Genome-Wide Association Study for Small Intestine Length in Qiandongnan Xiaoxiang Chickens

Abstract Small intestine length (SIL) is closely associated with nutrient absorption efficiency in farm animals. To elucidate the genetic basis of SIL in chickens, we measured SIL in 194 Qiandongnan Xiaoxiang chickens at 70 days of age. Using whole-genome resequencing data, we performed a genome-wide association study (GWAS) to identify key genes and pathways underlying SIL variation. Our results showed that SIL exhibited moderate heritability ( h ² = 0.41). Furthermore, correlation analysis revealed a highly significant positive correlation between SIL and 70-day body weight as well as average daily gain (ADG) ( P  < 0.01). Using both FarmCPU and GLM models, GWAS detected 11 significant SNPs or InDel associated with SIL ( P  < 5×10⁻⁶). These loci, which were distributed on chromosomes 1, 4, and 8, explained 0.13%-0.14% of the phenotypic variance in SIL. Gene annotation further indicated that these loci were located within three genes: IL1RAPL1 , PBX1 , and USP35 . Collectively, this study preliminarily dissects the genetic architecture of SIL in chickens and provides valuable candidate genes for improving growth performance through targeted molecular breeding.