Genetic basis and cecal microbiome markers associated with small intestine length in Qiandongnan Xiaoxiang chickens.
4 affiliations
- 1Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou Province, 550025, China.
- 2College of Animal Sciences, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, Guizhou Province, 550025, China.
- 3Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou Province, 550025, China. [email protected].
- 4College of Animal Sciences, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, Guizhou Province, 550025, China. [email protected].
Abstract
Background
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.Results
Our results indicated that SIL had a moderate heritability (h² = 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.Conclusions
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.
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BibTeX
@article{xiong2026genetic,
title = {{Genetic basis and cecal microbiome markers associated with small intestine length in Qiandongnan Xiaoxiang chickens.}},
author = {Tao Xiong and Xiaoling Yang and Haiqun Meng and Hongfa Zhang and Yongxian Yang and Xiongxia Long and Liqi Wang and Zhong Wang},
journal = {BMC genomics},
year = {2026},
month = aug,
doi = {10.1186/s12864-026-13263-z},
url = {https://europepmc.org/article/MED/42972239},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genetic basis and cecal microbiome markers associated with small intestine length in Qiandongnan Xiaoxiang chickens.
AU - Tao Xiong
AU - Xiaoling Yang
AU - Haiqun Meng
AU - Hongfa Zhang
AU - Yongxian Yang
AU - Xiongxia Long
AU - Liqi Wang
AU - Zhong Wang
PY - 2026
DA - 2026/08/06
JO - BMC genomics
DO - 10.1186/s12864-026-13263-z
UR - https://europepmc.org/article/MED/42972239
AB - Background 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.Results Our results indicated that SIL had a moderate heritability (h² = 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.Conclusions 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.
SN - 1471-2164
ER -