Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Abstract

Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

“…Besides, a female phenotype variation of 8.2% for DPW and 6.2% for SL12 was explained by L1. These associations are also consistent with the chicken and duck SNP-based GWAS results, which indicated that SNPs located near IGF2BP1 were associated with body weight, head weight, gizzard weight, chest width, leg weight, and wing weight ( Ma et al 2019 ; Zhou et al 2018 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). Unexpectedly, L2 allele was not found in the F2 population.…”

“…Since IGF2BP1 was also reported as the body size candidate gene using SNP-based studies ( Sheng et al 2013 ; Ma et al 2019 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ), we explored the SNPs within the region from 10 kb upstream of L1 deletion and 10 kb downstream in order to test whether any of the signal driving SNPs in previous studies could be the causal. SNP calling was done using the same 664 individual sequencing data for building the pan-genome; however, 210 individuals were excluded for the low quality of SNP calling or their heterozygous genotype.…”

“…Many QTGs or QTLs associated with chicken growth traits have been identified, of which loci located at chromosomes 27, 4, and 1 have the largest impact on growth in chicken ( Sheng et al 2013 ; Ma et al 2019 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). To our knowledge, the study in 2003 was the first time to report that a large QTL region located between 4.0 and 6.1 Mb in chromosome 27 was associated with chicken body size ( Kerje et al 2003 ).…”

“…Dwarfism and impaired gut development were also observed in IGF2BP1-deficient mice ( Hansen et al 2004 ). Evidence from genome-wide association studies (GWASs) and QTL mapping revealed that the genomic regions upstream of IGF2BP1 were significantly associated with body weight, head weight, gizzard weight, chest width, leg weight, and wing weight in chicken and duck ( Sheng et al 2013 ; Ma et al 2019 ; Zhou et al 2018 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). However, the causal variations of IGF2BP1 that responsible for body sizes in chicken and duck remain unclear.…”

Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

“…Therefore, identification of genetic determinants that affect growth traits in commercial chickens is fundamental to their industrial breeding. Growth traits are quantitative characteristics that are affected by various genes; therefore, it is hard to make rapid and efficient improvements using conventional selection methods [2].…”