Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection

Genetics Selection Evolution, Год журнала: 2022, Номер 54(1)

Опубликована: Янв. 24, 2022

The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation nineteenth century, establishment herd books, and selection for specific traits resulted 10 modern breeds Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 goats nine wild Bezoar aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used identification runs homozygosity (ROH) detection ROH islands.Across 226 caprine genomes 11 populations, we detected 344 islands that harbor 1220 annotated genes. compared between goats. As a proof principle, confirmed signature selection, which contains ASIP gene controls several breed-specific coat color patterns. In two other islands, identified missense variants, STC1:p.Lys139Arg TSHR:p.Ala239Thr, might represent causative functional signatures.We have shown information using WGS is suitable analysis signatures allowed protein coding may conferred beneficial phenotypes during domestication. hypothesize TSHR:p.Ala239Thr variant played role changing seasonality reproduction domesticated exact significance remains unclear requires further investigation. Nonetheless, STC1 new affecting relevant such as body size and/or milk yield

Язык: Английский

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Patterns of homozygosity in insular and continental goat breeds

Genetics Selection Evolution, Год журнала: 2018, Номер 50(1)

Опубликована: Ноя. 14, 2018

Genetic isolation of breeds may result in a significant loss diversity and have consequences on health performance. In this study, we examined the effect geographic caprine genetic patterns by genotyping 480 individuals from 25 European African with Goat SNP50 BeadChip comparing homozygosity insular nearby continental breeds.Among analysed, number total length ROH varied considerably depending breeds, could cover substantial fraction genome (up to 1.6 Gb Icelandic goats). When compared their counterparts, goats Iceland, Madagascar, La Palma Ireland (Bilberry Arran) displayed increase coverage, FROH values (P value < 0.05). Goats Mediterranean islands represent more complex case because certain populations significantly increased level (e.g. Girgentana) others did not Corse Sarda). Correlations for goat distance between nearest locations revealed an extremely long distances homozygosity.These results indicate that effects insularization are variable. raised Palma, show high levels homozygosity, whereas those bred display similar found populations. These is modulated multiple factors such as distribution, population size, demographic history, trading breed management.

Язык: Английский

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Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

Genetics Selection Evolution, Год журнала: 2019, Номер 51(1)

Опубликована: Ноя. 26, 2019

As one of the important livestock species around world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, genetic loci that underlie phenotypic variations in domestic are largely unknown, particularly for economically traits. In this study, we sequenced whole genome 38 from three Chinese breeds (Chengdu Brown, Jintang Black, Tibetan Cashmere) downloaded sequence data 30 five other (four non-Chinese breed) 21 Bezoar ibexes investigate composition selection signatures goat after domestication.Based on population structure analysis FST values (average = 0.22), Chengdu Brown differs considerably as a result geographic isolation. Strikingly, genes under identified Cashmere were significantly enriched categories hair growth bone nervous system development, possibly because they involved adaptation high-altitude. particular, found large difference allele frequency novel SNP (c.-253G>A) 5'-UTR FGF5 between with short hair. The mutation at site introduces start codon results occurrence premature protein is likely natural causal variant long phenotype cashmere goats. haplotype tagged AGG-allele exon 12 DSG3, which encodes cell adhesion molecule expressed mainly skin, was almost fixed goats, whereas locus still segregates lowland breeds. pigmentation gene KITLG showed strong signature ASIP LCORL being positive Black goats.After domestication, isolation some has resulted distinct structures. Furthermore, our work highlights several positively selected contributed breed-related traits

Язык: Английский

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Population Structure and Genetic Diversity of Sheep Breeds in the Kyrgyzstan

Frontiers in Genetics, Год журнала: 2019, Номер 10

Опубликована: Дек. 12, 2019

Sheep are a main livestock species of Kyrgyzstan, Central Asian country with predominating mountain terrain. The current gene pool local sheep resources has been forming under diverse climate conditions from the era trading caravans Great Silk Road, through Soviet period large-scale improvements, which was followed by deep crisis at end 20th century, up to now. However, not much is known about genetic background and variability populations. Therefore, our aims were provide characterization population structure relations within Kyrgyz breeds study their connections global using SNP analysis. Samples Alai (n = 31), Gissar 30), coarse wool 13), Aykol Tien-Shan 24) genotyped OvineSNP50 BeadChip or Ovine Infinium HD (Illumina Inc., USA). measure inbreeding based on runs homozygosity showed minimum value in breed (FROH 0.034), while maximum found 0.071). Short ROH segments (ROH ≤ 4 Mb) predominant all breeds. Long > 16 absent breed. had highest values effective sizes estimated for five generations ago (Ne5 660 563), whereas displayed lower 176 128, respectively). synthetic origin clearly evidenced analyses applied. Based network admixture breeds, Russian semi-fine demonstrated common ancestry that most likely due contribution Lincoln Gissar, Aykol, populations Iran China different type. revealed patterns probably resulted exchange trade during partly overlapped historical archeological findings.

