Integrative single-cell and multi-omic analysis resolves granulosa-cell programs during chicken follicle selection.

Ming Qu, Ji Cao, Xingjie He, Haiping Liang, Qing Wei, Jianzhen Huang, Yong Cui

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Article in Poultry science, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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7 authors.

Ming QuCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Ji CaoCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Xingjie HeCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Haiping LiangCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Qing WeiCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Jianzhen HuangCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Yong CuiCollege of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China. Electronic address: cuiyong@jxau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Follicle selection sustains the hierarchical ovulatory cycle in laying hens, yet granulosa-cell (GC) programs have not been integrated across transcriptomic, regulatory and trait-genetic datasets. We integrated GC single-cell RNA-seq with independent bulk transcriptomes, ATAC-seq, Hi-C and ChickenGTEx GWAS/eQTL resources. Integration of 62,997 cells resolved 18 fine states organized into eight major state groups and four broader programs spanning early/proliferative, pre-hierarchical/pre-selection, hierarchical/selected steroidogenic and post-ovulatory/remodeling states. Dataset-restricted analyses supported recovery of this shared state organization across sources. Slingshot ordered early/proliferative and pre-hierarchical states toward selected steroidogenic states, with early/pre-selection markers declining or peaking before steroidogenic markers increased. Across 36 independent bulk libraries, early/proliferative and DNA-replication programs were consistently depleted in large yellow follicles, whereas selected steroidogenic programs increased. Promoter accessibility and Hi-C compartment patterns provided stage-variable regulatory context. Rule-based multi-layer scoring prioritized LHCGR, AMH and CYP11A1 as Tier 1 candidates. Tier 1 and Tier 2 gene sets showed stronger local ChickenGTEx GWAS signals than matched random windows. Individual candidate-window signals remained below genome-wide and chromosome-wide significance thresholds. These results establish a cross-resource GC state framework for chicken follicle selection and nominate a focused candidate set for population-specific functional validation.

Indexed as

ChickenEgg-laying traitFollicle selectionGranulosa cellSingle-cell RNA-seq

Identifiers

PMID42767189

DOI10.1016/j.psj.2026.107771

PMCPMC13631913

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.