Integrated genomic and transcriptomic analysis reveals candidate genes associated with reproductive performance in Hetian Black chickens.

Hetian black chicken is an indigenous breed endemic to Xinjiang, China, known for its remarkable adaptability to harsh desert environments. Age at first egg (AFE) and egg number at 300 days of age (EN300) are important reproductive traits, yet their molecular genetic basis remains unclear. Here, we combined whole-genome resequencing (64 hens) and transcriptome sequencing (ovary and uterus from 13 hens) to identify candidate genes and SNPs associated with AFE and EN300. Using FST, Pi, and XP-CLR methods, we identified 7 overlapping candidate genes for AFE (core genes: ATAD5/CRLF3 on chr18, AGTR1 on chr9) and 20 overlapping candidate genes for EN300 (core genes: NRXN3 on chr5, AHR2/NDUFA10 on chr7, and PRSS2/PRSS3/PDE3A on chr1). AFE-associated core genes were significantly enriched in Apelin, adrenergic, and calcium signaling pathways, with 8 core SNPs detected (2 novel). Transcriptomic validation confirmed ovary-specific high expression of CRLF3 and ATAD5 (P < 0.01). EN300-associated core genes were significantly enriched in neuroactive ligand-receptor interaction and Influenza A pathways, with 16 core SNPs detected (all known). NRXN3 showed stable differential expression across all tissue and group comparisons, whereas AHR2 and PRSS2 exhibited tissue-specific expression patterns. These results indicate that ATAD5/CRLF3 on chr18, AGTR1 on chr9 and their SNPs are potential markers for AFE, while NRXN3 on chr5, AHR2 on chr7, PRSS2 on chr1 and their SNPs are potential markers for EN300. This study provides a theoretical basis for marker‑assisted selection of reproductive traits in Hetian black chickens.