Genome-wide association analyses reveal genomics basis for frizzled feather and candidate genes associated with growth traits in Yuexi frizzled feather chicken

Background Yuexi Frizzled Feather Chicken (YFC), an indigenous chicken breed in Western Guangdong of China (Yuexi region), is well known for its great adaptability and excellent tolerance to the high temperature and high humidity climates due to its frizzled feather characteristics. In order to investigate the genomic structure and genetic markers of frizzled feather in YFC, we conducted a genome wide analysis study (GWAS) for feather types using the whole genome resequencing data from 356 YFC and 85 non-frizzled feather chickens. Results Selective sweep analyses using Fst, ROD, and XPCLR were performed and a total of 267 overlapping genes were identified. Overlapping genes were subjected to GO and KEGG enrichment analysis, indicating that keratin filament, positive regulation of collateral sprouting, and positive regulation of protein kinase B signaling might be related to the frizzled feather formation. Further investigation by GWAS identified KRT5 and KRT3 as important linked genes, with sanger sequencing revealing one SNP and one InDel in KRT5 , as well as one SNP in KRT3 could be used as markers for frizzled feather characteristics. Although supplementary experiments targeting the 15‑bp deletion in KRT75L4 revealed that KRT5 and KRT3 are not the true causal genes but are merely in linkage disequilibrium with the causal variant, these association signals still provide valuable clues for the genetic dissection of the frizzle feather phenotype in this breed. Given genome-wide studies on body weight and body size traits of the YFC breed are limited, GWAS was also conducted on YFC for growth traits. The results demonstrated several genes associated with growth traits of YFC, including body weight ( ERC1 , RAD52 , ATP8A2 , PPARGC1A ), keel length ( RFX4 , TMPRSS15 , INPP4B , LUZP2 , CCNJL , IGF1 ), body slope length ( RBFOX1 ), tibia length ( IGF2BP1 ), tibia circumference ( SCRN1 , ERO1B , RAB4A , MAPK10 ), chest width ( MID1 , GRID1 , ARHGAP6 , FRMPD4 ), and chest depth ( LOC121109148 ). Conclusion Our studies not only provide new insights into the haplotype background and genetic variation landscape of the frizzled feather trait, but also identify several genes associated with growth traits that might contribute to genetic improvement of chickens.