Jun 2026· Vietnam Journal of Agricultural Sciences· Vol 9, pp. 3044-3052· 0 citations· 32 references
Abstract
Understanding the genomic basis of indigenous livestock is essential for both conservation and sustainable improvement. Korean native chickens (KNCs), although representing a small fraction of the poultry industry in Korea, are distinguished by their unique meat quality, robustness, and adaptability. Recent genomic studies have investigated their genetic diversity, evolutionary history, and economically important traits. High-density SNP arrays and population structure analyses have clarified the distinct identity of KNC lines, while runs of homozygosity have provided insights into inbreeding, conservation progress, and functional loci. Selection signature analyses have identified candidate genes related to growth, metabolism, reproduction, and immune function, reflecting line-specific adaptation. Genome-wide association studies have further identified variants associated with taste-active compounds, fatty acid composition, and growth traits, offering a foundation for genomic selection. Moreover, research on disease-related genes, such as the major histocompatibility complex B genes, has documented substantial genetic variability in KNCs, establishing important genomic resources for subsequent studies on avian immunity and pathogen response. Together, these findings highlight KNCs as valuable reservoirs of genetic variation with implications for both conservation and breeding. More broadly, the genomic insights obtained from KNCs provide a cautious yet informative model for indigenous livestock worldwide, demonstrating how genomic tools can support sustainable breeding programs that balance biodiversity preservation with productivity.
Abstract Investigating the genetic attributes of indigenous goat breeds is crucial for their conservation and breeding. The Matou goat, a valued native breed of Southern China, is characterized by high meat quality and reproductive efficiency, representing an important genetic resource for livestock production. Its genetic basis underlying productive traits remains unclear at the whole-genome level. Therefore, this study aimed to elucidate its genomic diversity and selection signatures with whole-genome sequencing (WGS), in order to provide a basis for its future conservation and breeding. Population structure analyses, including principal component analysis, phylogenetic tree construction, and admixture analysis, revealed that the 128 sampled individuals could be divided into two subgroups. One subgroup exhibited greater genetic diversity, as reflected by higher heterozygosity and lower inbreeding coefficients, along with a higher frequency of private alleles indicative of a more closed breeding history. The slower linkage disequilibrium decay observed in this subgroup suggests it has undergone stronger selection. By integrating Fst, XP‑CLR, and XP‑EHH analyses, we identified 215 genes within 306 candidate regions under selection. Several of these genes (ARHGAP31, CHURC1, ITGA11, and GFOD1) harbor variants that overlap with QTLs and are associated with production traits in livestock. These findings provide a basis for conservation and breeding of the Matou goat.
Lei Cheng, Jie Yu, Hongbo Chen et al.· Journal of Animal Science· 0 citations
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
Mostafa Ghaderi-Zefrehei, Effat Nasre Esfahani, Hassan Amini Pozveh et al.· Frontiers in Genetics· 0 citations
Single nucleotide polymorphisms represent the most abundant form of genetic variation in plant genomes and have become fundamental markers in modern plant genetics and breeding. Increasing global demand for food, combined with the pressures of climate change, environmental stress, and declining arable land, requires accelerated crop improvement strategies that exceed the capacity of conventional breeding approaches. In this context, SNP-based genomic technologies provide high-resolution tools for analyzing genetic diversity, identifying trait-associated loci, and enhancing selection efficiency in breeding programs. This review provides a comprehensive synthesis of SNP discovery methodologies, tracing their development from early Sanger sequencing approaches to advanced next-generation sequencing technologies, including whole-genome resequencing, genotyping-by-sequencing, and high-density SNP arrays. The article further examines the diverse applications of SNP markers in plant genetics, including genetic diversity analysis, linkage mapping, genome-wide association studies, marker-assisted selection, genomic selection, and evolutionary research. Key analytical and technical challenges, particularly those related to polyploid genome complexity, large-scale genomic data processing, and accurate variant interpretation, are critically discussed. In addition, emerging developments such as graph-based pangenomes, long-read sequencing technologies, machine learning-assisted SNP prioritization, and multi-omics integration are highlighted as promising directions for future research. By integrating recent technological advances with established genomic approaches, this review emphasizes the central role of SNP-based genomics in accelerating crop improvement and enabling climate-resilient, sustainable agricultural systems that support global food security.
Yucong Geng, Muhammad Zain ul Abideen, Alishba Shaukat et al.· International Journal of Bio...· 0 citations
Simple Summary The Jining Grey goat is a Chinese indigenous goat breed valued for its gray coat, high prolificacy, and adaptation to local production systems, but its growth performance still requires genetic improvement. This study used growth records and low-depth whole-genome sequencing from 70 performance-graded goats to search for candidate genomic regions associated with growth traits. We also examined 47 seven-day-old goats from the same project to explore whether prioritized markers showed early-life trait trends. To reduce reliance on any single analysis in a small population, we combined phenotype comparisons, population-structure analysis, selective-sweep scans, genome-wide association analysis, superior-genotype screening, positional annotation, and exploratory genomic prediction. The results identified a 99-SNP candidate marker panel and showed limited physical overlap between growth-associated candidate regions and major selective-sweep regions related to breed background. However, the findings should be interpreted as preliminary because the cohort was small, sequencing depth was low, imputation was performed within the cohort, and the seven-day analysis did not provide independent validation. Overall, this study provides a conservative candidate-marker resource for future validation and for balanced improvement of growth traits while conserving key characteristics of Jining Grey goats.
Zhangmu goats and Chentang black goats are valuable local goat genetic resources in Shigatse, Xizang. Due to long-term geographic isolation and small population size, their genetic diversity and adaptive genetic basis remain poorly understood. In this study, whole-genome resequencing was performed on 30 Zhangmu goats and 30 Chentang black goats. By calculating indicators such as observed heterozygosity (HO), expected heterozygosity (HE), nucleotide diversity (π), and inbreeding coefficient (FIS), the genetic diversity of the two populations was comprehensively assessed, and their selection signatures were analyzed using both Fst and XP-CLR. The results showed that both Zhangmu goats and Chentang black goats exhibited relatively low but detectable levels of genetic diversity, with clear genetic differentiation from wild goats. Population structure analysis indicated that the two indigenous populations possessed relatively independent genetic backgrounds. Combined Fst and XP-CLR analyses identified multiple candidate genes associated with hypoxia adaptation (ARNT), immune response (CD274, PTPN7), growth and development (FGF5, MYOM3), and reproductive regulation (GDF5, MEIOB). Functional enrichment analysis revealed that these candidate genes were mainly enriched in GO terms such as nucleoplasm, and in pathways such as the calcium signaling pathway and propanoate metabolism. These results provide genomic insights into the genetic characteristics of Zhangmu goats and Chentang black goats, and offer a theoretical basis for the conservation and sustainable utilization of indigenous goat genetic resources in Xizang.
Tingxiang Chen, Ting Wang, Wenrui Ye et al.· Animal Genetics· 0 citations