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18 pages, 4265 KB

Open AccessArticle

Multi-Omics Revealed Breed Dominates over Plumage Color in Regulating Pigeon Meat Quality and Flavor

by Yuanxin Guan, Fei Ye, Xiaofei Xu, Jixiang Wei, Shen Liu, Miaomiao Yang, Jing Wang, Zhengsheng Li and Hai Xiang

Animals 2026, 16(7), 1047; https://doi.org/10.3390/ani16071047 - 30 Mar 2026

Viewed by 459

Abstract

Both breed and plumage color are considered potential genetic factors influencing meat quality in pigeons, yet their independent effects remain poorly distinguished. This study aimed to disentangle the regulatory roles of breed and plumage color on meat quality, nutritional composition, and flavor-related metabolites [...] Read more.

Both breed and plumage color are considered potential genetic factors influencing meat quality in pigeons, yet their independent effects remain poorly distinguished. This study aimed to disentangle the regulatory roles of breed and plumage color on meat quality, nutritional composition, and flavor-related metabolites in meat pigeons. White-feathered (SQB) and grey-feathered (SQH) Shiqi pigeons were compared with European Mimas white pigeons (MMS) under identical rearing conditions. Slaughter performance, meat quality traits, and flavor profiles were assessed, followed by untargeted metabolomics and transcriptomics sequencing of pectoral muscle tissues. The results demonstrated that breed exerted a significant influence on carcass traits, water-holding capacity, collagen content, as well as the composition of fatty acids and free amino acids. In contrast, no notable disparity in meat quality was observed between the white- and gray-feathered varieties within the same Shiqi pigeon breed. A total of 114 and 205 differentially expressed metabolites (DEMs), and 11 and 327 differentially expressed genes (DEGs) were identified in plumage color and breed comparisons, respectively. Key flavor-associated metabolites, including glutathione, L-histidine, L-carnosine, and cytidine-5′-monophosphate, were identified as candidate biomarkers for breed-specific flavor differentiation. Breed is the dominant genetic factor determining meat quality and flavor in meat pigeons, while plumage color variation within breed has a limited impact. The identified pathways and regulatory networks provide actionable targets for the precision breeding and flavor enhancement of local pigeon breeds. Full article

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

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11 pages, 753 KB

Open AccessArticle

Occurrence and Genetic Parameters Estimation of Blood and Meat Spots in Brown-Shelled Eggs During the Extended Laying Period

by Honglei Jin, Bingxin Luo, Lin Xuan, Runzhe Wang, Jiahui Lai, Guiyun Xu and Jiangxia Zheng

Animals 2026, 16(3), 404; https://doi.org/10.3390/ani16030404 - 28 Jan 2026

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Abstract

Blood and meat spots are key internal egg quality indicators, and clarifying their genetic characteristics in late laying periods is critical for quality improvement via selective breeding. This study collected 392 eggs from 421 96-week-old Rhode Island Red hens across 69 families, analyzing [...] Read more.

Blood and meat spots are key internal egg quality indicators, and clarifying their genetic characteristics in late laying periods is critical for quality improvement via selective breeding. This study collected 392 eggs from 421 96-week-old Rhode Island Red hens across 69 families, analyzing 10 traits including blood/meat spots and standard egg quality traits. Heritability, genetic and phenotypic correlations were estimated using the DMU package. The incidences of blood and meat spots were 15.8% and 64.8%, respectively. Blood spots were yolk-localized, single and <1 mm in diameter, while meat spots mostly occurred on chalazae (83.5%) and thick albumen (33.1%), mostly multiple (56.1% with 2–5 spots) and 1.80 ± 1.53 mm in diameter (30% >2 mm). Blood spots had low heritability (0.05), meat spots moderate heritability (0.20). The two traits showed high positive genetic correlation (r_G = 0.93), and strong negative genetic correlations with albumen height and eggshell strength. In conclusion, blood and meat spots in late-laying hens differ in distribution, size and number, and meat spots are amenable to genetic selection for internal egg quality enhancement. Full article

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

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20 pages, 4455 KB

Open AccessArticle

A Comparative Analysis of Transcriptome-Wide Differential Gene Expression and Alternative Polyadenylation in the Ovaries of Meat Ducks and Laying Ducks

by Sike Wang, Yaomei Wang, Shiwei Li, Chao Jia, Debing Yu and Weiling Huang

Animals 2026, 16(2), 313; https://doi.org/10.3390/ani16020313 - 20 Jan 2026

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Abstract

Significant differences in reproductive performance exist between meat-type ducks (e.g., Qiangying Duck, QD) and laying-type ducks (e.g., Shaoxing Duck, SD). The molecular mechanisms underlying these differences, particularly concerning ovarian development and function, remain incompletely understood. This study aimed to comprehensively characterize the ovarian [...] Read more.

