基于SNP芯片分析新浦东鸡的遗传多样性和遗传结构

doi:10.11843/j.issn.0366-6964.2023.12.008

Abstract

Abstract: The study aimed to explore the genetic diversity, relationship and family structure of the New Pudong chickens population. In order to reveal the genetic relationship between individuals, "Jingxin No.1" SNP chip was used to detect the SNPs in the whole genome of 368 New Pudong chickens. The genetic structure, genetic relationship and inbreeding coefficient of New Pudong chickens were also analyzed. The result showed that a total of 55 023 SNPs were obtained. According to the quality control of Plink (V1.90) software, there were 42 267 remaining SNPs, among which 78% were polymorphic. The effective allele number was 1.552, the PIC was 0.237, the MAF was 0.226, the H_O was 0.355, and the H_E was 0.353. The average IBS genetic distance of New Pudong chickens was 0.280 9. The average IBS genetic distance of 110 roosters was 0.280 1. According to the cluster analysis (the standard is that the coefficient of genetic relationship was greater than or equal to 0.1), 110 roosters were divided into 32 families. The ROH length of each New Pudong chicken were 0-350 Mb, and the proportion of individuals with ROH length of 100-150 Mb was the largest. The average inbreeding coefficient calculated based on ROH value was 0.155, indicating a high degree of inbreeding. According to these results, this study reveals the population genetic structure and genetic diversity of New Pudong chickens at the genomic level, which can provide reference for future breeding and utilization.

Key words: New Pudong chicken, SNP chip, genetic diversity, population genetic structure

CLC Number:

S831.2

QI Lina, LU Xuelin, YANG Kaixuan, ZHOU Jin, LI Xianyu, LIU Ke, ZHANG Wengang, GU Xin, ZHANG Weijian. Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4962-4971.

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Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips

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