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Agriculture
Special Issues
Genetic Resource Evaluation and Germplasm Innovation of Poultry
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Genetic Resource Evaluation and Germplasm Innovation of Poultry

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Farm Animal Production".

Deadline for manuscript submissions: 20 December 2025 | Viewed by 1911

Special Issue Editors

Prof. Dr. Zhonghua Ning

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Guest Editor
National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Interests: hen breeding; genetic mechanism analysis; disease resistance breeding; feather color; healthy farming
Prof. Dr. Dehe Wang

E-Mail Website
Guest Editor
College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China
Interests: quantitative genetics; genomics; molecular markers; egg quality; eggshell ultrastructure; biomineralization
Dr. Long Liu

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: quantitative genetics; duck; chicken; reproductive traits; biological breeding; genome editing; fat deposition

Special Issue Information

Dear Colleagues,

Poultry species, such as chickens, ducks, geese, and turkeys, provide humans with a vital source of protein. These avian species exhibit a rich genetic and phenotypic diversity due to their large populations and high reproductive capacity. Multi-omics technologies, including genomics, transcriptomics, proteomics, and epigenetics, support the exploration of trait formation, yet there remains debate over the regulatory mechanisms of phenotypic traits.

This Special Issue focuses on the phenotypic diversity and characterization methods of poultry traits; the identification, function, and role of key candidate genes in trait regulation; the contribution of the polygene hypothesis and related models to the formation of poultry traits; and the latest advancements and discoveries in the epigenetic analysis of poultry traits. We aim to provide an overview and discussion on these topics, hoping to offer insights that will enrich and deepen our understanding of the regulatory mechanisms behind livestock phenotypic traits.

This journal particularly welcomes articles that present viewpoints and reviews, with the intention of enhancing and expanding the regulatory mechanisms of livestock phenotypic traits.

Prof. Dr. Zhonghua Ning
Prof. Dr. Dehe Wang
Dr. Long Liu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phenotypic characterization
  • polygene hypothesis
  • regulatory mechanisms
  • epigenetic

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Published Papers (2 papers)

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Research

16 pages, 1978 KB  
Article
Metabolic Basis of Breast Muscle Flavor in Houdan Chicken Crossbreeds Revealed by GC/LC-MS Metabolomics
by Yanru Lei, Chengpeng Xiao, Chenxi Zhang, Wanying Xie, Junlai Shi, Xintao Jia, Shu Wang, Yulong Ma, Zhao Cai, Donghua Li, Ruirui Jiang, Guirong Sun, Xiangtao Kang and Wenting Li
Agriculture 2025, 15(22), 2360; https://doi.org/10.3390/agriculture15222360 - 14 Nov 2025
Viewed by 447
Abstract
The quality and flavor of chicken meat are fundamentally determined by muscle metabolite composition, which reflects the regulatory effects of genetic background on metabolic pathways and muscle development. In this study, we profiled the meat quality of breast muscle across 3 crossbreeding combinations [...] Read more.
The quality and flavor of chicken meat are fundamentally determined by muscle metabolite composition, which reflects the regulatory effects of genetic background on metabolic pathways and muscle development. In this study, we profiled the meat quality of breast muscle across 3 crossbreeding combinations (D×HD, HD×D, and D×LD) between the Yunong D line and Houdan chickens to elucidate the metabolic mechanisms underlying flavor variation. Eighteen representative breast muscle samples were analyzed using common physicochemical indexes, untargeted metabolomics based on Gas Chromatography-Time-of-Flight Mass Spectrometry (GC-TOF-MS) and Ultra-High-Performance Liquid Chromatography coupled with Quadrupole Exactive Mass Spectrometry (UHPLC-QE-MS). Differential metabolites were identified through Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Multivariate analysis revealed distinct metabolic signatures among crossbreeding combinations, with HD×D exhibiting the most favorable tenderness, color, and water-holding capacity. A total of nine differential metabolites (5 upregulated and 4 downregulated) were identified between D×HD and HD×D, and thirty-eight metabolites (18 upregulated and 27 downregulated) between D×HD and D×LD. The identified metabolites were predominantly associated with amino acid metabolism, lipid biosynthesis, nucleotide turnover, and energy metabolism. Among these, arachidonic acid, taurine, L-alanine, and citric acid exhibited marked intergroup differences. Enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated significant involvement of pathways such as amino acid biosynthesis, taurine and hypotaurine metabolism, and ABC transporters in flavor formation. Hierarchical clustering and Pearson correlation analyses further delineated synergistic or antagonistic interactions among key metabolites, suggesting the existence of intricate regulatory mechanisms. These findings reveal critical metabolites and metabolic pathways associated with flavor attributes, offering both a theoretical framework and potential molecular targets for enhancing poultry meat quality through breeding strategies. Full article
(This article belongs to the Special Issue Genetic Resource Evaluation and Germplasm Innovation of Poultry)
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24 pages, 4611 KB  
Article
Combined Genomic and Transcriptomic Screening of Candidate Genes for Asymmetric Oviduct Development in Hens
by Ruijie Li, Xiang Song, Xiao Lin, Mingli Deng, Yin Liu, Tuoyu Geng, Daoqing Gong, Minmeng Zhao and Long Liu
Agriculture 2025, 15(12), 1245; https://doi.org/10.3390/agriculture15121245 - 7 Jun 2025
Cited by 1 | Viewed by 1067
Abstract
Background: While the mechanism of asymmetric gonadal development is generally understood, the mechanism of asymmetric oviduct development remains unclear. Methods: Right and left oviducts were collected from chick embryos at three developmental stages (Embryonic day 7.5, E9.5, and E11.5) for RNA-seq analysis (RNA-seq). [...] Read more.
Background: While the mechanism of asymmetric gonadal development is generally understood, the mechanism of asymmetric oviduct development remains unclear. Methods: Right and left oviducts were collected from chick embryos at three developmental stages (Embryonic day 7.5, E9.5, and E11.5) for RNA-seq analysis (RNA-seq). Whole-genome resequencing (WGRS) was performed on hens with bilateral reproductive systems (a rare natural occurrence) and unilateral controls. These data were co-analyzed with public RNA-seq data of female embryonic gonads at different developmental stages (E4.5, E5.5, and E6.5) to screen for candidate genes affecting oviduct degeneration/development. Results: RNA-seq analyses showed that a total of 27, 10, and 38 DEGs were identified between the left and right oviducts at E7.5, E9.5, and E11.5, respectively. WGRS analyses revealed 1045 differentially mutated genes (DMGs) between bilateral (D) and unilateral (S) groups. Preliminary validation highlighted BMP7, PAK3, SLC6A11, PITX2, and SMC1B as candidate genes influencing oviduct asymmetry. Conclusions: This study provides insights into the genetic basis of asymmetric oviduct development and lays the groundwork for breeding hens with bilateral reproductive systems. Full article
(This article belongs to the Special Issue Genetic Resource Evaluation and Germplasm Innovation of Poultry)
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