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Advances in Genetic Analysis of Important Traits in Poultry

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Poultry".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 6843

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Dr. Minli Yu

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Guest Editor

College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
Interests: poultry breeding; follicle development; skeletal muscle development; meat quality regulation; epigenetic regulation

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the latest advancements in genetic research, aiming to understand and improve important traits in poultry, including growth, reproduction, disease resistance, and product quality. With the rapid development of genomic technologies such as single-cell RNA sequencing, genome-wide association studies (GWASs), and CRISPR-based gene editing, significant progress has been made in identifying key genes, regulatory pathways, and molecular mechanisms underlying these traits. This Special Issue invites original research articles, reviews, and methodological studies that explore the genetic basis of poultry traits, the application of genomic tools in breeding programs, and the integration of multi-omics approaches to enhance poultry production and welfare. By highlighting cutting-edge research, this Special Issue aims to provide a comprehensive resource for scientists, breeders, and industry stakeholders to advance genetic improvement strategies and address challenges in sustainable poultry farming.

Dr. Minli Yu
Guest Editor

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Keywords

poultry
breeding
economic traits
genetics
multi-omics integration
reproductive performance

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Published Papers (7 papers)

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Research

13 pages, 542 KB

Open AccessArticle

Genome-Wide Association Study of Abdominal and Intramuscular Fat Deposition Traits in Huainan Yellow-Feathered Chickens

by Zichun Dai, Yaxin Li, Jie Liu, Rong Chen, Huanxi Zhu and Mingming Lei

Animals 2025, 15(22), 3342; https://doi.org/10.3390/ani15223342 - 19 Nov 2025

Viewed by 404

Abstract

The Huainan yellow-feathered chicken is a prized local breed known for its high-quality meat. However, excessive abdominal fat deposition adversely affects feed efficiency and carcass quality. This study aimed to identify genetic markers and candidate genes associated with fat traits to facilitate marker-assisted selection (MAS) using genome-wide association studies (GWAS). A total of 220 chickens were phenotyped for abdominal fat weight (AFW), abdominal fat percentage (AFP), intramuscular fat of pectoral muscle (IFPM), and intramuscular fat of leg muscle (IFLM). GWAS based on whole-genome resequencing revealed significant SNPs for AFW and AFP on chromosomes 1, 2, 7, 10, 13, and 35, annotating genes including GRIA1, CYP1A1, CYP1A2, and SCAMP2. For IFPM and IFLM, significant loci were identified on chromosomes 1, 2, 4, 5, 6, 9, 12, 23, 25, 26, and 28, highlighting genes such as LRP4, FABP3, and ADAMTS9. Functional enrichment analysis showed involvement of steroid hormone biosynthesis, retinol metabolism, and cytochrome P450 pathways in abdominal fat deposition, while Wnt and MAPK signaling pathways regulated intramuscular fat. These findings provide molecular targets for genetic selection to improve fat traits in Huainan chickens. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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26 pages, 6764 KB

Open AccessArticle

Integrative Transcriptome Analysis Across Follicles Highlights Key Regulatory Pathways in Low and High-Egg-Laying Hens

