Genetic basis and cecal microbiome markers associated with small intestine length in Qiandongnan Xiaoxiang chickens

Small intestine length (SIL) is tightly correlated with nutrient utilization efficiency in livestock and poultry. As a vital indigenous chicken genetic resource in China, Qiandongnan Xiaoxiang chicken exhibits unique growth and intestinal physiological characteristics. To dissect the genetic and microbial regulatory mechanisms of SIL variation and provide universal theoretical references for chicken growth improvement, we measured SIL phenotypes from 194 seventy-day-old Qiandongnan Xiaoxiang chickens to dissect the genetic and microbial foundations of SIL variation. With whole-genome resequencing and cecal microbiota datasets, we implemented GWAS and microbial association analysis to excavate core host genes and intestinal microbial markers regulating SIL phenotypes. Our results indicated that SIL had a moderate heritability ( h ² = 0.41). Correlation analysis showed that SIL was significantly and positively correlated with 70-day body weight and average daily gain (ADG) ( P < 0.01). Based on both FarmCPU and GLM models, a total of 11 suggestive SNPs and InDels were identified to be significantly associated with SIL ( P < 1 × 10⁻⁶). These loci were located on chromosomes 1, 4, and 8, each explaining 0.13%-0.14% of the phenotypic variance in SIL. Gene annotation successfully annotated these variants to three candidate genes: IL1RAPL1 , PBX1 , and USP35 . Furthermore, sixteen gut microbial ASVs were strongly associated with SIL, among which the genus Parasutterella showed significant correlations with intestinal length. When SIL-related microbial and metabolite abundances were treated as phenotypic traits for GWAS analysis, no host genomic loci reached the genome-wide suggestive significance threshold, indicating that host genetics may not regulate SIL through gut microbiota or serum metabolites. We preliminarily uncovered the genetic and gut microbial determinants underlying small intestine length of Qiandongnan Xiaoxiang chickens. The identified key genes and microbial biomarkers not only clarify the regulatory mechanism of intestinal development in local chicken breeds but also provide valuable candidate targets and theoretical support for molecular breeding and growth performance improvement in commercial chickens. Considering the limitation of the present sample quantity, larger experimental cohorts should be used in follow-up validation tests to verify the general applicability of the findings.