基于RAD-seq静原鸡保种群体的遗传变异分析

旨在分析静原鸡白羽、麻羽、黑羽保种群之间的遗传变异，挖掘调控特征性状的关键候选基因。本研究利用RAD-seq技术对180日龄特征明显、发育正常且健康的白羽、麻羽、黑羽静原鸡(每个羽色选取60个个体，40只母鸡，20只公鸡)进行测序，基于SNP标记计算观察杂合度(Ho)、群体内核酸多态性(Pi)、群体的平均近交系数(Fis)等指标，分析静原鸡3个类群的遗传多样性和群体结构，并通过选择性清除分析和全基因组关联分析(GWAS)筛选出候选基因，利用KOBAS对候选基因进行KEGG (Kyoto Encyclopedia of Genes and Genomes)通路富集,最终筛选出调控静原鸡羽色的候选基因。测序结果表明，静原鸡180个样品共产生198.83 Gb Clean Data，Q30达到93%以上。遗传多样性分析表明，白羽、麻羽、黑羽静原鸡分别鉴定出238 533、233 562和240 820个SNPs标记，Ho、Pi和Fis分别在0.273 2~0.278 2、0.304 9~0.309 6和0.096 1~0.109 8之间。群体结构分析表明，静原鸡根据不同羽色分为不同类群。通过选择性清除分析和全基因组关联分析共筛选出11个(FZD4、WNT16、EDNRB、TYR、KRAS、CTNNB1、DDC、MC1R、CAMK2A、PRKCB、PRKCA)与静原鸡羽色相关的候选基因，富集结果显示这些基因主要与黑色素生成、酪氨酸代谢和Wnt信号传导等通路相关。综上所述，本研究利用SNPs标记信息可以全面地评价静原鸡的保种现状，为静原鸡的遗传资源保护奠定理论基础。同时，筛选出了与静原鸡羽色性状相关的候选基因，为静原鸡不同羽色的品系化培育提供新的遗传标记和基因靶点。

Analysis of Genetic Variation in a Conserved Population of Jingyuan Chickens Based on RAD-seq

The aim of this study was to analyze the genetic variation among the white-, hemp- and black-feathered breeding populations of Jingyuan chickens, and to explore the key candidate genes regulating the characteristic traits. In this study, the RAD-seq technology was used to sequence 180-day-old white-, hemp- and black-feathered Jingyuan chickens (60 individuals of each plumage color, 40 hens and 20 roosters) with distinctive features, normal development and health, and the observed heterozygosity (Ho), nucleic acid polymorphism (Pi) within the population and the average inbreeding coefficient (Fis) of the population based on SNPs markers were calculated to analyze the genetic diversity and population structure of Jingyuan chickens. The candidate genes were screened by selective sweep analysis and genome-wide association analysis (GWAS), and enriched by KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways using KOBAS. The candidate genes regulating plumage color of Jingyuan chickens were finally screened. The sequencing results showed that a total of 198.83 Gb of clean data was obtained from 180 samples of Jingyuan chickens, with Q30 reaching more than 93%. Genetic diversity analysis showed that 238 533, 233 562 and 240 820 SNPs markers were identified for the white-, hemp-, and black- feathers of Jingyuan chickens, with Ho, Pi and Fis range of 0.273 2-0.278 2, 0.304 9-0.309 6 and 0.096 1-0.109 8, respectively. The analysis of population structure showed that Jingyuan chickens were divided into different groups according to different feather colors. A total of 11 candidate genes (FZD4, WNT16, EDNRB, TYR, KRAS, CTNNB1, DDC, MC1R, CAMK2A, PRKCB, PRKCA) associated with plumage color in Jingyuan chickens were screened by selective sweep analysis and genome-wide association analysis, and the enrichment results showed that these genes were related to the pathways of melanogenesis, tyrosine metabolism, and Wnt signaling. In summary, the breeding status of the Jingyuan chicken can be comprehensively evaluated using SNPs marker information and lay a theoretical foundation for the conservation of the genetic resources of the Jingyuan chicken in this study. At the same time, the candidate genes related to the plumage color trait of Jingyuan chicken were screened to provide new genetic markers and gene targets for the breeding of different plumage colors of Jingyuan chicken.