Significant differences in reproductive performance exist between meat-type ducks (e.g., Qiangying Duck, QD) and laying-type ducks (e.g., Shaoxing Duck, SD). The molecular mechanisms underlying these differences, particularly concerning ovarian development and function, remain incompletely understood. This study aimed to comprehensively characterize the ovarian transcriptomes of these two duck types, focusing on differential gene expression and post-transcriptional regulatory events. We performed an integrated full-length transcriptome analysis of ovarian tissues from these two breeds using PacBio SMRT and Illumina sequencing. Bioinformatic analyses, including functional annotation, differential expression analysis, and the identification of APA events, were used. We discovered substantial breed-specific differences in alternative polyadenylation (APA), with SD ducks exhibiting significant 3′UTR shortening in 3799 genes and 3′UTR lengthening in 1626 genes compared to QD. The integrated analysis of differential gene expression and APA events highlighted key genes related to steroid hormone synthesis (HMGCS1, DHCR24), lipid metabolism (SCD), signal transduction (HRAS), and antioxidant defense (SOD1). The functional enrichment implicated critical pathways such as mitochondrial energy metabolism, oxidative phosphorylation, and fatty acid degradation. Our study provides a comprehensive atlas of post-transcriptional regulation in the duck ovary and reveals APA as a crucial process of gene regulation. APA may contribute to the differential ovarian function and egg-laying capacity between meat and laying ducks, thus offering valuable targets for genetic selection. Full article

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

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17 pages, 4500 KB

Open AccessArticle

Molecular Characterization and Functional Insights into Goose IGF2BP2 During Skeletal Muscle Development

by Cui Wang, Yi Liu, Jiuli Dai, Shufang Chen and Daqian He

Animals 2026, 16(1), 58; https://doi.org/10.3390/ani16010058 - 24 Dec 2025

Cited by 1 | Viewed by 654

Abstract

Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is an RNA-binding protein known to play critical roles in metabolism, cell proliferation, and tumorigenesis. Although its involvement in muscle development has been documented in several species, the function of goose IGF2BP2 remains largely unexplored. [...] Read more.

Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is an RNA-binding protein known to play critical roles in metabolism, cell proliferation, and tumorigenesis. Although its involvement in muscle development has been documented in several species, the function of goose IGF2BP2 remains largely unexplored. In this study, we cloned and characterized the full-length cDNA and genomic DNA sequences of goose IGF2BP2. The cDNA is 2957 bp in length and contains a 1662 bp open reading frame encoding a 553-amino acid protein with five conserved RNA-binding domains. The genomic sequence spans 12,183 bp and consists of 12 exons and 11 introns. A total of 60 genetic variants were identified, including a deletion of a G base at position 2299 (g.2299delG) that results in a frameshift mutation. Expression analysis revealed high levels of IGF2BP2 mRNA in the liver, heart, and muscle tissues of female geese across embryonic (E25d), growing (A70d), and laying (L270d) stages, consistent with a potential role in muscle development (p < 0.05). Functionally, overexpression of IGF2BP2 in skeletal muscle satellite cells (SMSCs) was associated with significant changes in the expression of several genes linked to muscle development and signaling pathways, including upregulation of IGF1, EGFR, FGF19, BMP6, BMP2, ACVR1C and WNT5A and downregulation of MYBPC3, NODAL, HOXD13, TNXB, and ADD2 (Padj < 0.01). Furthermore, protein–protein interaction (PPI) network analysis of these genes suggests that IGF2BP2 may coordinate key genes, contributing to its potential role in skeletal muscle development in geese. Full article

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

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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

Cited by 1 | Viewed by 968

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 [...] Read more.

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

Cited by 2 | Viewed by 1097

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 [...] Read more.

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 1689

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 [...] Read more.

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

Cited by 1 | Viewed by 1845

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 [...] Read more.

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 3 | Viewed by 1733

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 [...] Read more.

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 1595

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 [...] Read more.

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 3 | Viewed by 1586

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 [...] Read more.

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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Review

Jump to: Research

15 pages, 855 KB

Open AccessReview

An Integrative Genetic Strategy for Identifying Causal Genes at Quantitative Trait Loci in Chickens

by Akira Ishikawa

Animals 2026, 16(2), 155; https://doi.org/10.3390/ani16020155 - 6 Jan 2026

Viewed by 650

Abstract

Background: Identifying causal genes underlying quantitative trait loci (QTLs) remains challenging due to small effect sizes and the prevalence of non-coding variants. Although multi-omics integration frameworks such as eQTL- and epigenomic-based approaches and TWAS have advanced gene prioritization, their application in poultry and [...] Read more.

Background: Identifying causal genes underlying quantitative trait loci (QTLs) remains challenging due to small effect sizes and the prevalence of non-coding variants. Although multi-omics integration frameworks such as eQTL- and epigenomic-based approaches and TWAS have advanced gene prioritization, their application in poultry and livestock is often constrained by limited reference panels and tissue resources. This review introduces a cost-effective F₂-based integrative framework and compares it with existing multi-omics strategies. Methods: The proposed framework combines QTL remapping, transcriptome analysis, haplotype frequency comparison, association analysis, and conditional correlation analysis within a single workflow. Causal analysis and quantitative complementation tests using knockout birds are incorporated to identify causal genes. Results: By reusing the original F₂ population employed for QTL mapping, this approach enables hypothesis-independent gene prioritization without requiring additional fine-mapping crosses. Its effectiveness is demonstrated through comparison with conventional multi-omics methods, and the integration of causal analysis and quantitative complementation testing provides robust genetic evidence for pinpointing causal genes. Conclusions: This F₂-based framework efficiently prioritizes and verifies causal gene candidates directly within the mapping population, offering a cost-effective alternative to multi-omics approaches that require large-scale resources. It is broadly applicable to diverse chicken crosses and readily transferable to other small livestock species and model organisms. Full article

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

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