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Open access Aug 2026

Identification of candidate genes for reproductive traits in Chinese Holstein cattle using single-step genome-wide association study.

In dairy farming, reproductive efficiency is vital to both profitability and sustainability. However, years of selective breeding for increased milk yield have adversely affected reproductive potential. This study aimed to pinpoint genomic regions and identify potential candidate genes associated with reproductive traits in Chinese Holstein cattle. In this study, a single-step genome-wide association study (ssGWAS) was conducted using 33,202 phenotypic records from 16,379 animals, 55,244 pedigree records, and genomic data from 1,698 cows. These data were integrated into the ssGWAS analysis, resulting in a total pedigree structure of 21,635 animals. A total of 12 significant markers were identified for calving interval (IC), days open (DO), number of services per conception (NS), and conception rate (CR). Among these significant SNPs, 3 SNPs were for IC, 2 SNPs were for DO, 3 SNPs were for NS, and 4 SNPs were for CR. Several promising candidate genes located near these SNPs have been identified, including SFXN4, B3GAT2, GRK5, PRDX3, and MTHFD1L, highlighting their potential involvement in fertility-related biological processes. Furthermore, functional enrichment analysis identified significant enrichment of pathways associated with cell adhesion and embryonic development, suggesting a potential mechanistic role for DSG family members (DSG1, DSG2, DSG3, and DSG4) in fertility regulation. Collectively, our findings enhance understanding of the complex genetic basis of reproductive traits in dairy cattle and may offer a valuable set of genomic targets for precision breeding of Chinese Holsteins. Integrating these markers into genomic selection programs may contribute to genetic improvements in reproductive efficiency and support the long-term sustainability of dairy production.

W. A. Lombebo, Mingxin Du, G. M. Tarekegn et al. · 0 citations
Open access Jul 2026

Genome-wide association studies on growth performance trait of Nigerian indigenous Chicken genotypes

Meat from Nigerian indigenous chickens (NICs) has high consumer demands but slow growth rate with high variability in body weight (BW). A study was carried out at T&R farm of FUNAAB identifying chromosomes associated with body weights of NICs in a GWAS study using the chicken 60K Single Nucleotide Polymorphisms (SNPs) Panel for 53313 markers subjected to test. Body weight was taken for 8 week. Blood samples were collected from 42 purebreds and F2 upgrades of NICs to extract DNA and amplify through PCR-RFLP technique to obtain Amplicons used for sequencing. Sequenced molecular analysis involving many Molecular software packages and bioinformatics approach were were done to trim and compare the sequence. The raw phenotypic data which comprised of the sex and body weight (>2 kg as 1 (case)) and <1 kg as 0 (control)) were analyzed using Gen Abel of the R Software Package to carry out quality checks through some filtering techniques on these chickens. The results from Selective sweep analysis identified ten chromosomes and SNPs associated with BWT of the NICs F2 upgrades Nigerian Chickens resource population. However, ten chromosomes with SNPs associated with BWT at the suggestive Bonferroni significant threshold level (p < 0.05) were discovered. These findings made it clear that F2 upgrades had better trait association on chromosomes when compared to those of the Purebreds and should be included as a genetic marker in the breeding programs by breeders for genetic improvement due to the potentialities found in this NICs genotypes studied.

U. J. Ezekiel, Ekanem, Nsikan Joseph, Udo, Mfoniso Ezekiel · 0 citations
Open access Jul 2026

Association of TGFβ2 gene polymorphism with growth performance and meat quality traits in Kampung Unggul Balitbangtan chickens under multienzyme supplementation

ABSTRACT Background and Aim: Improving growth performance and meat quality is a major objective in genetic improvement programs for indigenous poultry breeds. Kampung Unggul Balitbangtan (KUB) chickens are an improved Indonesian native breed with considerable potential for sustainable tropical poultry production. Transforming growth factor-beta 2 (TGFβ2) plays an important role in regulating skeletal muscle development, cell proliferation, and tissue remodeling; however, its genetic variation and association with economically important traits in KUB chickens remain unknown. This study aimed to characterize TGFβ2 gene polymorphisms and evaluate their associations with growth performance and meat quality traits in KUB chickens receiving dietary multienzyme supplementation. Materials and Methods: Twenty-five one-day-old male KUB chickens were assigned to five dietary treatments containing different combinations of phytase and protease and reared for 90 days. Growth performance was assessed using feed intake (FI), body weight (BW), feed conversion ratio (FCR), and carcass weight (CW). Meat quality traits, including pH, texture, cooking loss (CL), water holding capacity, and color characteristics (L*, a*, and b*), were evaluated after slaughter. Genomic DNA extracted from muscle tissue was analyzed using polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing to identify TGFβ2 polymorphisms. Functional enrichment of differentially expressed genes was investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Results: Three TGFβ2 genotypes (CC, TC, and TT) were identified, with allele frequencies of 0.48 (C) and 0.52 (T). The TGFβ2 genotype was significantly associated with BW, CW, and FCR (p < 0.05), whereas FI was unaffected. Multienzyme supplementation significantly reduced CL, improved water holding capacity, and enhanced meat color characteristics without affecting pH or texture. Two exon single nucleotide polymorphisms, c.103C>T and c.99G>A, were identified, representing novel variants in KUB chickens. Functional enrichment analyses demonstrated significant involvement of extracellular matrix-receptor interaction, metabolic pathways, and biological processes related to muscle development and cell proliferation, supporting a nutrigenetic interaction between TGFβ2 polymorphism and enzyme supplementation. Conclusion: This study provides the first characterization of TGFβ2 polymorphisms in KUB chickens and demonstrates their association with growth performance and meat quality traits under multienzyme supplementation. The identified polymorphisms represent promising molecular markers for marker-assisted selection and precision nutrition strategies to improve productivity in indigenous tropical chicken populations.

