Selection signatures in livestock genome: A review of concepts, approaches and applications

Livestock Science, Год журнала: 2020, Номер 241, С. 104257 - 104257

Опубликована: Сен. 19, 2020

Язык: Английский

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Evolution and domestication of the Bovini species

Animal Genetics, Год журнала: 2020, Номер 51(5), С. 637 - 657

Опубликована: Июль 27, 2020

Summary Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since early Holocene (ca. 10 000 BCE) has contributed significantly to development human civilization. In this study, we review recent literature on origin phylogeny, domestication dispersal three major Bos – taurine zebu yak their genetic interactions. The global dispersion cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation mitochondrial Y‐chromosomal DNA. high diversity European breeds been shaped through isolation‐by‐distance, different production objectives, breed formation expansion popular breeds. overlapping broad ranges led hybridization with each other bovine species. For instance, Chinese gayal carries DNA; several Indonesian descend from bull × banteng cow crossings; Tibetan have exchanged gene variants; about 5% American bison contain mtDNA. Analysis at genomic level indicates that introgression may played role environmental adaptation.

Язык: Английский

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Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals, Год журнала: 2021, Номер 11(3), С. 904 - 904

Опубликована: Март 22, 2021

The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, draught animal. remained underutilized in terms of the development well-annotated assembled reference genome de novo. It is mandatory to explore genetic architecture species understand biology that helps manage its variability, which ultimately used for selective breeding genomic selection. Morphological molecular data have revealed swamp population strong geographical diversity with low gene flow but phenotypic consistency, while river higher weak phylogeographic structure. availability recent high-quality genotyping marker panels invigorated many genome-based studies on evolutionary history, diversity, functional elements, performance traits. increasing knowledge syndicate should pave way improvement climatic resilience, disease resistance, production water populations globally.

Язык: Английский

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BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis

Database, Год журнала: 2025, Номер 2025

Опубликована: Янв. 1, 2025

Abstract Amidst the global challenge of extreme poverty, livestock sector can significantly contribute to sustainable development goals by enhancing resilience, smallholder productivity, and market participation. The Indian is one largest in world with a total population 535.82 million, ∼10.7% world’s population. Buffalo (Bubalus bubalis) holds significant importance India other Asian countries, notably contributing their economies surpassing cattle milk production providing various valuable products. limited availability genomic transcriptomic resources for buffaloes hinders efforts enhance traits increased meat production. To address this gap, study adopted state-of-the-art bioinformatics tools analyse 2429 transcriptomes representing 438 BioSamples from 23 BioProjects obtained public domain database, 76 different types tissues cell all major organ systems buffalo species (river swamp). outcome exhaustive data led relational expression database based on three-tier architecture named as BuffExDb (http://46.202.167.198/buffex/). user-friendliness flexibilities retrieval tissue-specific genes (TSGs) functional annotation are characteristics BuffExDb. This first its kind that offers an effortlessly navigable filterable enabling users examine visualize levels each tissue across multiple samples, simultaneously. It also provides Tau score parameter identification TSGs along essential roles development, maintenance, function observed through enrichment test gene ontologies. work would pave way biological, functional, evolutionary studies easy access. prior information mechanisms be used future research, especially association endeavour enhanced breeding conservation programmes. Database URL: http://46.202.167.198/buffex/

Язык: Английский

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Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia

Animals, Год журнала: 2025, Номер 15(6), С. 831 - 831

Опубликована: Март 13, 2025

Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning data to the genome, WGRS enables precise detection genetic variations in individuals or populations. As core technology genomic research, WGS holds profound significance ruminant studies. It not only reveals intricate structure genomes but also provides essential for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing exploration mechanisms. However, still faces several challenges, such as incomplete inaccurate genome assembly, well annotation numerous unknown genes functions. Although can identify vast number variations, specific relationships between these phenotypes often remain unclear, which limits its potential functional studies breeding applications. performing on multiple samples, assembly challenges be effectively addressed, particularly regions high repeat content complex structural variations. accurately subtle among different populations further elucidate their associations traits, overcoming limitations providing more information research This review systematically summarizes latest applications analysis structures, diversity, economic adaptive while discussing faced by this technology. aims provide scientific foundation improvement conservation resources.

Язык: Английский

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New Insights into Genetic Diversity and Differentiation of 11 Buffalo Populations Using Validated SNPs for Dairy Improvement

Genes, Год журнала: 2025, Номер 16(4), С. 400 - 400

Опубликована: Март 30, 2025

Background/Objectives: Buffalo populations exhibit distinct genetic variations influenced by domestication history, geographic distribution, and selection pressures. This study investigates the structure differentiation of 11 buffalo populations, focusing on five loci related to milk protein (CSN1S1 CSN3) fat metabolism (LPL, DGAT1 SCD). The aim is assess variation between river, swamp, wild-type buffaloes identify key contributing population differentiation. Methods: Genetic diversity was analyzed through allele frequency Hardy−Weinberg equilibrium testing, observed (Ho) expected heterozygosity (He) calculations. Population assessed using principal component analysis (PCA), FST statistics, phylogenetic clustering (k-means UPGMA tree). silhouette score (SS) Davies−Bouldin index (DBI) were applied determine optimal clustering. Results: Significant river swamp (p < 0.001). CSN3 emerged as markers distinguishing types. Italian Mediterranean exhibited highest (Ho = 0.464; He 0.454), while Indonesian, Chinese, Vietnamese showed low heterozygosity, likely due pressures isolation. global (0.2143; p 0.001) confirmed moderate differentiation, with closely (e.g., Nepal Pakistan) exhibiting minimal divergence, distant Egypt Indonesia) marked differences, Romanian a unique position. Conclusions: These findings contribute deeper understanding provide valuable basis for exploiting potential this species in light future breeding conservation strategies specific each type.

