) consistently detected 25 putative regions under selection. Nine pigmentation- associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2) reside within these regions, and these genes are interesting candidates for black plumage and provide a starting point for further identification of causative mutations for black feathers in chicken.