Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

animal, Год журнала: 2024, Номер 18(6), С. 101147 - 101147

Опубликована: Март 28, 2024

Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed south China's tropical island province Hainan, possess distinctive traits such hair, moderate growth rate, good meat quality, small body size. However, they exhibit exceptional resilience to rough feeding conditions, high-quality meat, show remarkable resistance stress heat. In this study, we resequenced whole genome goats study economic basis these leveraged whole-genome sequencing data from 33 analyze single nucleotide polymorphism(SNP) density, Runs homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) selection characteristics. Our findings revealed that harbor substantial degree variation, with total 23 608 983 polymorphisms (SNPs) identified. ROHs identified 53 710 segments, predominantly composed short fragments, inbreeding events mainly occurring in ancient ancestors, estimates based on ROH typically values ranging 0.107 0.186. This primarily attributed significant declines over recent generations. Moreover, 921 candidate genes within intersection region iHS. Several are associated immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 LEPR), quality (ACOX1, SSTR1, CAMK2B, PPP2CA PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 CDK19), (TLR2, IFI44, ENPP1, STK3 NFATC1). The presence may be adaptation local climate conditions. insights gained provide valuable references solid foundation preservation, breeding, utilization resources.

Язык: Английский

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Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken

Animals, Год журнала: 2023, Номер 13(10), С. 1645 - 1645

Опубликована: Май 15, 2023

Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management conservation, present study, we systematically investigated characteristics genetic variations runs homozygosity (ROH) along genome using re-sequenced whole-genome sequencing data from 235 chickens. A total 16,511,769 single nucleotide polymorphisms (SNPs) 53,506 ROH segments were identified all individuals, chicken mainly composed short (0-1 megabases (Mb)). On average, 5.664% was located across samples. According several parameters, diversity relatively high. The average inbreeding coefficient chickens based on FHOM, FGRM, FROH 0.060 ± 0.014, 0.561 0.020, 0.0566 0.01, respectively. 19 islands containing 393 genes detected 9 different autosomes. Some these putatively associated with growth performance (AMY1a), stress resistance (THEMIS2, PIK3C2B), traits (MBTPS1, DLK1, EPS8L2), fat deposition (LANCL2, PPARγ). These findings provide better understanding degree hereditary basis shaped under selection. results valuable future breeding, utilization other breeds.

Язык: Английский

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Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs

Animals, Год журнала: 2024, Номер 14(2), С. 201 - 201

Опубликована: Янв. 8, 2024

Tunchang pigs are an indigenous pig population in China known for their high tolerance to roughage, delicious meat, and fecundity. However, the number of has been declining due influence commercial breeds African swine fever, which could potentially lead inbreeding. To assess inbreeding level genetic basis important traits pigs, our research investigated patterns "runs homozygosity" (ROHs) using whole genome resequencing data from 32 pigs. The study aimed determine length, number, coverage, distribution model ROHs as well genomic regions with ROH frequencies. results revealed that a total 20,499,374 single-nucleotide polymorphisms (SNPs) 1953 fragments were recognized individuals. predominantly short, ranging 0.5 1 megabases (Mb) length. Furthermore, coverage varied across chromosomes, chromosome 3 having highest 11 lowest coverage. diversity was found be relatively based on values

Язык: Английский

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Conservation and Selection of Genes Related to Environmental Adaptation in Native Small Ruminant Breeds: A Review

Ruminants, Год журнала: 2022, Номер 2(2), С. 255 - 270

Опубликована: Июнь 8, 2022

Environmental stressors have, over generations, influenced the morphology, anatomy, behaviour, physiology, and genetic structure of small ruminants. The widespread dispersal ruminants vast geographical areas occurred along with human migration, thereby promoting adaptative process to different environmental conditions mainly through natural selection. Ongoing global warming prompted scientific efforts deepen knowledge understanding adaptation traits in Compared other ruminants, sheep goats seem have a better ability stressors, as evident by their presence across geographic on level. Adaptation specific environment leads variations precise genomic regions, allowing for identification selection animals high capacity stressors. Rapid development sequencing technologies, together bioinformatics tools, make it possible analyse regions related adaptation. Hence, aims this review were (i) outline main steps evolution goat species, (ii) summarise candidate genes adaptation, (iii) evaluate both conservation possibilities these native ruminant breeds future challenges face warming.

Язык: Английский

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Genomic regions underlying positive selection in local, Alpine cattle breeds

Animal Genetics, Год журнала: 2023, Номер 54(3), С. 239 - 253

Опубликована: Фев. 3, 2023

We used genome-wide SNP data from 18 local cattle breeds six countries of the Alpine region to characterize population structure and identify genomic regions underlying positive selection. The geographically close Evolèner, Eringer, Valdostana Pezzata Nera, Castana were found differ all other breeds. In addition, three breeds, Simmental, Original Braunvieh Switzerland Pinzgauer Austria built separate clusters. Of studied, intra-alpine Swiss breed Evolèner had highest average inbreeding based on runs homozygosity (FROH ) relationship within breed. contrast, Slovenian Cika lowest selection signatures chromosome 6 near known genes such as KIT LCORL explaining variation in coat color body size cattle. most prominent similar regardless marker density set. using available high-density 14 we identified 47 genome ROH islands. proportion homozygous animals was higher studied than Holstein Brown cattle, two important commercial region. report islands related thermoregulation, color, production, stature. results this study serve a basis for search causal variants adaptation alpine environment specific characteristics selected during evolution