Язык: Английский

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Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India

Animal Biotechnology, Год журнала: 2020, Номер 33(2), С. 297 - 311

Опубликована: Июль 30, 2020

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock resources. In this study, we presented a comprehensive genome-wide analysis diversity, ROH, inbreeding, linkage disequilibrium, effective population size haplotype block structure in Tharparkar cattle India. A total 24 animals used study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs retained, which HWE, MAF > 0.05 genotyping rate >90%. The overall mean observed (HO) expected heterozygosity (HE) 0.339 ± 0.156 0.325 0.129, respectively. average minor allele frequency was 0.234 standard deviation 0.131. We identified 1832 ROH segments highest autosomal coverage 13.87% on chromosome 23. genomic inbreeding coefficients estimates by FROH, FHOM, FGRM FUNI 0.0589, 0.0215, 0.0532 0.0160 disequilibrium (LD) 133,532 pairwise measured D' r2 0.6452 0.1339, addition, gradual decline over past generations.

Язык: Английский

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Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Animal Genetics, Год журнала: 2021, Номер 52(2), С. 155 - 170

Опубликована: Фев. 5, 2021

Summary ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion genome covered by and their length indicators the level origin inbreeding. Frequent common within same population define ROH islands indicate hotspots selection. In this work, we investigated in a total 1131 pigs from 20 European local pig breeds three cosmopolitan breeds, genotyped with GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes genomic inbreeding parameters were evaluated. defined evaluating different thresholds SNP frequency. A functional overview breed‐specific obtained via over‐representation analyses GO biological processes. Mora Romagnola Turopolje had largest proportions (~1003 ~955 Mb respectively), whereas Nero Siciliano Sarda lowest (~207 247 respectively). highest (>16 Mb) Apulo‐Calabrese, Casertana. number identified Italian Landrace ( n = 32), Cinta Senese 26) Lithuanian White Old Type 22) breeds. Several regions encompassing genes known affect morphological traits. Comparative structure analysis among indicated similar genetic across Europe. This study contributed understanding history provided information manage these resources.

Язык: Английский

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VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Genetics Selection Evolution, Год журнала: 2021, Номер 53(1)

Опубликована: Ноя. 8, 2021

Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed understand the consequences on diversity domestic goats elucidate how speciation hybridization modeled genomes set species representative genus Capra.A dataset comprising 652 sequenced 507 public sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) 13,607,850 insertion-deletions (InDels) by aligning these sequences latest version reference genome (ARS1). A Neighbor-joining tree based Reynolds distances showed that from Africa, Asia Europe tend group into independent clusters. Because breeds Oceania Caribbean (Creole) all derive imported animals, they are distributed along according ancestral geographic origin.We report unprecedented effort characterize genome-wide goats. This large range individuals represents unique opportunity ascertain demographic selection processes associated post-domestication history shaped this species. Data generated for will also be extremely useful identify deleterious mutations causal effects complex traits, thus contribute new knowledge could used in genomic prediction association studies.

Язык: Английский

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A near complete genome for goat genetic and genomic research

Genetics Selection Evolution, Год журнала: 2021, Номер 53(1)

Опубликована: Сен. 10, 2021

Abstract Background Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, reported nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome highly fragmented Y scaffolds. Results Here, we present very high-quality de novo assembly, Saanen_v1, male Saanen dairy goat, with scaffold based on 117× long-read sequencing 118× Hi-C data. Saanen_v1 displays high level completeness thanks to presence centromeric telomeric repeats at proximal distal ends two-thirds autosomes, much reduced number gaps (169 vs. 773). accuracy are also evidenced by more assembled sequences chromosomes (2.63 Gb for 2.58 ARS1), slightly increased mapping ratio transcriptomic data, genes anchored chromosomes. eight putative large errors (1 ~ 7 Mb each) found in were amended, time, substitution rate this ruminant was estimated. Furthermore, sequence improvement compared enables us assign likely correct positions 4.4% single nucleotide polymorphism (SNP) probes widely used GoatSNP50 chip. Conclusions updated including sex (X Y) autosomes high-resolution quality will serve valuable resource genetic research applications.

Язык: 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, Год журнала: 2022, Номер 13

Опубликована: Апрель 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

Язык: Английский

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Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds

BMC Genomics, Год журнала: 2022, Номер 23(1)

Опубликована: Июль 12, 2022

Abstract Background Understanding inbreeding and its impact on fitness evolutionary potential is fundamental to species conservation agriculture. Long stretches of homozygous genotypes, known as runs homozygosity (ROH), result from their number length can provide useful population-level information characteristics locations signatures selection. However, the utility ROH for limited natural populations where baseline data genomic tools are lacking. Comparing metrics in recently feral vs. domestic well understood like horse could genetic health those offer insight into how such compare between managed unmanaged populations. Here we characterized ROH, coefficients, islands a population Sable Island, Canada, using ~41 000 SNPs contrasted results with 33 breeds assess impacts isolation abundance, length, distribution, islands. Results number, ROH-based coefficients (F ) Island horses were generally greater than breeds. Short runs, which typically coalesce many generations prior, more abundant long all populations, but run distributions indicated recent bottlenecks horses. Nine detected horses, exhibiting very little overlap found Gene ontology (GO) enrichment analysis revealed genes associated 3 clusters biological pathways largely metabolism immune function. Conclusions This study indicates that tend be inbred counterparts most this due historical founder effects rather mating close relatives. Unique suggest adaptation local selective pressures and/or strong drift highlight value reservoir equine variation. research illustrates analyses applied gain insights history, health, divergence wild or concern.

Язык: Английский

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