by Armughan Ahmed Wadood, Farhad Bordbar and Xiquan Zhang

Animals 2025, 15(22), 3300; https://doi.org/10.3390/ani15223300 - 15 Nov 2025

Viewed by 492

Abstract

Egg-laying performance in hens is regulated by complex molecular mechanisms within the hypothalamic–pituitary–gonadal (HPG) axis and ovarian follicles. This study employed integrative transcriptome profiling of primordial (PR), primary (PM), small white (SW), and small yellow (SY) follicles in hens with low and high egg-laying capacities to explain regulatory pathways influencing reproductive outcomes. Specific gene expression patterns were observed that correlated with follicular growth, steroidogenesis, and granulosa cell proliferation. Heatmap clustering and principal component analysis revealed transcriptional divergence between low- and high-laying hens, suggesting that coordinated changes in signaling pathways influence egg-laying performance. High-laying hens intricated an upregulation of the PI3K-AKT-FOXO3, TGF-β, and Wnt/β-catenin pathways, which facilitate early follicular development, granulosa cell proliferation, and folliculogenesis. Higher phosphorylation of AKT and reduced nuclear FOXO3 activity were associated with enhanced primordial follicle growth. Increased TGF-β signaling, as demonstrated by higher levels of SMAD2/3/4 and cell cycle regulators, promoted granulosa cell proliferation in primary follicles (PMF). In SWF, higher levels of β-catenin and its downstream genes, such as c-Myc and cyclin D1, promoted follicle development. High-laying hens revealed increased expression of FSHR, CYP19A1, 17β-HSD, CYP1A1, and CYP1B1 in SYF, signifying enhanced FSH level and steroidogenesis. Similarly, low-laying hens exhibited downregulation of key genes, suggesting reduced follicular development and hormone signaling. These findings identify key regulatory networks and molecular markers associated with reproductive performance, providing targets for genetic selection and interventions to enhance egg production while reducing the risk of hormonal overstimulation. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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20 pages, 1707 KB

Open AccessArticle

Comparative Study on Growth Performance and Meat Production Traits of Reciprocal Crosses Between Guizhou Recessive White Chickens and Qiandongnan Xiaoxiang Chickens

by Yingping Tian, Xiaoya Wang, Yong Yue, Muhammad Arif, Yaozhou Jiang, Qinsong Liu, Yun Du, Xudong Zhao and Fuping Zhang

Animals 2025, 15(22), 3262; https://doi.org/10.3390/ani15223262 - 11 Nov 2025

Viewed by 578

Abstract

Indigenous chicken breeds often exhibit desirable meat quality but slower growth. This study evaluated growth, body size, slaughter traits, meat quality, and heterosis in reciprocal crosses between Guizhou recessive white (GW) and Qiandongnan Xiaoxiang (QX) chickens. A complete diallel cross produced four populations (WW: GW♂ × GW♀; QQ: QX♂ × QX♀; QW: QX♂ × GW♀; WQ: GW♂ × QX♀). To assess growth dynamics, body weight was recorded from hatch to 18 weeks and fitted with Logistic, Gompertz, and Von Bertalanffy models. At 18 weeks, 160 birds (40 per group, equal sex ratio) were assessed for body size, carcass yield, and meat quality. The results showed clear paternal effects. For instance, WQ (GW sire) outperformed QW (QX sire): WQ roosters had higher body weight at 18 weeks (1784.1 g vs. QW, p < 0.05) and greater heterosis (12.38%, 95%CI: 9.15–15.61 vs. 2.54%, 95%CI: −0.66–5.74). WQ hens also showed stronger heterosis despite similar body weight to QW hens (8.05%, 95%CI: 5.04–11.04 vs. 4.05%, 95%CI: 0.67–7.43). Growth curves were generally best described by the Von Bertalanffy model (R² ≥ 0.998), except in QW roosters, where the Gompertz model fitted better. Hybrid progeny (WQ and QW) showed improved slaughter traits over QQ, with WQ roosters exhibiting higher heterosis rates (14.09–30.71%) than QW (1.08–21.93%). Meat tenderness was superior in QQ, while QW showed advantages over WQ in tenderness and water retention. Overall, crossbreeding enhanced growth and carcass traits, and using GW as the male parent (WQ) was most effective. These findings provide practical evidence for improving Qiandongnan Xiaoxiang chickens through crossbreeding. Moreover, the observed paternal effects on growth traits suggest the need for further investigation into underlying mechanisms such as genomic imprinting and growth-related hormonal pathways. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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13 pages, 3548 KB

Open AccessArticle

Analysis of Carcass and Meat Characteristics in Breast Muscle Between Hubbard White Broilers and Xueshan Chickens

by Fan Li, Xingyu Zhang, Jiajia Yu, Jiaxue Yuan, Yuanfeng Zhang, Huiting He, Qing Ma, Yinglin Lu, Xiaoe Xiang and Minli Yu

