Identification of the genetic basis of the duck growth rate in multiple growth stages using genome-wide association analysis

Yang Xi; Qifan Wu; Yutian Zeng; Jingjing Qi; Junpeng Li; Hua He; Hengyong Xu; Jiwei Hu; Xiping Yan; Lili Bai; Chunchun Han; Shenqiang Hu; Jiwen Wang; Hehe Liu; Liang Li

doi:10.1186/s12864-023-09302-8

Identification of the genetic basis of the duck growth rate in multiple growth stages using genome-wide association analysis

BMC Genomics. 2023 May 26;24(1):285. doi: 10.1186/s12864-023-09302-8.

Authors

Yang Xi¹, Qifan Wu¹, Yutian Zeng¹, Jingjing Qi¹, Junpeng Li¹, Hua He¹, Hengyong Xu¹, Jiwei Hu¹, Xiping Yan¹, Lili Bai¹, Chunchun Han¹, Shenqiang Hu¹, Jiwen Wang¹, Hehe Liu², Liang Li³

Affiliations

¹ Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China.
² Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China. liuee1985@sicau.edu.cn.
³ Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China. liliang@sicau.edu.cn.

Abstract

Background: The genetic locus responsible for duck body size has been fully explained before, but the growth trait-related genetic basis is still waiting to be explored. For example, the genetic site related to growth rate, an important economic trait affecting marketing weight and feeding cost, is still unclear. Here, we performed genome wide association study (GWAS) to identify growth rate-associated genes and mutations.

Result: In the current study, the body weight data of 358 ducks were recorded every 10 days from hatching to 120 days of age. According to the growth curve, we evaluated the relative and absolute growth rates (RGR and AGR) of 5 stages during the early rapid growth period. GWAS results for RGRs identified 31 significant SNPs on autosomes, and these SNPs were annotated by 24 protein-coding genes. Fourteen autosomal SNPs were significantly associated with AGRs. In addition, 4 shared significant SNPs were identified as having an association with both AGR and RGR, which were Chr2: 11483045 C>T, Chr2: 13750217 G>A, Chr2: 42508231 G>A and Chr2: 43644612 C>T. Among them, Chr2: 11483045 C>T, Chr2: 42508231 G>A, and Chr2: 43644612 C>T were annotated by ASAP1, LYN and CABYR, respectively. ASAP1 and LYN have already been proven to play roles in the growth and development of other species. In addition, we genotyped every duck using the most significant SNP (Chr2: 42508231 G>A) and compared the growth rate difference among each genotype population. The results showed that the growth rates of individuals carrying the Chr2: 42508231 A allele were significantly lower than those without this allele. Moreover, the results of the Mendelian randomization (MR) analysis supported the idea that the growth rate and birth weight had a causal effect on the adult body weight, with the growth rate having a greater effect size.

Conclusion: In this study, 41 SNPs significantly related to growth rate were identified. In addition, we considered that the ASAP1 and LYN genes are essential candidate genes affecting the duck growth rate. The growth rate also showed the potential to be used as a reliable predictor of adult weight, providing a theoretical reference for preselection.

Keywords: Duck; GWAS; Growth rate.

MeSH terms

Adult
Animals
Body Weight / genetics
Ducks* / genetics
Genome-Wide Association Study*
Genotype
Humans
Polymorphism, Single Nucleotide
Quantitative Trait Loci