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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Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

animal, Год журнала: 2024, Номер 18(5), С. 101159 - 101159

Опубликована: Апрель 16, 2024

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed diversity. This study assesses inbreeding levels via pedigree genomic approaches analyzes old recent using runs of homozygosity (ROH), selection signals Alpine Grey cattle. Pedigree from 165 575 individuals, analyzed with INBUPGF90 software, computed coefficients. Genomic-based coefficients derived PLINK v1.9. or DetectRUNS R package analyses 1 180 individuals' genotypes. Common SNPs within ROH pinpointed regions, aggregating "ROH islands" indicative pressure. Overlaps USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between coefficients, most estimators having higher (>0.8) correlation values. averaged 0.04 <8 Mb segments, 0.03 >16 segments; >90% ROHs were Mb, indicating ancient prevalence. Recent proved less detrimental than cosmopolitan breeds. Two major islands on chromosomes 6 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), fertility (EIF4EBP3, SRA1). underscores the need for detailed understand characteristics historical changes local breeds like insights, especially ROH, facilitated overcoming limitations, illuminating Our findings reveal inbreeding's enduring impact potential selective sweeps, elucidating traits

Язык: Английский

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Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds

Genes, Год журнала: 2025, Номер 16(3), С. 316 - 316

Опубликована: Март 7, 2025

Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for long-term sustainability of animal husbandry. However, extent has not been fully understood sheep on a global scale. Methods: Here, we analyzed high-depth genomes 210 from 20 worldwide breeds to identify pattern distribution genome-wide runs homozygosity (ROH) detect candidate selected genes ROH islands agronomic phenotypic traits. Results: Leveraging whole-genome sequencing data, found large number short (e.g., <1.0 Mb) all observed overall higher values statistics coefficient European than Asian Dorper sheep. We identified some well-known CAMK4, HOXA gene family, ALOX12, FGF11, MTOR) 40 novel KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, PAX1) that are functionally associated with fecundity, body size, wool-related traits Based genes, revealed different genetic bases fecundity Conclusions: This study improves resolution detection provides new insights into genomic trait architecture as well useful markers future breeding practice.

Язык: Английский

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Genome-wide detection of runs of homozygosity in Ding’an pigs revealed candidate genes relating to meat quality traits

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Март 31, 2025

Ding'an (DA) pig, a native Chinese breed, is renowned for its excellent meat quality, disease resistance, high reproductive performance, and adaptability. Its quality traits hold significant economic value. However, conservation population has been declining due to the impact of commercialized breeds African swine fever, which not conducive development utilization. This study utilized whole-genome resequencing data from 15 DA pigs reveal their genetic characteristics current resource status. We analyzed length, number, distribution patterns Runs Homozygosity (ROH) in pigs, as well high-frequency ROH regions. The results identified 23,208,098 single nucleotide polymorphisms (SNPs), 4,497,242 insertion deletion (InDels), 13,622 copy number variation (CNVs), 399,934 structure (SVs). Further analysis revealed relatively diversity low inbreeding levels pigs. Through functional gene enrichment regions, we multiple candidate genes associated with specific including (ANKRD1, CPNE5, MYOM1), fat deposition (OBSCN, MAPK4, PNPLA1, PACSIN1, GRM4), skeletal muscle (LRPPRC, WNT9A). conducted sequencing on revealing within population. deposition, development. These findings only enhance our understanding mechanisms underlying unique but also provide valuable insights practical applications. Specifically, genomic regions can guide efforts maintain mitigate risks. Meanwhile, these be integrated into breeding programs improve other economically important traits, thereby supporting sustainable utilization

Язык: Английский

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Visualization of Runs of Homozygosity and Classification Using Convolutional Neural Networks

Biology, Год журнала: 2025, Номер 14(4), С. 426 - 426

Опубликована: Апрель 16, 2025

Runs of homozygosity (ROH) are key elements the genetic structure populations, reflecting inbreeding levels, selection history, and potential associations with phenotypic traits. This study proposes a novel approach to ROH analysis through visualization classification using convolutional neural networks (CNNs). Genetic data from Large White (n = 568) Duroc 600) pigs were used construct maps, where each homozygous segment was classified by length visualized as color-coded image. The conducted in two stages: (1) animals breed based on maps (2) identification presence or absence trait (limb defects). Genotyping performed GeneSeek® GGP SNP80x1_XT chip (Illumina Inc., San Diego, CA, USA), segments identified software tool PLINK v1.9. To visualize individual we utilized modified function HandyCNV package. results showed that CNN model achieved 100% accuracy, sensitivity, specificity classifying pig breeds maps. When analyzing binary (presence limb defects), demonstrated an accuracy 78.57%. Despite moderate predicting trait, high negative predictive value (84.62%) indicates model’s reliability identifying healthy animals. method can be applied not only animal breeding research but also medicine association between hereditary diseases. Future plans include expanding other types developing mechanisms improve interpretability deep learning models.

Язык: Английский

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