Animals 2025, 15(14), 2099; https://doi.org/10.3390/ani15142099 - 16 Jul 2025

Viewed by 1331

Abstract

The focus on selecting broilers for rapid growth rates and enhanced breast muscle yield has resulted in a decline in meat quality. The differences in carcass characteristics and meat quality between Hubbard white broilers (HWs, a commercial breed) and Xueshan chickens (XSs, an indigenous breed) at market age were analyzed to determine the potential mechanisms responsible for these differences. The results show that HWs exhibited significantly better carcass performance than XSs, including the larger weight of the carcass, the breast muscle, and the thigh muscle (p < 0.01). In addition, based on HE staining analysis, HWs’ breast muscles had a considerably larger average myofiber area and diameter than those of XSs (p < 0.01). Furthermore, the physical characteristics of the meat revealed that XSs had higher redness and yellowness and also higher lightness. HW meat had a higher pH and thermal loss, but a lower shear force and drip loss than XS meat (p < 0.01). The content of saturated fatty acids (SFAs) and polyunsaturated fatty acids (PUFAs) was, remarkably, lower in the breast muscles of HWs than of XSs (p < 0.01). In contrast, HWs had a larger concentration of monounsaturated fatty acids (MUFAs) than XSs (p < 0.01). Finally, the breast muscles of XSs had lower levels of mRNA expression for genes linked to lipid metabolism, such as fatty acid binding protein 4 (Fabp4) and peroxisome proliferator-activated receptor alpha (Pparα), and had higher levels of the phosphofructokinase muscle type (Pfkm) compared to HWs (p < 0.01). These results indicate that a lower carcass yield was observed in XSs compared with HWs, but that XSs showed better performance in terms of meat quality than HW. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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18 pages, 4762 KB

Open AccessArticle

Precise Editing of chNHE1 Gene via CRISPR/Cas9 Generates ALV-J-Resistant Chicken Primordial Germ Cell

by Xinyi Zhou, Ruyu Liao, Min Tan, Yu Zhang, Haiwei Wang, Keshan Zhang, Qigui Wang and Xi Lan

Animals 2025, 15(14), 2018; https://doi.org/10.3390/ani15142018 - 9 Jul 2025

Cited by 1 | Viewed by 1070

Abstract

Avian leukosis virus subgroup J (ALV-J), an α-retrovirus, mediates infection by binding to the host-specific receptor chNHE1 (chicken sodium–hydrogen exchanger type 1), leading to immunosuppression and tumorigenesis, which severely threatens the sustainable development of the poultry industry. Studies have shown that the tryptophan residue at position 38 (W38) of the chNHE1 protein is the critical site for ALV-J infection. In this study, we employed the CRISPR/Cas9 system to construct a lentiviral vector targeting the W38 site of chNHE1, transfected it into chicken primordial germ cells (PGCs), and validated its antiviral efficacy through ALV-J infection assays, successfully establishing an in vitro gene-editing system for chicken PGCs. The constructed dual lentiviral vector efficiently targeted the W38 site. PGCs isolated from 5.5- to 7-day-old chicken embryos were suitable for in vitro gene editing. Stable fluorescence expression was observed within 24–72 h post-transfection, confirming high transfection efficiency. ALV-J challenge tests demonstrated that no viral env gene expression was detected in transfected PGCs at 48 h or 72 h post-infection, while high env expression was observed in control groups. After 7 days of infection, p27 antigen ELISA tests were negative in transfected groups but positive in controls, indicating that W38-deleted PGCs exhibited strong resistance to ALV-J. This study successfully generated ALV-J-resistant gene-edited PGCs using CRISPR/Cas9 technology, providing a novel strategy for disease-resistant poultry breeding and advancing avian gene-editing applications. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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15 pages, 1622 KB

Open AccessFeature PaperArticle

Chicken Primordial Germ Cell Surface Marker

by Tamara J. Gough, Terry G. Wise, Matthew P. Bruce, Timothy J. Doran, Daniel S. Layton and Andrew G. D. Bean

