Whole‐genome resequencing reveals diversity and selective signals in the Wuxue goat

Animal Genetics, Journal Year: 2024, Volume and Issue: 55(4), P. 575 - 587

Published: May 28, 2024

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline the diversity of livestock has occurred worldwide. This is pronounced developing countries, where management these insufficient. In current study, we performed whole genome sequencing 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, utilized published genomes 131 samples representing different goat breeds from various regions China. We investigated compared selection signatures WX Whole analysis GW populations yielded 120 425 063 SNPs, which resided primarily intergenic intron regions. Population structure revealed that exhibited resemblance to GW, Chengdu Brown, Jintang Black significant differentiation other breeds. addition, three methods (nucleotide diversity, linkage disequilibrium decay, runs homozygosity) showed moderate used nucleotide composite likelihood ratio identify within-breed positive A total 369 genes were identified using both detection methods, including related reproduction (GRID2, ZNF276, TCF25, SPIRE2), growth (HMGA2 GJA3), immunity (IRF3 SRSF3). Overall, this study explored adaptability goats, shedding light on their richness potential thrive challenges posed by climatic changes diseases. Further investigations warranted harness insights enhance more efficient sustainable breeding initiatives.

Language: Английский

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Genetic diversity and population structure of Pacific abalone (Haliotis discus hannai) using SNP genotyping data

Aquaculture, Journal Year: 2024, Volume and Issue: 593, P. 741335 - 741335

Published: July 14, 2024

Language: Английский

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West African cattle share non-random heterozygosity-rich region islands enriched on adaptation-related genes despite their different origins

Frontiers in Animal Science, Journal Year: 2024, Volume and Issue: 5

Published: Nov. 19, 2024

Methods Up to 237 individuals belonging 10 different taurine ( Bos taurus ), zebu B. indicus and × sanga cattle populations sampled in Benin, Burkina Faso, Niger were typed using the BovineHD BeadChip of Illumina ascertain patterns importance heterozygosity-rich regions (HRRs) West African cattle. To account for among-population gene flow, further classified into three groups (Qtaurine, Qzebu, admixed) according maximum likelihood estimates individual ancestries q^ ) obtained program Admixture v1.23. Results discussion The 967 HRRs identified on 27 out 29 bovine chromosomes 231 summarized 103 HRR islands, covering 40.7 Mb genome. Only islands at least 10% animals or type admixture class considered relevant characterize genomic background. one taurine- zebu-specific, respectively. Most (14) present despite which they (waHRR), suggesting that can give advantages adaptation harsh environments. A total 202 potential candidate genes 14 waHRR islands. them belonged families coding zinc finger, protocadherin, adhesion G protein-coupled receptors, solute carrier, arachidonate lipoxygenase proteins, involved immune response, with a putative role adaptation. Furthermore, waHRRs also enriched 18 11 olfactory receptors pregnancy-associated glycoproteins, respectively, giving additional support suggested adaptive ability Our research new areas be targeted ability.

Language: Английский

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Transcriptomic profiling identifies differentially expressed genes and related pathways associated with wound healing and cuproptosis-related genes in Ganxi goats

Frontiers in Veterinary Science, Journal Year: 2023, Volume and Issue: 10

Published: May 3, 2023

Introduction Wound healing is very important for the maintenance of immune barrier integrity, which has attracted wide attention in past 10 years. However, no studies on regulation cuproptosis wound have been reported. Methods In this study, skin injury model was constructed Gnxi goats, and function, regulatory network hub genes before after were comprehensively analyzed by transcriptomics. Results The results showed that there 1,438 differentially expressed (DEGs), up-regulated 545 down-regulated 893, detected comparing day 0 5 posttraumatic skin. Based GO-KEGG analysis, DEGs tended to be enriched lysosome, phagosome, leukocyte transendothelial migration pathways, while significantly adrenergic signaling cardiomyocytes calcium pathway. There 166 overlapped (DE-CUGs) between cuproptosis-related genes, with 72 DE-CUGs 94 DE-CUGs. GOKEGG analysis ferroptosis, lysosome Apelin pathway tyrosine metabolism pathways. By constructing analyzing protein–protein interaction (PPI) networks DE-CUGs, (ENSCHIG00000020079, PLK1, AURKA, ASPM, CENPE, KIF20A, CCNB2, KIF2C, PRC1 KIF4A) (MMP2, TIMP1, MMP9, MMP14, TIMP3, MMP1, EDN1, GCAT, SARDH, DCT) obtained, respectively. Discussion This study revealed pathways Ganxi identified correlation first time, found MMP2, EDN1 core associated. transcriptome data goats expanded research direction cuproptosis.

