Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 2, 2024

Abstract Heterozygosity-rich regions (HRR) are genomic of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim work was inter-breed relationships HRR patterns using Sliding Window (SW) Consecutive Runs (CR) detection methods. Genetic highlighted a clear separation between non-European European breeds, well north–south geographic cline within latter. Pearson correlation coefficients descriptive parameters obtained SW CR methods were higher than 0.9. A total 166 islands detected. CHI1, CHI11, CHI12 CHI18 chromosomes harboring highest number islands. genes annotated in linked various factors productive, reproductive, immune, environmental adaptation mechanisms. Notably, Montecristo feral showed despite level inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying species-specific pattern could provide clearer view mechanisms regulating genome modelling following anthropogenic combined interaction.

Язык: Английский

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Heterozygosity-Rich Regions in Canine Genome: Can They Serve as Indicators of Balancing Selection?

Animals, Год журнала: 2025, Номер 15(4), С. 612 - 612

Опубликована: Фев. 19, 2025

Compared to the negative effect of directional selection on genetic diversity, balancing acts oppositely and maintains variability across genome. This study aims articulate whether leads heterozygosity-rich region islands (HRRIs) forming in canine genome by investigating 1000 animals belonging 50 dog breeds via 153,733 autosomal SNPs. A consecutive SNP-based approach was used identify regions (HRRs). Signals studied were then assessed with Tajima's D statistics. total 72,062 HRRs an average length 324 kb detected be unevenly distributed 509 450 genomic classified as HRRIs signals, respectively. Although genome-wide distributions varied breeds, several found same locations multiple breeds. 109 both signals selection. Even though coordinates did not fully overlap all regions, may play a significant role maintaining diversity associated various cancer diseases, immune response, bone, skin, cartilage tissue development.

Язык: Английский

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Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Май 16, 2024

Abstract Background Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation these modern breeds via admixture events. However, their confusing genetic backgrounds include genomic footprint regulating complex traits, which is not conducive animal breeding. Results To better evaluate candidate regions under domestication indigenous chickens, we considered both runs homozygosity (ROHs) selective signatures 13 chickens. The Silkie feather presented highest heterozygosity, whereas inbreeding status ROH number found Luhua Short (< 1 Mb), principal type all A total 291 islands detected, QTLdb mapping results indicated that body weight carcass traits most important traits. An on chromosome 2 covering VSTM2A gene was detected 12 populations. Combined analysis with Tajima’s D index revealed 18 genes (e.g., , BBOX1 RYR2 ) selection covered by islands. Transcriptional showed specifically expressed heart muscle tissue, respectively. Conclusion Based genome-wide scanning for signatures, evaluated characteristics significant signatures. findings this study facilitated understanding diversity provided valuable insights chicken breeding conservation strategies.

Язык: Английский

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Identification of population‐informative markers from high‐density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds

Animal Genetics, Год журнала: 2024, Номер 55(2), С. 193 - 205

Опубликована: Янв. 8, 2024

Abstract Large genotyping datasets, obtained from high‐density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied Boruta algorithm, wrapper machine learning random forest on database 23 European pig (20 autochthonous three cosmopolitan breeds) with 70k SNP chip, pre‐select informative SNPs. sets these pre‐selected were then ranked based their mean decrease accuracy gene indexes. We evaluated efficiency subsets breed classification usefulness approach detect candidate genes affecting breed‐specific phenotypes relevant production traits that might differ breeds. The lowest overall error (2.3%) was reached subpanel including only 398 SNPs (ranked accuracy), no in seven using up 49 Several selected subpanels genomic regions which previous studies had identified signatures selection associated morphological distinguish analysed Therefore, even if not originally designed selection, results showed they could potentially useful purpose.

Язык: Английский

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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

Animals, Год журнала: 2022, Номер 12(18), С. 2365 - 2365

Опубликована: Сен. 10, 2022

Understanding the genetic composition of indigenous goats is essential to promote scientific conservation and sustainable utilization these breeds. The Jianchang Black (JC) goat, a Chinese native breed, solid black exhibits crude feed tolerance, but characterized by low growth rate small body size. Based on whole-genome sequencing data for 30 JC, 41 Jintang (JT), 40 Yunshang (YS) goats, 21 Bezoar ibexes, here, we investigated JC conducting analyses population structure, runs homozygosity (ROH), genomic inbreeding, selection signature. Our results revealed that JT YS showed close relationship with non-negligible amount gene flows were genetically distant from apart Bezoars. An average 2039 ROHs present in autosomal genome per individual. ROH-based inbreeding estimates generally moderate values ranging 0.134 0.264, mainly due rapid declines effective size during recent generations. annotated genes (e.g., IL2, IL7, KIT) overlapping ROH islands significantly enriched immune-related biological processes. Further, found 61 STIM1, MYO9A, KHDRBS2) under positive via three complementary approaches, which may underly adaptations local environmental conditions. findings provided references goats.