Animals 2025, 15(13), 1868; https://doi.org/10.3390/ani15131868 - 24 Jun 2025

Viewed by 1135

Abstract

The creation of transgenic chickens holds significant promise for the agricultural and biotechnological sectors, offering potential improvements in disease resistance and production efficiency. The preferred method for generating gene-edited chickens involves the genetic manipulation of primordial germ cells (PGCs), making the identification and isolation of these cells a growing focus of research. PGCs are the precursors to sperm and oocytes, responsible for transmitting genetic material to the next generation. In humans, PGCs are characterized by their large size, round nuclei, and refractive lipids in the cytoplasm, and can be identified using periodic acid–Schiff (PAS) staining and the surface marker stage-specific embryonic antigen 1 (SSEA1). Similarly, chicken PGCs express SSEA1, but their most specific marker is the chicken vasa homologue (CVH), the avian equivalent of the RNA-binding factor gene vasa. However, SSEA1, along with other known surface markers, does not bind to all PGCs or lacks specificity, while CVH, although highly specific to PGCs, is intracellular and unsuitable for isolating viable cells. This study aims to develop an antibody targeting a PGC surface marker with the same specificity as CVH. Despite the importance of identifying surface markers for PGC characterization, to date, such reagents are limited. To address this, whole chicken PGCs were injected into mice, leading to the generation of a panel of monoclonal antibodies. One antibody was found to bind cultured chicken PGCs and showed reduced expression upon differentiation with retinoic acid, indicating its specificity to PGCs. Immunoprecipitation followed by mass spectrometry identified the antigen as myosin heavy chain-like (MYH9) protein. The antibody, αMYH9, was further characterized and shown to bind circulating PGCs and embryonic gonadal PGCs (Hamburger Hamilton (H-H) stage 30, embryonic day 6.5–7). Whilst our primary aim was to determine the binding to PGCs, further investigation is required to determine potential binding to somatic cells. In conclusion, this study provides the characterization of a surface marker for chicken PGCs, with significant implications for advancements in avian genetic preservation, agriculture, and biotechnology. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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13 pages, 3346 KB

Open AccessArticle

Integrative Transcriptomic and Metabolomic Analysis of Muscle and Liver Reveals Key Molecular Pathways Influencing Growth Traits in Zhedong White Geese

by Kai Shi, Xiao Zhou, Jiuli Dai, Yuefeng Gao, Linna Gao, Yangyang Shen and Shufang Chen

Animals 2025, 15(9), 1341; https://doi.org/10.3390/ani15091341 - 6 May 2025

Cited by 2 | Viewed by 1198

Abstract

Geese (Anser cygnoides) are popular worldwide with consumers for their unique meat quality, egg production, foie gras, and goose down; however, the key genes that influence geese growth remain elusive. To explore the mechanism of geese growth, a total of 500 Zhedong White geese were raised; four high-weight (HW) and four low-weight (LW) male geese were selected to collect carcass traits and for further transcriptomic and metabolomic analysis. The body weight and average daily gain of HW geese were significantly higher than those of the LW geese (p-value < 0.05), and the yields of the liver, gizzard, glandular stomach, and pancreas showed no significant difference between the HW and the LW group (p-value > 0.05). Compared with the LW geese, 19 differentially expressed genes (DEGs) (i.e., COL11A2, COL22A1, and TF) were detected in the breast muscle from the HW geese, which were involved in the PPAR signaling pathway, adipocytokine signaling pathway, fatty acid biosynthesis, and ferroptosis. A total of 59 differential accumulation metabolites (DAMs), which influence the pathways of glutathione metabolism and vitamin B6 metabolism, were detected in the breast muscle between the HW and LW geese. In the liver, 106 DEGs (i.e., THSD4, CREB3L3, and CNST) and 202 DAMs were found in the livers of the HW and LW groups, respectively. DEGs regulated the pathways of the TGF-beta signaling pathway, pyruvate metabolism, and adipocytokine signaling pathway; DAMs were involved in pyrimidine metabolism, nitrogen metabolism, and phenylalanine metabolism. Correlation analysis between the top DEGs and DAMs revealed that in the breast muscle, the expression levels of COL11A2 and COL22A1 were positively correlated with the content of S-(2-Hydroxy-3-buten-1-yl)glutathione. In the liver, the expression of THSD4 was positively correlated with the content of 2-Hydroxyhexadecanoic acid. In addition, one DEG (LOC106049048) and four DAMs (mogrol, brassidic acid, flabelline, and L-Leucyl-L-alanine) were shared in the breast muscle and liver. These important results contribute to improving the knowledge of goose growth and exploring the effective molecular markers that could be adopted for Zhedong White goose breeding. Full article

(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)

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