Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 6, 2023

The importance of sheep breeding in the Mediterranean part eastern Adriatic has a long tradition since its arrival during Neolithic migrations. Sheep production system is extensive and generally carried out traditional systems without intensive systematic programmes for high uniform trait (carcass, wool milk yield). Therefore, eight indigenous Croatian breeds from treated here as metapopulation (EAS), are considered multipurpose (milk, meat wool), not specialised particular type production, but known their robustness resistance to certain environmental conditions. Our objective was identify genomic regions genes that exhibit patterns positive selection signatures, decipher biological productive functionality, provide "genomic" characterization EAS adaptation determine type.We identified signatures using several methods based on reduced local variation, linkage disequilibrium site frequency spectrum (eROHi, iHS, nSL CLR). analyses numerous (e.g., desmosomal cadherin desmoglein gene families) associated with economically important traits. Most candidate were related meat/production health/immune response traits, while some discovered domestication evolutionary processes HOXa family FSIP2). These results also confirmed by GO QTL enrichment analysis.Our contribute better understanding unique adaptive genetic architecture define type, ultimately providing new opportunity future programmes. At same time, will improve our ruminant (sheep) harsh specific environment.

Language: Английский

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Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Animals, Journal Year: 2021, Volume and Issue: 11(9), P. 2696 - 2696

Published: Sept. 15, 2021

In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), locally-adapted in order to identify and characterize factors impacting the detection runs homozygosity (ROH) heterozygosity-rich regions (HRRs) sheep. We also applied a business intelligence (BI) tool integrate visualize outputs from complementary analyses. observed prevalence short ROH, clear distinction between ROH profiles across populations. The visualizations showed fragmentation medium long segments. Furthermore, tested scenarios HRR evaluated impact parameters used. Our findings suggest that HRRs are small frequent genome; however, further studies with higher density SNP chips methods suggested future research. defined islands identified common populations, where genes related variety traits reported, such as body size, muscle development, brain functions. These results indicate associated many traits, thus under selective pressure breeds raised purposes. Interestingly, candidate detected within integrity. strong association high linkage disequilibrium pattern compared HRR, despite fact not located regions.

Language: Английский

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Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: April 26, 2022

Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history adaptive evolution. Numerous studies have shown that deleterious mutations enriched in the ROH humans, pigs, cattle, chickens. However, relationship variants to pattern ROHet goats been largely understudied. Here, 240 Guangfeng Ganxi from Jiangxi Province, China, were genotyped using Illumina GoatSNP50 BeadChip genome-wide ROH, ROHet, genetic load analyses performed context 32 global goat breeds. The classes with highest percentage 0.5-2 Mb 0.5-1 Mb, respectively. results inbreeding coefficients (based on SNP ROH) measurements showed had higher variability than most Chinese goats, while a high degree inbreeding, even exceeding commercial Next, predicted damaging homozygotes more long ROHs, especially goats. Therefore, we suggest information alleles should also be incorporated design breeding conservation programs. A list genes related fecundity, growth, environmental adaptation identified hotspots two sense-related hotspot (chromosome 12: 50.55-50.81 Mb) was shared across breeds may undergone selection prior domestication. Furthermore, an identical 1: 132.21-132.54 containing associated embryonic development (STAG1 PCCB) detected domestic worldwide. Tajima's D BetaScan2 statistics indicated this region caused by long-term balancing selection. These findings not only provide guidance for strategies but enrich our understanding evolution

Language: Английский

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Detection of selection signatures in South African Mutton Merino sheep using whole‐genome sequencing data

Animal Genetics, Journal Year: 2022, Volume and Issue: 53(2), P. 224 - 229

Published: Jan. 31, 2022

The South African Mutton Merino (SAMM), a dual-purpose (meat and wool) sheep breed, is characterized by its excellent performance on growth, carcass traits meat quality compared to other fine-wool breeds. Nowadays, the SAMM breed has been widely used cross with commercial indigenous or coarse-wool breeds improve growth in many countries. To date, however, little known about genetic basis for prominent characteristics. In this study, whole-genome sequences of 10 were sequenced selection signatures analyzed together those 39 Australian Chinese (wool-type Merino) FST , iHS, XP-EHH methods. total, 313 genes 277 regions identified at least 2 methods signal 21 them all three We highlighted list interesting genes, including GHR, LCORL, SMO, NCAPG, DCC, IBSP, PPARGC1A, PACRGL, PRDM5, XYLB, AHCYL2, TEFM, AFG1L, FAM184B, which have shown be involved traits, previous studies. Herein, encoding transmembrane receptor hormone, most notable one. report first study analysis sequence level. These results provide new insights into mechanisms underlying SAMM.

Language: Английский

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Comparative genomic characterization of indigenous fat‐tailed Akkaraman sheep with local and transboundary sheep breeds

Food and Energy Security, Journal Year: 2023, Volume and Issue: 13(1)

Published: Oct. 1, 2023

Abstract The domestic sheep with over 1200 breeds descended from those early domesticated animals that are bred for a variety of resources such as meat, milk and wool. Akkaraman, fat‐tailed indigenous breed Türkiye, is widespread throughout Central Anatolia, the largest population. Assessing genetic diversity genomic structure animal among key contributors to deciphering adaptation environmental extremes constructing efficient improvement strategies. Therefore, this study aimed characterize genome Akkaraman against various world‐renowned transboundary fat thin tails. Genetic similarities differences between have been displayed by estimating comparing indices, linkage disequilibrium (LD) estimates fixation index ( F ST ), runs homozygosity (ROH) well PCA neighbour‐joining tree analysis. were observed form cluster alongside Moghani, Karakas, Tibetan Cyprus Fat Tail sheep, which primarily sole representatives in study. This clustering was evident both also lowest inbreeding one numbers ROHs, might indicate has not exposed historical intensive selection pressure, inbred mating or massive population bottleneck leave strong marks homozygosity. results improve our understanding comparison certain mainstream around world. Additionally, findings will provide valuable insights perform further GWAS effectively considering structure, LD patterns while providing practical knowledge contribute designing successful genome‐based programmes worldwide production systems.

