Simple Summary Sheep play an important role in food production and rural livelihoods, especially in regions where locally adapted breeds have developed unique traits. Two key characteristics that influence sheep productivity are the number of lambs born per ewe (prolificacy) and coat color, which can affect adaptation and market value. This study evaluated genetic variations in 15 Brazilian sheep breeds using a set of 48 genetic markers related to these traits. Our findings suggest that a specific mutation in the GDF9 gene may be associated with increased lamb production in the Brazilian Blackbelly, in addition to Santa Inês and Morada Nova breeds where it has previously been associated with prolificacy. Other genes formerly linked with enhanced reproductive performance did not show relevant effects in these locally adapted breeds. Genetic differences were also identified in genes influencing coat color, helping to explain the diversity observed between hair and wool sheep. Importantly, the genetic material stored in the Brazilian Animal Germplasm Bank (BBGA) preserves much of the diversity found in populations conserved in situ. These findings contribute to the conservation and sustainable use of local sheep breeds, supporting genetic improvement programs and helping ensure food security and biodiversity for future generations.
Background/Objectives: Brazilian locally adapted sheep breeds represent valuable genetic resources. However, the commercial valorization of these breeds depends in part on genetic certification to support traceability and verify product origin. This study aimed to identify and evaluate a minimum set of highly informative SNPs for accurate and efficient breed assignment across five Brazilian locally adapted sheep breeds. Methods: A total of 677 samples were genotyped using the Embrapa Multispecies 65 K Illumina Infinium 1 chip, which contains 2926 markers for Ovis aries. The dataset was partitioned into training (n = 566) and independent testing (n = 111) sets. Markers were ranked according to genetic differentiation based on pairwise Wright’s fixation index (FST) using the Toolbox for Ranking and Evaluation of SNPs (TRES), generating three nested reduced panels of 288, 192, and 96 SNPs. Panel performance and preservation of population structure were evaluated using Random Forest classification, Principal Component Analysis (PCA), and ADMIXTURE. Results: The 96-SNP panel achieved classification accuracy comparable to that of the 2145-SNP post-QC baseline and the 192- and 288-SNP panels (Cochran’s Q test: Q = 6.00, df = 3, p = 0.112), with no statistically significant difference in classification performance despite the substantial reduction in marker number. PCA and ADMIXTURE analyses indicated that the 96-SNP panel preserved the major population structure observed with the full post-QC marker set. Conclusions: Although formal analytical validation of a dedicated low-density genotyping assay remains necessary before routine implementation, the in-silico marker selection and empirical validation performed here provide an evidence-based framework for translating high-density genomic information into accessible and cost-effective applications for breed assignment, traceability, and conservation of Brazilian locally adapted sheep genetic resources.
Camila Souza Rodrigues, Danielle Assis de Faria, S. Paiva et al.· Genes· 0 citations
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
Coat color in cattle is a phenotypic trait of high biological, zootechnical, and economic relevance, having historically been used as a visual criterion in selection programs and as a marker associated with adaptive and productive processes. In zebu breeds such as Gir (Bos indicus), this trait exhibits wide phenotypic variability, constituting an important component of breed identity and attracting scientific interest in tropical dairy production systems. Pigmentation results from the activity of melanocytes, which are responsible for melanin synthesis within melanosomes and is regulated by molecular networks that control the production of eumelanin and pheomelanin through specific signaling pathways. Within the context of population genomics, parameters such as linkage disequilibrium (LD) and effective population size (Ne) allow the characterization of population genetic structure, whereas genome-wide association studies (GWAS) enable the investigation of the genetic architecture underlying coat color. In this study, phenotypic records from 50,341 animals classified into 25 coat color categories were used, along with genomic data from 55,154 Gir cattle. After quality control, 389,172 SNPs were retained for the analyses. Heritability estimates ranged from 0.16 to 0.75, indicating moderate to high genetic control. The average LD (r²) was 0.064 at 50 kb, while effective population size declined from 53.9 individuals in generation 50 to 13.8 individuals in generation 5. Genomic windows of 0.5 Mb explained up to 24% of the additive genetic variance, enabling the identification of 52 candidate genes associated with coat color variation. The identified genes are related to processes such as melanocyte migration and development, cellular differentiation, cytoskeleton organization, signal transduction, and melanogenesis pathways. Taken together, the results indicate that coat color variation in the Gir breed is controlled by a complex and polygenic genetic architecture, involving multiple genes with pleiotropic effects, with implications for genetic improvement programs, conservation strategies, and the valorization of the breed in tropical production systems. Keywords: pigmentation; genetic variability; coat color.
