基于RAD-seq静原鸡保种群体的遗传变异分析

doi:10.11843/j.issn.0366-6964.2022.07.008

Abstract

Abstract: 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.

Key words: Jingyuan chicken, RAD-seq, genetic diversity analysis, selective sweep analysis, genome-wide association analysis

CLC Number:

S831.2

MA Lixia, CAO Guowei, ZHU Hongfang, DENG Zhanzhao, CAI Zhengyun, ZHOU Chenghao, HAN Wei, GU Yaling, ZHANG Juan. Analysis of Genetic Variation in a Conserved Population of Jingyuan Chickens Based on RAD-seq[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2104-2117.

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

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