S. Ayuti, M. Lamid, M. Arif et al. · 0 citations
Open access Jul 2026

Association of polymorphisms in the GHRL, GAST, and SCTR genes with feed conversion and productivity indicators of meat chickens bred at the Smena Breeding Centre

The study was conducted to identify the genotypes of single-nucleotide polymorphisms (SNPs) in the GHRL, GAST, and SCTR genes for early performance assessment in Smena 9 poultry. The study was performed on 170 CM5/CM7 roosters and 750 final-hybrid CM5679 broiler chickens with individual feed intake monitoring at ages 36-42 days and 21-42 days, respectively. Groups were formed randomly. Polymorphisms were identified using genotyping using real-time PCR with fluorescently labelled probes. CM5 roosters homozygous for the T allele and heterozygous (TC) for the rs312295326 polymorphism demonstrated improved feed conversion in the 36-42-day period. The feed conversion ratio (FCR) for this period was 1.89 for birds with the TT genotype and 1.91 for TC. The CC genotype was associated with a 7.3-8.5% decrease in FCR (p<0.05). Statistically significant differences in feed conversion efficiency (FCR) were observed in broilers with polymorphic variants of the SCTR gene (rs314830059 and rs736374789). In birds of both sexes with the GG genotype of the rs314830059 polymorphic variant, a decrease in FCR by 8.6-16.9% was observed compared to the GT and TT genotypes from the 24th to the 33rd day (p<0.05). Females with the GG genotype of the rs736374789 polymorphism showed a lower FCR (2.18 to 2.48) compared to individuals with the GT genotype (2.41 to 2.89) on days 39, 40, and 42 (p < 0.05). The identified SNPs in the GHRL (rs312295326), SCTR (rs314830059), and SCTR (rs736374789) genes can be integrated into genomic selection programmes aimed at reducing FCR in meat-producing chickens.

L. G. Korshunova, E. I. Kulikov, D. M. Dmitrenko et al. · 0 citations
Open access Aug 2026

Bayesian Genome-Wide Association Study of Feed Efficiency Traits in Pigs

Feed efficiency traits are increasingly important in pig production for improving profitability and environmental sustainability. Understanding their genetic basis is crucial for uncovering underlying biological mechanisms and informing selection strategies. In this study, we analyzed residual feed intake (RFI), feed conversion ratio (FCR), and average daily feed intake (ADFI) in 201 animals. Three separate Bayesian GWASs were conducted using 29,844 SNPs in a case–control design, with the lowest and highest 15% of the phenotypic distribution selected as controls and cases (N = 30 per group), respectively, for each trait. The results confirmed the polygenic nature of the traits, identifying 4 SNPs for RFI on Sus scrofa chromosomes (SSC) 3, 13, and 15 with high posterior probability for the direction of their effects; 4 SNPs for FCR on SSC 8, 14, and 17; and 8 SNPs for ADFI on SSC 1, 2, 6, 8, and 11. A candidate gene search identified 41 potential genes involved in diverse biological processes, including feed efficiency, intestinal development, tissue remodeling and integrity, nutrient transport and absorption, metabolic homeostasis, cellular signaling, energy sensing, and neurological regulation. These genes formed a highly interconnected network, highlighting the complexity of feed efficiency and the interplay among multiple physiological, metabolic, and regulatory pathways.

S. Faggion, V. Bonfatti, A. Bergamasco et al. · 0 citations
Open access 2026

Characterization of IGF1 gene marker as potential genes in improving growth performance of Indonesian goats

Background: Goat farming development begins with the availability of genetically and phenotypically superior livestock to ensure optimal productivity and reproduction. Aim: This study aimed to identify polymorphisms in the IGF1 gene and to evaluate their association with growth performance. Methods: A total of 105 goats were sampled, including 35 individuals from each of three Indonesian goat breeds: Peranakan Etawah (PE), Jawarandu, and Kacang, aged between 12 and 24 months. Growth parameters measured included body weight and morphometric characteristics. Genetic variation of the IGF1 gene was analyzed using Sanger sequencing. Morphometric data were analyzed using principal component analysis (PCA) in R software to explore variation patterns, while associations between IGF1 gene polymorphisms and growth traits were evaluated using analysis of variance (ANOVA). Results: Sequence analysis revealed significant nucleotide variations at certain positions, indicated by overlapping guanine (G) and thymine (T) chromatogram peaks, indicating a heterozygous genotype (G/T) at this locus. The IGF1 gene has diverse genotypes in all goat breeds, namely GG, GT, and TT. All genotypes were present except in the JW breed, where the TT genotype was absent. IGF1 gene diversity was significantly associated (P<0.05) with morphometric characteristics, including muzzle circumference, head length, ear length, ear width, rump length, and leg circumferenc. The GT genotype had the highest morphometric performance compared to the other genotypes. Conclusion: The IGF1 gene may serve as a potential candidate marker for marker-assisted selection (MAS) to improve the growth performance of Indonesian goats, although further validation is required.

Depison Depison, R. Harahap, Gushairiyanto Gushairiyanto et al. · 0 citations