Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks

Hehe Liu,Yaxi Xu,Ming Xie,Shuisheng Hou,Lei Wang,Zhengkui Zhou,Zhanbao Guo,Yunsheng Zhang,Jing Tang,Wenlei Fan,Jian Hu,Qian Xu

doi:10.1186/s12711-021-00684-5

Abstract

BackgroundAs a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks.ResultsFeed conversation ratio (FCR) was positively correlated with feed intake but negatively correlated with egg-related traits, including egg weight and egg production, both phenotypically and genetically. Estimates of pedigree-based heritability were higher than 0.2 for all traits investigated, except hip-width. Based on whole-genome sequencing data, we conducted genome-wide association studies to identify genomic regions associated with these traits. In total, 11 genomic regions were associated with FCR. No genomic regions were identified as significantly associated with hip-width, total feed intake, average daily feed intake, and total egg production. Analysis of selective sweeps between mallard and Pekin ducks confirmed three of these genomic regions on chromosomes 13, 3 and 6. Within these three regions, variants in candidate genes that were in linkage disequilibrium with the GWAS leader single nucleotide polymorphisms (SNPs) (Chr13:2,196,728, P = 7.05 × 10–14; Chr3:76,991,524, P = 1.06 × 10–12; Chr6:20,356,803, P = 1.14 × 10–10) were detected. Thus, we identified 31 potential candidate genes associated with FCR, among which the strongest candidates are those that are highly expressed in tissues involved in reproduction and nervous system functions of ducks: CNTN4, CRBR, GPR63, KLHL32, FHL5, TRNT1, MANEA, NDUFAF4, and SCD.ConclusionsFor the first time, we report the identification of genomic regions that are associated with FCR in ducks and our results illustrate the genomic changes that occurred during their domestication and are involved in egg production efficiency.

Highlights

As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production
Phenotypic statistics and estimates of genetic parameters The phenotypic statistics for each trait are in Table 1 and show that the coefficient of variation was greater than 10% for all traits, except for HP, and was largest for Feed conversation ratio (FCR), at 50%
We have reported genetic parameters for six egg production traits in ducks based on an F2 population that was constructed from mallard and Pekin ducks

Summary

Introduction

As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. Limited information is available about the underlying genetic architecture of egg production traits in ducks. Achieving breeding progress in egg production efficiency through conventional selection using phenotypic information only is difficult. With the advances in molecular genetic technologies and the availability of DNA markers, identifying QTL that control egg production traits in poultry for application in marker-assisted selection (MAS) has progressed rapidly [9]. Based on GWAS, QTL for egg production traits in poultry can be screened much more quickly than before. Based on the records available in the chicken QTL database, to date, 600 QTL related to egg production traits have been identified [14]

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Discussion

Conclusion