Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping DOI Creative Commons
Vera Mukhina, G. R. Svishcheva, В. Н. Воронкова

et al.

Animals, Journal Year: 2022, Volume and Issue: 12(3), P. 221 - 221

Published: Jan. 18, 2022

Mongolian goats are of great interest for studying ancient migration routes and domestication, also represent a good model adaptability to harsh environments. Recent climatic disasters uncontrolled massive breeding endangered the valuable genetic resources raised question their conservation status. Meanwhile, have never been studied on genomic scale. We used Illumina Goat SNP50 estimate risks in five goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, Dorgon) explored phylogenic relationships among these populations context other breeds. Various clustering methods showed that grouped with Asian were especially close some neighboring Russian Chinese The Buural breed lowest estimates inbreeding exhibited shortest distances within breeds, especially, Red GS. These three formed single core group, being weakly differentiated from each other. Among them, GS displayed obvious signs probably resulted artificial selection pressure. Dorgon Erchim stand apart according various types analyses, bear unique features pointing different histories or distinct origins All strong decline effective population size. However, none them met formal criteria be considered as SNP data obtained this study improved knowledge could future management decisions order preserve diversity.

Language: Английский

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

Z.X. An,

Liangyu Shi, Guanyu Hou

et al.

animal, Journal Year: 2024, Volume and Issue: 18(6), P. 101147 - 101147

Published: March 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.

Language: Английский

Citations

5
Combined approaches to reveal genes associated with litter size in Yunshang black goats DOI
Lin Tao, Xiaoyun He,

Yanting Jiang

et al.

Animal Genetics, Journal Year: 2020, Volume and Issue: 51(6), P. 924 - 934

Published: Sept. 28, 2020

Summary Intensive artificial selection has been imposed in Yunshang black goats, the first specialist mutton goat breed China, with a breeding object of improving reproductive performance, which contributed to reshaping genome including characterization SNP, ROH and haplotype. However, variation ability exists present population. A WGS was implemented two subpopulations (polytocous group, PG, monotocous MG) evident differences litter size. Following mapping reference genome, SNP calling pruning, three approaches – GWAS, analysis detection signatures were employed unveil candidate genes responsible for Consequently, 12 containing OSBPL8 minimum P ‐value uncovered by GWAS. Differences observed pattern between that shared similar low inbreeding coefficients. Two hotspots corresponding emerged from pool association analysis. Based on n S L statistic, 15 61 promising disclosed under MG PG respectively. Of them, some participate ovarian function ( PPP2R5C , CDC25A ESR1 RPS26 SERPINB s), seasonal reproduction DIO3 BTG1 CRYM ) metabolism SLC39A5 s). Our study pinpointed novel influencing size, provided comprehensive insight into genetic makeup size might facilitate selective goats.

Language: Английский

Citations

35
Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds DOI Creative Commons
Guixin Li, Jianhong Tang, Jinyan Huang

et al.

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

Citations

22
Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep DOI Open Access
Zully Ramos, Dorian J. Garrick, H. T. Blair

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(1), P. 167 - 167

Published: Jan. 7, 2023

The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live (LW), body condition score (BCS), pregnancy rate (PR) lambing potential (LP) Uruguayan Merino sheep. Phenotypic records approximately 2000 mixed-age ewes were obtained from a nucleus flock. Genome-wide association studies performed utilizing single-step Bayesian analysis. For wool traits, total 35 windows surpassed significance threshold (PVE ≥ 0.25%). proportion additive genetic variance explained by those 4.85 9.06% for FD CFW, respectively. There 42 significantly LWM, which collectively 43.2% variance. BCS, 22 relevant accounted more than 40% variance, whereas reproduction 53 (24 29 PR LP, respectively) reached suggestive 0.25% PVE. Within top 10 each trait, we identified several showing associations (e.g., IGF-1, TGFB2R, PRKCA), CAST, LAP3, MED28, HERC6), CDH10, TMC2, SIRPA, CPXM1) or traits ADCY1, LEPR, GHR, LPAR2) ewes.

Language: Английский

Citations

12
Discovering novel clues of natural selection on four worldwide goat breeds DOI Creative Commons
Arianna Manunza, Johanna Ramírez-Díaz,

Brian L Sayre

et al.

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

Citations

12
Screening Indels from the whole genome to identify the candidates and their association with economic traits in several goat breeds DOI
Ahmed A. Saleh, Lei Xue, Yongju Zhao

et al.

Functional & Integrative Genomics, Journal Year: 2023, Volume and Issue: 23(1)

Published: Feb. 9, 2023

Language: Английский

Citations

10
Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat (Capra hircus) Using Whole-Genome Resequencing DOI Open Access
Xingqiang Fang, Bowen Gu, Meixi Chen

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(10), P. 1960 - 1960

Published: Oct. 19, 2023

Reproductive traits are the basic economic of goats and important indicators in goat breeding. In this study, Dazu black (DBGs; n = 150), an Chinese local breed with excellent reproductive performance, were used to screen for variation loci genes traits. Through genome-wide association studies (GWAS), 18 SNPs found be associated kidding (average litter size, average size first three parity, six parity), 10 udder (udder depth, teat diameter, length, supernumerary teat). After gene annotation combination relevant references, candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, FGFR2, traits, while ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, ENSCHIG00000026285 size. These can provide useful biological information improvement goats.

Language: Английский

Citations

10
Genomic insights into selection signatures and candidate genes for milk production traits in buffalo population DOI Creative Commons
Tingxian Deng,

X Y,

Anqi Duan

et al.

animal, Journal Year: 2025, Volume and Issue: unknown, P. 101427 - 101427

Published: Jan. 1, 2025

Language: Английский

Citations

0
Genome-wide landscape of genetic diversity, runs of homozygosity, and runs of heterozygosity in five Alpine and Mediterranean goat breeds DOI Creative Commons
Sara Pegolo, Vittoria Bisutti, Lúcio Flávio Macêdo Mota

et al.

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 3, 2025

Abstract Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience productivity, especially as we are facing important climate agriculture challenges. To this aim genomic architecture 480 goats belonging five (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared Sardinia Island were genotyped evaluated find molecular basis traits. Inbreeding, runs homozygosity (ROH) heterozygosity (ROHet) identified. Finally, candidate genes ROH ROHet regions explored through pathway analysis assess role. Results In total, detected 10,341 SAA genome, 11,063 CAM 12,250 MUR 8,939 MAL 18,441 SAR genome. Moreover, identified 4,087 for SAA, 3,360 CAM, 2,927 MUR, 3,701 MAL, 3,576 SAR, with having highest coefficient. Interestingly, when computing inbreeding coefficient using homozygous segment ( F ), showed lowest value while one, suggesting need improve selecting strategies preserve diversity within population. Among most significant genes, several ones linked different physiological functions, such milk production (e.g., DGAT1 , B4GALT1 immunity GABARAP GPS2 ) adaptation environment GJA3 GJB2 GJB6 ). Conclusions This study highlighted among goat breeds. The high levels some might indicate lack variation, which negatively impact animal Conversely, diversity, beneficial breed health resilience. Therefore, these findings could managing preserving diversity.

Language: Английский

Citations

0
Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds DOI Open Access
Rui Ma, Jiaxin Liu, Xiao Ma

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(3), P. 316 - 316

Published: March 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.

Language: Английский

Citations

0