Language: Английский

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Runs of Homozygosity and Selection Signature In Santa Inês Sheep: A Genomic Analysis

Small Ruminant Research, Journal Year: 2025, Volume and Issue: unknown, P. 107478 - 107478

Published: Feb. 1, 2025

Language: Английский

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Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides)

Poultry Science, Journal Year: 2025, Volume and Issue: 104(5), P. 105004 - 105004

Published: March 8, 2025

In recent years, the dwindling population of these endangered geese has hindered our understanding their phenotypic variations and genes associated with important traits. To investigate structure genetic diversity this breed, whole-genome data 90 individuals from a conservation farm were obtained using Illumina 6000 paired-end platform. The research results indicate that each locally goose variety formed monophyletic population. Baizi (BZ), Lingxian White (LX), Xupu (XP) exhibiting higher than other breeds. Tree-Mix analysis revealed presence five gene flows events between populations, Yangjiang (YJ) consistently significant distance Under strong pressures natural environment artificial selection, selective scanning 394 overlapping genes. Gene Ontology (GO) enrichment putative candidate (PCGs) 20 terms (P < 0.05). Similarly, Kyoto Encyclopedia Genes Genomes (KEGG) PCGs in 23 Examination identified through at least two selection methods set key traits, including growth development (CCND1, DES, CCNO, SMC5, NUBP1), immunity (ABCA2, ABCC8, UHRF2, ABCA1), body aging (KAT6B). Our findings provide insights into basis level, laying foundation for future molecular on variation changes. summary, invaluable resources delineating uniqueness

Language: Английский

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Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 18, 2025

Runs of Homozygosity (ROH) are homozygous genomic fragments inherited from parents to offspring. ROH can be used indicate the level inbreeding, as well identify possible signatures artificial or natural selection. Indigenous sheep populations on southern edge Taklimakan Desert have evolved unique genetic traits adapted extreme desert environments. In an attempt better understand adaptive mechanisms these under harsh conditions, we Illumina® Ovine SNP50K BeadChip perform a characterization three recognized breeds (Duolang: n = 36, Hetian: 84, Qira black: 189) and one ecotypic breed (Kunlun: 27) in region. Additionally, assessed inbreeding coefficients through analysis, revealing insights into history populations. Subsequently, retrieved candidate genes associated with economic islands each breed. To autozygosity distribution indigenous relative international breeds, also included commercial mutton (Poll Dorset: 108, Suffolk: 163, Texel: 150). The study revealed that among seven Hetian exhibited shortest linkage disequilibrium (LD) decay distance, while Kunlun demonstrated highest LD levels. A total 10,916 ROHs were obtained. number per ranged 34 (Kunlun) 2,826 (Texel). length was mainly 1–5 Mb (63.54%). Furthermore, 991 specific identified, including those heat tolerance, adaptability, energy metabolism, reproduction, immune response. These findings elucidate adaptation Desert, uncovering distinctive characteristics formation, advocating for conservation enhancement local

Language: Английский

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Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Frontiers in Veterinary Science, Journal Year: 2022, Volume and Issue: 9

Published: March 8, 2022

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures livestock. Commercial breeds provide excellent materials reveal the landscape ROH shaped during intense process. Here, we GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data 3,770 American Duroc (AD) 2,096 Canadian (CD) pigs analyze genome-wide ROH. First, showed that AD had a moderate differentiation with CD pigs, more abundant diversity significantly lower level inbreeding than pigs. In addition, sows larger levels boars in These differences may be caused by selective intensity. Next, hotspots revealed many candidate genes putatively under for growth, sperm, muscle development two lines. Population-specific ROHs inferred have special female reproduction, while immunity. Moreover, overlapping populations, observed missense mutation (rs81216249) located growth fat deposition-related supergene (

Language: Английский

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Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Genes, Journal Year: 2024, Volume and Issue: 15(4), P. 524 - 524

Published: April 22, 2024

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact artificial selection on genomic architecture genetic markers sought remains a key area research. Here, we used whole-genome resequencing data analyze architecture, diversity, selective sweeps in Cornish White (CRW) Plymouth Rock (PRW) transboundary breeds selected for meat production and, comparatively, an aboriginal Russian breed Ushanka (USH). Reads were aligned reference genome bGalGal1.mat.broiler.GRCg7b filtered remove PCR duplicates low-quality reads using BWA-MEM2 bcftools software; 12,563,892 SNPs produced subsequent analyses. Compared CRW PRW, USH had lower diversity higher distinctiveness. Selective sweep regions corresponding candidate genes examined based ZFST, hapFLK, ROH assessment procedures. Twenty-seven prioritized chicken functional projection from human homologs suggest their importance signals studied breeds. These have relationship with such categories as body weight, muscles, fat metabolism deposition, reproduction, etc., mainly QTLs regions. This information is pivotal further executing enhance phenotypic traits.

Language: Английский

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