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

Abstract

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

“…Similarly, IGF2BP1 was shown to affect body size in ducks [ 19 ]. In this study, the candidate region was located in the promoter and up-stream region of IGF2BP1 , which is consistent with the previous report [ 20 ]. Further, GIP is important to bone size and growth traits in chicken [ 13 , 50 ], but zero expression was detected in muscle.…”

“…We found that only the mRNA level of IGF2BP1 was negatively related to BrW. Wang et al reported higher transcription level of IGF2BP1 was detected in Ross compared with that in Gushi chickens [ 20 ]. This indicates that body size and muscle development are likely regulated in a positive manner by IGF2BP1 .…”

“…By annotation, IGF2BP1 , GIP , SNF8 , UBE2Z , ATP5MC1 , CALCOCO2 , HOXB gene family members, and two microRNAs were found in the region. Wang et al have reported that IGF2BP1 affected chicken body size (e.g., claw weight, shank length, and carcass weight), and a deletion mutation in the promoter region has been validated as a causal variant [ 20 ]. Similarly, IGF2BP1 was shown to affect body size in ducks [ 19 ].…”

“…However, the IGF2BP1 gene has been studied widely in muscle development and lipid metabolism in animals [ 17 , 18 ]. Zhou et al and Wang et al demonstrated that IGF2BP1 had a predominant role in body size as judged by GWAS and quantitative trait locus (QTL) mapping in duck and chicken, respectively [ 19 , 20 ]. In chicken advanced intercross line, an interval of chromosome 27 was recognized as a candidate genomic region (containing IGF2BP1 , GIP , and other genes) that affected growth traits [ 13 ].…”

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome

“…The deletion of IGF2BP1 in intestinal epithelial cells was shown to compromise barrier function and ameliorate experimental colitis in mice, thus suggesting a role for IGF2BP1 in maintaining intestinal homeostasis ( 56 , 57 ). More recently, Wang et al confirmed the association of IGF2BP1 with chicken body weight by large-scale genomic screening and functional studies ( 58 ). However, the way IGF2BP1 affects the weight of the host is still poorly understood.…”