Language: Английский

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Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle

Journal of Animal Science, Journal Year: 2024, Volume and Issue: 102

Published: Jan. 1, 2024

Abstract Runs of homozygosity (ROHom) are contiguous stretches homozygous regions the genome. In contrast, runs heterozygosity (ROHet) heterozygosity-rich regions. The detection these two types genomic (ROHom and ROHet) is influenced by parameters involved in their identification number available single-nucleotide polymorphisms (SNPs). present study aimed to test effect chip density detecting ROHom ROHet Italian Simmental cattle breed. A sample 897 animals were genotyped at low (50k SNP; 397 individuals), medium (140k 348 or high (800k 152 individuals). per animal (nROHom nROHet, respectively) average length calculated. shared more than one times a particular SNP was inside run also computed (SNPROHom SNPROHet). As increased, nROHom whereas decreased. nROHet decreased increased as increased. most repeated harbored no genes, four genes (SNRPN, SNURF, UBE3A, ATP10A) previously associated with reproductive traits found. Across 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, 37 (located BTA21) exceeded 99th percentile distribution SNPROHom SNPROHet, respectively. region BTA6 mapped SLIT2, PACRGL, KCNIP4 19 18 BTA16 BTA21, Interestingly, found through analysis reported be related health, reproduction, fitness traits. results confirm that reliable when increases, trend seems opposite. Genes quantitative trait loci (QTL) highlighted can due balancing selection, thus traits, mainly production strengthened usefulness analyzing genomes livestock biological meaning.

Language: Английский

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Examination of homozygosity runs and selection signatures in native goat breeds of Henan, China

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

Published: Dec. 6, 2024

Language: Английский

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Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Annals of Animal Science, Journal Year: 2023, Volume and Issue: 24(2), P. 431 - 444

Published: Oct. 21, 2023

Abstract This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population Holstein cattle on the basis two microarrays medium (50k; 2163 animals; 54 609 SNPs) high single nucleotide polymorphism (SNP) density (HD; 600 777 692 SNPs). To assess inbreeding values cattle, ROH-based genomic coefficient (F ROH ) was calculated. The comparison SNP panels suggested that F above 4 Mb should be considered for densities as relatively reliable measure inbreeding. Moreover, hotspots coldspots were identified compared between HD 50k carefully examined association with production functional traits. obtained results pinpointed regions presumably under selection pressure cattle. overlapped number genes, including GHR , GBF1 SUMF1 CCL28 NIM1K U6 BTRC FABP1, many which are involved important characteristics. We also found some panel not detected panel, mainly because insufficient certain regions. suggests using medium-density might best choice when precise identification patterns is main goal. In summary, this work, we confirmed high-density to allows more patterns, especially case short could associated ancestral

Language: Английский

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Genetic diversity and runs of homozygosity (ROH): A portrait of the quantitative academic publication dynamic and scientific metadata

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 10, 2024

Abstract Background Autozygosity is the homozygous state of identical-by-descent (IBD) alleles, which can result from several phenomena. The increase in inbreeding (F) leads to different negative effects such as a reduction genetic variance, with individual performance (inbreeding depression) and lower population viability. Nowadays, among alternative methods estimate inbreeding, F estimated Run Homozygosity (FROH) considered most powerful. This study aimed provide systematic review comprehensive understanding structure dynamics genomic diversity impact ROH studies over last decade, highlighting directions opportunities for future research. Results 406 publications were identified on WoS core collection applied bibliometric analysis available R environment. revealed an increased number per year. China, Italy, United States are countries that published topic, main contributions journals Animals Frontiers Genetics. highlights growing interest functional ROHs driven by computational tools capable characterizing these regions. Noteworthy PLINK software detectRUNS package, utilizing sliding window methodology SNP genome. Beyond global crisis loss, challenges encompass ecological issues, habitat fragmentation, isolated populations, well availability variation species domesticated humans, forms foundation our food supply. Conclusion A progress research breeds homozygosity (ROH) diversity, advancement technology international collaboration. Asia, America Europe lead knowledge production. Advances like mean quest more accurate analysis. Emerging topics migration correlation indicate increasing focus standards. Challenges include refining analytical techniques exploring regions high heterozygosity, promising directions.

Language: Английский

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Genomic analysis revealed hotspots of genetic adaptation and risk of disappearance in the Brazilian goat populations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 4, 2024

Abstract We accessed a 50K Illumina SNP genotype dataset from two important goat breeds of the Brazilian semi- arid region to analyze abundance and length runs homozygosity (ROH). This analysis aims elucidate importance adaptation history in genome populations measure genomic inbreeding. Heterozygosity-rich regions (HRR) or high genetic variability provide clues about how diversity might be associated with increased fitness, avoiding deleterious homozygous alleles. Overall, 22,872 ROH were identified. The average number per individual ranged 74.73 (Anglo-Nubian commercial breed) 173.85 (Marota landrace). Analysis distribution according their size showed that, for both breeds, majority short (<2.0 Mb) category (65.6%). ROH-based inbreeding (F ) revealed low levels Anglo-Nubian (0.0627) Marota (0.1419), likely due reduction effective population over generations landrace. defined islands HRR identified common goat, where genes related various traits such as embryonic development, body growth, lipid homeostasis, brain functions are located. These results indicate that many have therefore been under selective pressure these reared different purposes.

Language: Английский

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Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds

Genes & Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 31, 2024

Language: Английский

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