The Baicheng-You chicken is an indigenous Chinese breed known for its superior egg quality and stress resistance, yet the genetic basis of these traits is not fully understood. This study investigated the genomic architecture of 10 egg quality traits in 1 002 Baicheng-You chickens using whole-genome resequencing. The estimated genomic heritabilities for these traits ranged from 0.30 to 0.83. Genome-wide association studies identified 30 single nucleotide polymorphisms reaching genome-wide significant or suggestive association thresholds, which were mapped to 386 candidate genes, including ALAS1, LCORL, and CTNNBL1. Functional enrichment analysis indicated these genes are primarily involved in developmental patterning and embryonic skeletal system morphogenesis. To prioritise candidate variants, statistical fine-mapping using the Sum of Single Effects method (SuSiE) was integrated with epigenomic data (H3K27ac and ATAC-seq). Furthermore, the activity-by-contact model prioritised putative regulatory variants within enhancer regions on chromosomes 20 and 6 that may contribute to the regulation of eggshell colour and thickness, respectively. These findings improve our understanding of the molecular mechanisms regulating egg quality and provide potential genetic markers for breeding programmes in indigenous poultry.
Eggshell color is an important economic trait in poultry. In green-eggshell chickens, eggshell color intensity is primarily determined by the amount of biliverdin deposited in the shell, but its genetic basis remains unclear. In this study, 230 Dongxiang green-eggshell chickens at 29 weeks of age were genotyped for the green-shell locus. Homozygous green-shell individuals were identified and subjected to a genome-wide association study (GWAS) using eggshell biliverdin concentration as the phenotype. The results showed that all 230 individuals were homozygous for the green-shell genotype, and eggshell biliverdin concentration was approximately normally distributed in the population. GWAS identified seven SNPs that exceeded the genome-wide significance threshold within a 110-kb region (3035804-3143838 bp) on chromosome 12. Functional annotation of the significant loci identified ALAS1 as a candidate gene. ALAS1 encodes the rate-limiting enzyme in heme biosynthesis and is therefore biologically linked to biliverdin production. Haplotype analysis further revealed a strong linkage block encompassing the ALAS1 region, supporting its potential role in regulating green eggshell color intensity. These findings provide candidate genetic markers for improving green eggshell color intensity in breeding programs.
1. Egg production is a primary economic driver in the poultry industry, determining the total yield of commercial layers. However, the complex polygenic mechanism remains largely elusive. This study investigated the phase-specific genetic mechanisms of egg production using a high-precision genomic approach.2. A genome-wide association study (GWAS) was conducted on a layer population (n = 3,587). Egg numbers were recorded across four distinct production phases: onset to 300 days, 301 to 560 days, 561 to 651 days and the cumulative onset to 651 days period. Following whole-genome SNP genotyping, GWAS signals were integrated with functional enrichment analyses to prioritise key loci and candidate genes associated with egg‑number traits.3. A total of 425 significant SNP were identified across the evaluated phases. Functional annotation revealed significant enrichment in 47 GO terms and four KEGG pathways, primarily involved in cell cycle regulation, cytoskeleton assembly and reproductive development. MAP2K3, TRIM37 and ACTR3were highlighted as compelling candidate genes. Potential genetic markers were identified, including rs14072717 within MAP2K3, a cluster of nine SNP within the ACTR3 locus and three variants within TRIM37.4. These findings elucidated the dynamic genetic regulation of egg production throughout the laying cycle and highlight MAP2K3, TRIM37 and ACTR3 as genomic targets. These markers provide a foundation for marker-assisted selection to enhance egg yield and production persistency in poultry.
Y. Ni, S. Huang, T. Bai et al.· British Poultry Science· 0 citations
Simple Summary Growth and body conformation traits are important determinants of meat production and economic performance in sheep. Understanding their genetic basis can enhance breeding efficiency and support sustainable genetic improvement. In this study, we conducted a genome-wide association study (GWAS) to identify genomic regions associated with seven growth and body conformation traits in 401 sheep from four populations: Qira Black, Kyrgyz, Dorset × Hu crossbred, and Suffolk × Karakul crossbred sheep. After genotype quality control, 47,674 SNP markers were analyzed using a mixed linear model accounting for population structure and genetic relatedness. A total of 44 independent genomic regions were detected at a nominal significance threshold, containing 112 candidate genes potentially involved in skeletal development, cartilage formation, muscle growth, and metabolic regulation.
Erkinbay Azbergenov, Tao Jiang, Rui-zhi Yang et al.· Animals· 0 citations
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.· Journal of Animal Science· 0 citations
Background Complex traits are influenced by numerous variants, most of which have regulatory effects on gene expression that can be mediated by DNA methylation. Molecular QTL mapping is an approach that aims to dissect these effects. However, obtaining molecular phenotypes on a large scale is challenging, particularly in livestock species. In cattle, an epigenotyping array called EpiChip has recently been developed in the European RUMIGEN project. The EpiChip, which contains 43,317 CpG sites distributed all over the bovine genome, enables large-scale measurement of DNA methylation. This study aims to characterize the genetic determinism of blood DNA methylation in cows by estimating heritability and mapping cis- and trans-methylation QTLs (meQTLs). Results Whole blood samples from 4,457 genotyped Holstein cows were epigenotyped. Across all CpG sites, the heritability estimates averaged 24.6%. The local meQTL mapping at sequence-level for variable CpG sites (SD > 2.5%; n = 28,806) detected cis-meQTLs for 80.1% of the CpG sites, with sentinel SNPs located close to their associated CpGs. A two-step analysis was also conducted to identify long-range associations, with a particular focus on trans-meQTL hotspots. First, we identified CpG-SNP trans-associations using medium-density genotypes (50k SNPs) that revealed 31,846 SNPs with significant effects on 1 to 530 trans-CpG sites. Then, regions associated with at least 34 independent trans-CpGs were retained defining 31 hotpots. For each hotspot, a local sequence-level GWAS was conducted using the first principal component derived from the associated trans-CpGs. Out of the 31 detected hotspots, three were located close to transcription factor genes (RUNX1, NFIC and FOXA3) for which the associated trans-CpGs were enriched for the corresponding binding motif. Two other hotspots were located within KDM5A and KDM5B, and their corresponding trans-CpGs were strongly overrepresented in H3K4me3 narrow peaks in blood as well as in other tissues. Conclusions By identifying functional candidate genes associated with blood DNA methylation in cattle, these findings provide new insights into the regulatory architecture of DNA methylation in mammals, highlighting the value of large-scale molecular data from livestock populations.
Corentin Fouéré, V. Costes, Florian Besnard et al.· bioRxiv· 0 citations
Objective
Litter size is a key trait for evaluating reproductive performance of goats, which can directly influence the breeding efficiency and profitability of production cycles. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, thus hindering its application in precision breed-ing.
Methods
A total of 92 female Leizhou goats were genotyped through whole-genome se-quencing (WGS), and their litter size were measured for three consecutive births. Subsequently, based on the genotype and phenotype data, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed.
Results
We identified a total of 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was detected between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. In GWAS results, we identified 63 quantitative trait loci (QTLs) for litter size at suggestive significance (P＜1×10-5). After, 207 candidate genes were annotated, and 4 of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcrip-tion factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats.
Conclusion
Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.
Da Feng, Siyi Hu, Jian Ma et al.· Animal bioscience· 0 citations