Язык: Английский

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Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

Frontiers in Genetics, Год журнала: 2023, Номер 14

Опубликована: Март 17, 2023

The erosion of genetic diversity limits long-term gain and impedes the sustainability livestock production. In South African (SA) dairy industry, major commercial breeds have been applying estimated breeding values (EBVs) and/or participating in Multiple Across Country Evaluations (MACE). transition to genomic (GEBVs) selection strategies requires monitoring inbreeding current genotyped animals, especially considering comparatively small population sizes global SA. This study aimed perform a homozygosity-based evaluation SA Ayrshire (AYR), Holstein (HST), Jersey (JER) cattle breeds. Three sources information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), 3) identified runs homozygosity (ROH) segments were used quantify related parameters. lowest completeness was HST reducing from value 0.990 0.186 generation depths one six. all breeds, 46.7% detected ROH between 4 megabase pairs (Mb) 8 Mb length. Two conserved homozygous haplotypes more than 70% JER on Bos taurus autosome (BTA) 7. breed displayed highest level across coefficients. mean (± standard deviation) pedigree-based coefficient (F PED ) ranged 0.051 (±0.020) AYR 0.062 (±0.027) JER, whereas SNP-based coefficients SNP 0.020 (HST) 0.190 ROH-based coefficients, segment coverage ), 0.053 (AYR) 0.085 (JER). Within-breed Spearman correlations genome-based estimates weak (AYR: 0.132 FPED F calculated &lt;4Mb size) moderate (HST: 0.584 ). Correlations strengthened as length category considered lengthened, suggesting dependency breed-specific depth. parameters studied proved useful investigating status reference populations implement three most prominent

Язык: Английский

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Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Animal Genetics, Год журнала: 2023, Номер 54(5), С. 591 - 605

Опубликована: Июнь 28, 2023

Analysis of genomic data is becoming more and common for the effective management livestock breeding programmes, even in case local populations. In this work, genome-wide Nero Siciliano pig breed were compared to that wild boar, Italian cosmopolitan breeds investigate its genetic structure, runs homozygosity (ROH) heterozygosity patterns. The has been reported have highest rate diversity among breeds, a variability comparable breeds. Analyses structure relationships underlined proximity an internal substructure probably linked different family lines. showed low value inbreeding estimated from ROH, index if lower than cosmopolitans. Four ROH islands three chromosomes (SSC8, SSC11, SSC14) one heterozygosity-rich region (SSC1) identified Siciliano, highlighting regions related productive QTL. Across SSC8 SSC14 with most islands, Mora Romagnola boar showing level autozygosity. Chromosomes SSC2, SSC6, SSC13 majority regions, mainly found which several genes associated health-related outlined results can help better identify profile order plan matings, maintain adequate exploit production system.

Язык: Английский

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Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Genes, Год журнала: 2024, Номер 15(3), С. 313 - 313

Опубликована: Фев. 28, 2024

Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits livestock. In this study, we analyzed resequencing data from 10 local goat breeds Yunnan province China five additional populations obtained a public database. The ROH analysis revealed 21,029 across 15 populations, an average length 1.27 Mb, pattern ROH, assessment coefficient indicating diversity varying levels inbreeding. iHS (integrated haplotype score) was analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) regions, related economic such as coat color weight variation. These candidate include OCA2 (OCA2 melanosomal transmembrane protein) MLPH (melanophilin) color, EPHA6 (EPH receptor A6) involved litter size, CDKAL1 (CDK5 regulatory subunit protein 1 like 1) POMC (proopiomelanocortin) linked variation some putative high-altitude adaptability immune. This study uncovers within province, China. identification provides actionable insights for utilization conservation efforts.

Язык: Английский

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Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation

Journal of Applied Genetics, Год журнала: 2024, Номер 65(2), С. 383 - 394

Опубликована: Март 25, 2024

Язык: Английский

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Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity

animal, Год журнала: 2024, Номер 18(5), С. 101142 - 101142

Опубликована: Март 25, 2024

The analysis of livestock heterozygosity is less common compared to the study homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, was conducted investigate characterize patterns four beef cattle breeds, which included two cosmopolitan breeds (Limousine Charolaise) local (Sarda Sardo Bruna). Our identified regions with a high degree using consecutive runs approach, Tajima D test, nucleotide diversity estimation, Hardy Weinberg equilibrium test. These exhibited recurrent peaks were consistently found on specific chromosomes across all specifically autosomes 15, 16, 20, 23. Bruna also displayed 2 21, respectively. Thirty-five top shared by more than 25% populations identified. genomic fragments encompassed 18 genes, are directly linked male fertility, while associated lactation. Two other genes play roles in response. detected region related growth carcass Limousine breed. heterozygosity-rich revealed particular segments genome various traits. It appears that balancing selection occurring within examined unexpectedly, they breeds. hold potential applications breeding programs conservation studies phenotypes these heterozygous genotypes. In addition, Nucleotide diversity, test confirmed presence analysis.

Язык: Английский

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