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

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: July 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.

Language: Английский

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Discovering novel clues of natural selection on four worldwide goat breeds

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Feb. 6, 2023

Abstract In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to fixation of specific alleles traits. This led formation and evolution many different breeds specialised raised a particular purpose. However, despite intensity selection, natural continues acting, possibly leaving more diluted contribution over time, whose traces may be difficult capture. order explore footprints as response environmental adaptation, we analysed total 993 goats from four transboundary (Angora, Boer, Nubian Saanen) genotyped with SNP chip 50 K using outlier detection, runs homozygosity haplotype-based detection methods. Our results showed that all methods identified on chromosome 6 (from 30 49 Mb) two populations sampled in Egypt. Angora Saanen detected selective sweeps HapFLK, 21 52 55 25 1 5 respectively. The analysis some hotspots breeds. overall investigation selected regions combining approaches gene ontology exploration revealed both novel well-known loci related especially heat stress. findings can help better understand balance between pressures commercial providing new insights molecular mechanisms adaptation.

Language: Английский

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Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 2, 2024

Abstract Background Jianli pig, a renowned indigenous breed in China, has the characteristics of two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding genetic diversity, population structure genomic regions under selection pig. On other hand, mechanism TEB color remained largely unknown. Results In this study, whole genome resequencing 30 pigs within context 153 individuals representing 13 diverse breeds was performed. The analysis revealed that have close relationships with Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected runs homozygosity) implied relatively high level diversity and, low inbreeding coefficient compared pigs. We used Fst XP-EHH to detect signatures Asian wild boar. A total 451 candidate genes influencing quality ( CREBBP , ADCY9 EEPD1 HDAC9 ), reproduction ESR1 FANCA EDNRB MITF MC1R were detected by gene annotation analysis. Finally, fine-map region for phenotype pigs, we performed three signature between no-TEB breeds. current further confirmed found Chinese including Jinhua haplotype harboring 25 SNPs may promote formation color. Further ATAC-seq luciferase reporter assays these suggest 25-SNPs causative mutation regulates altering enhancer function. Conclusion Our results advanced understanding behind artificial selection, provided resources protection breeding improvement

Language: Английский

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Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds

Poultry Science, Journal Year: 2020, Volume and Issue: 100(2), P. 441 - 451

Published: Nov. 16, 2020

The aim of this study was to conduct a genome-wide comparative analysis 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori Lonigo [PML], Polverara Bianca, Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Maculata), all under conservation plan, understand their genetic diversity population structure. A total 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. levels highest lowest in PML PPP, respectively. results genomic inbreeding based on runs homozygosity (ROH; FROH) showed marked differences among ranged from 0.161 (PML) 0.478 (PPP). Furthermore, breeds, short ROH (<4 Mb length) more frequent than long segments. Patterns differentiation, model-based clustering, neighbor networks that most formed nonoverlapping clusters clearly separate populations. 2 shared similar background differentiation comparison with purebred lines; populations separated groups. PPP closer group broiler lines (BRSA, BRSB, BRDA, BRDB). Six regions are presented as hotspots autozygosity candidate genes involved multiple morphological phenotypes breast muscle, muscle dry matter content, body weight. This is first exhaustive these chickens Veneto region. We conclude have conserved authentic patterns. significant importance because they will help design implement strategies. In fact, may also positive impacts economy, niche traditional markets, offering source high-quality products consumers. context, information play crucial role management breeds.

Language: Английский

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