Acta Veterinaria et Zootechnica Sinica ›› 2024, Vol. 55 ›› Issue (9): 3914-3924.doi: 10.11843/j.issn.0366-6964.2024.09.016

• Animal Genetics and Breeding • Previous Articles     Next Articles

The Study on Population Genetic Diversity and Genome-wide Association Study of Body Weight and Size Traits for Lion-head Geese

Hongyan HUANG1(), Liyun ZHANG1(), Zhirong HUANG1, Zhongping WU1, Xumeng ZHANG1, Hongjia OUYANG1, Junpeng CHEN2, Zhenping LIN2, Yunbo TIAN1, Xiujin LI1,*(), Yunmao HUANG1,*()   

  1. 1. Science & Technology Innovation Platform of Guangdong Waterfowl Health Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
    2. Baisha Poultry and Livestock Origin Research Institute, Shantou 515821, China
  • Received:2024-03-18 Online:2024-09-23 Published:2024-09-27
  • Contact: Xiujin LI, Yunmao HUANG E-mail:huanghongyan@zhku.edu.cn;zhangliyun@zhku.edu.cn;lixiujin996@126.com;huangyunmao@zhku.edu.cn

Abstract:

The aim of this study was to investigate the genetic diversity of Lion-head geese and to perform the genome-wide association study of body weight and size traits. In this study, the 111 lion-head geese (20 males and 91 females) were randomly selected. They are two years old and off-season. The phenotypes detection of body weight and size traits and the second-generation genome sequencing (5×) for these geese were performed. SNPs from the sequencing data was called, the genetic diversity indexes was calculated and the association between SNPs and body weight and size traits was performed using the single SNP regression mixed model. The Bonferroni correction was used, i.e., the genome-wide threshold (0.05/a total of SNPs) and the chromosome-wide threshold (0.05/number of SNPs on each chromosome) to define the significant SNPs. The gene annotation was performed based on the 50 kb upstream and downstream of chromosome-wide significant SNPs. By the quality control, a total of 7 577 552 SNPs was obtained for the further analysis. The analysis of genetic diversity found that effective population size, minor allele frequency, polymorphic information content, observed heterozygosity, expected heterozygosity and inbreeding coefficient were 234, 0.25, 0.34, 0.26, 0.34 and 0.22, respectively. A total of 6 164 runs of homozygosity was detected, the high proportion (74.4%) of which ranged from 1.0 Mb to 2.0 Mb. We found 38 chromosome-wide significant SNPs by the association between SNPs and body weight and size traits, and these significant SNPs were involved in 90 genes. Among these genes, D2HDH, THAP4, ESPNL, EPT1, TNPO3, MCF2L and AIP1 were previously reported to affect the growth and development.In this study, by using the second generation genome sequencing data, we found a certain degree of inbreeding phenomenon for the Lion-head geese population and detected 7 candidate genes affecting the body weight and size traits, which can provide important references for the subsequent conservation of the Lion-head geese, the study of gene function and the application of molecular breeding.

Key words: Lion-head goose, population genetic diversity, body weight and size traits, genome-wide association study

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