Язык: Английский

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Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia

Frontiers in Genetics, Год журнала: 2021, Номер 12

Опубликована: Март 22, 2021

The swamp buffalo is a domesticated animal commonly found in Southeast Asia. It highly valued agricultural for smallholders, but the production of this species has unfortunately declined recent decades due to rising farm mechanization. While still plays role farmland cultivation, species' purposes shifted from draft power meat, milk, and hide production. current status buffaloes Asia understudied compared its counterparts such as riverine cattle. This review discusses background buffalo, with an emphasis on work Asia, associated genetics genomics cytogenetic studies, phylogeny, domestication migration, genetic sequences resources. Recent challenges realize potential agriculture industry are also discussed. Limited resource called more be done including decoding genome. As economy progresses mechanization increases, research development focused enhancing productivity through understanding agriculturally important traits. use genomic markers powerful tool efficiently utilize food security conservation. Understanding retaining maximizing adaptability harsher environments strategic move poorer nations face climate change.

Язык: Английский

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Analysis of genetic diversity and selection characteristics using the whole genome sequencing data of five buffaloes, including Xilin buffalo, in Guangxi, China

Frontiers in Genetics, Год журнала: 2023, Номер 13

Опубликована: Янв. 9, 2023

Buffalo is an economically important livestock that renders useful services to manhood in terms of meat, milk, leather, and draught. The Xilin buffalo among the native breeds China. In present study, genetic architecture selection signature signals have been explored. Correlation analysis population structure was conducted by constructing NJ tree, PCA, ADMIXTURE other methods. A total twenty-five (n = 25) whole genome data forty-six 46) buffaloes published were used. showed belong Middle-Lower Yangtze. diversity relatively high. CLR, π ratio, FST, XP-EHH used detect candidate genes characteristics positive buffalo. Among identified genes, most enriched signal pathways related nervous system metabolism. mainly reported (GRM5, GRIK2, GRIA4), reproductive (CSNK1G2, KCNIP4), lactation (TP63). results this study are great significance for understanding molecular basis phenotypic variation traits We provide a comprehensive overview sequence variations genomes. Selection signatures detected genomic regions possibly help future breeding conservation programs resource.

Язык: Английский

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Genomic analyses reveal distinct genetic architectures and selective pressures in buffaloes

GigaScience, Год журнала: 2020, Номер 9(2)

Опубликована: Фев. 1, 2020

Abstract Background The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity yet to be fully discovered. Results In this study, we describe the demographic events selective pressures of by analyzing 121 whole genomes (98 newly reported) from 25 swamp river breeds. Both uniparental biparental markers were investigated provide final scenario. ancestors diverged ~0.23 million years ago then experienced independent histories. They domesticated different at border between southwest China southeast Asia, while south Asia. stocks migrated other regions further differentiated, as testified (at least) 2 ancestral components identified each subspecies. Different signals also detected these types buffalo. buffalo, historically used a draft animal, shows selection signatures genes associated with nervous system, dairy breeds, under are related heat stress immunity. Conclusions Our findings substantially expand catalogue genetic variants reveal new insights into evolutionary history distinct

Язык: Английский

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Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes

Journal of Dairy Science, Год журнала: 2023, Номер 107(2), С. 992 - 1021

Опубликована: Сен. 18, 2023

Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to: 1) compare single-trait random regression models under a Single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) setting based on alternative covariance functions (i.e., Wood – WD, Wilmink WL, Ali-and-Schaeffer AS) describe (MY), fat (FY), protein (PY), mozzarella (MZY) yields, fat-to-protein ratio (FPR), somatic cell score (SCS), lactation length (LL), persistency (LP) in Murrah dairy (Bubalus bubalis); 2) combine the best each trait multiple-trait framework; 3) estimate time-dependent SNP effects all studied traits; and, 5) identify most likely candidate genes associated with traits. A total 323,140 test-day records from first 4,588 were made available study. The model included average curve population nested within herd-year-season calving, systematic number milkings per day, age at calving as linear quadratic covariates, additive genetic, permanent environment, residual effects. WD had goodness fit deviance information criterion posterior probabilities Moderate heritabilities estimated over time (0.30 ± 0.02 MY; 0.26 0.03 FY; 0.45 0.04 PY; 0.28 0.05 MZY; 0.13 FPR; 0.15 SCS). heritability estimates LP ranged 0.38 0.65 depending definition used. Similarly, LL 0.10 0.01 0.14 0.03. genetic correlation across DIM −0.06 (186 215 MY-SCS) 0.78 (66 95 PY-MZY). calculated coefficients used throughout (from 5 305 d). Numerous relevant regions identified traits, confirming their polygenic nature. contribute better understanding background milk-related reinforce value incorporating programs.

Язык: Английский

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