Modern breeding of agricultural animals has transitioned from phenotype-based selection to high-precision genomic prediction based on hundreds of thousands of DNA markers. This has not only accelerated the development of breeds with target traits but also enhanced their adaptability and stress resistance through the design of balanced selection programs. In this context, the present work involved the selection and validation of various DNA markers associated with adaptation potential in rabbits (Oryctolagus cuniculus) and fur-bearing animals (using the sable Martes zibellina as an example). Studies were conducted using PCR and real-time PCR. In the population-genetic study of female sables (n=9, yearlings born in 2023; n=5, two-year-olds born in 2022; n=7, born before 2022), highly polymorphic markers ((ACC)6G, LTR-BERV-K1) were identified, demonstrating high discriminatory power in analyzing differences between animal generations. In the study of feed additive effectiveness in rabbits (n=12, Rodnik cross), reduced expression of metabolic genes g6pd and slc15a1 was observed when using a vitamin-mineral premix during the fattening period. The micronucleus test revealed the potential genome-destabilizing effect of the premix on blood cells, despite the absence of a statistically significant effect on body weight gain. In the behavior genetics study (n=8, rabbits of the Soviet Chinchilla and White Giant breeds), breed and sex differences in the expression of glutamatergic system genes grik3 and gria2 were discovered, opening prospects for selection aimed at reducing aggression in captive animal populations. The proposed approaches create new opportunities for fur farming and rabbit breeding through targeted selection of DNA markers to control genetic variability across generations and the functional activity of key metabolic network components.
A.V. Leonov, T. Glazko, O. Skobel et al.· №4 (2018)· 0 citations
Goats (Capra hircus) are among the world’s most important livestock, providing milk, meat, and fiber across diverse agro-ecological zones. Traditional breeding relying on pedigree-based estimated breeding values (EBVs) has driven steady genetic progress but is constrained by long generation intervals and limited accuracy for sex-limited or difficult-to-measure traits. High-throughput single nucleotide polymorphism (SNP) chips and genomic selection (GS) have transformed goat breeding by enabling early, accurate selection independent of phenotypic records. This review synthesizes the development of goat SNP chip platforms from the foundational 52 K GoatSNP50 BeadChip through high-density solid-phase arrays and low-cost liquid-phase capture panels, with emphasis on their relative performance, cost-effectiveness, imputation potential, and suitability for different breeding systems. In addition to genomic selection (GS), genome-wide association studies (GWAS), and genetic diversity assessment, we also discuss candidate-gene selection and marker-assisted selection (MAS) as practical intermediate approaches that remain relevant in many goat breeding programs. GS has achieved genomic estimated breeding value (GEBV) prediction accuracies of 0.35–0.79 for key production traits across multiple countries and breeds. GWAS has identified candidate genes for milk composition (DGAT1, CSN1S1), growth (PLAG1, HMGA2), reproduction (BMPR1B, GDF9), and fiber quality (KRT, KRTAP families). We compare GS with traditional BLUP-based approaches, assess economic benefits, and discuss key challenges including reference population construction, genotype imputation, inbreeding management via Optimum Contribution Selection (OCS), and multi-omics integration. Future directions include customized chip design, AI-assisted genomic prediction, climate adaptation breeding, and CRISPR/Cas9 gene editing for precision improvement.
Ting-Chieh Kang, Hisn-Hung Lin, Kai-Fei Tseng et al.· Frontiers in Veterinary Scie...· 0 citations
Simple Summary Morphometric traits are important in beef cattle breeding because they directly affect meat production and economic value. Differences in these traits among cattle breeds are partly influenced by genetic variation. In this study, we examined copy number variation (CNV) in the MYC-associated factor X gene in 572 Chinese cattle from five breeds, including Qinchuan, Ji’an, Jinnan, Nanyang, and Xianan cattle. CNVs are defined as differences in the number of copies of genomic DNA segments among individuals within a population. The copy number variation in this gene showed different distribution patterns among the five breeds. Based on raw p values, MAX CNVs showed nominal associations with chest girth in Jinnan cattle and with chest girth and hucklebone width in Nanyang cattle. Animals with the medium copy type, defined as two copies, showed higher values for the nominally associated traits than those with the loss type (<2 copies) or gain type (>2 copies). These findings suggest that copy number variation in the MYC-associated factor X gene may represent a potential candidate locus related to morphometric traits in Chinese cattle. Further validation in larger cattle populations is still needed before it can be used in breeding programs.
Shiyi Lv, Boyu Li, Suyun Fan et al.· Animals· 0 citations