A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Genome Research, Journal Year: 2023, Volume and Issue: 33(3), P. 463 - 477

Published: March 1, 2023

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence functions in domestic animals largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, 14,707 multiallelic with precise breakpoints discovered. The SV spectrum is characterized by an excess derived insertions compared deletions (94,422 vs. 33,571), suggesting recent active LINE expansions sheep. Nearly half the SVs display low moderate linkage disequilibrium surrounding single-nucleotide polymorphisms (SNPs) most cannot be tagged SNP probes widely used ovine 50K chip. We identified 865 population-stratified including 122 possibly domestication process among 690 worldwide. novel 168-bp insertion 5' untranslated region (5' UTR)

Language: Английский

---

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

---

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 6, 2023

The dairy goat is one of the earliest livestock species, which plays an important role in economic development, especially for developing countries. With development agricultural civilization, goats have been widely distributed across world. However, few studies conducted on specific characteristics goat. In this study, we collected whole-genome data 89 individuals by sequencing 48 and employing 41 publicly available goats, including five breeds (Saanen, Nubian, Alpine, Toggenburg, Guanzhong goat; n = 24, 15, 11, 6, 6), three (Guishan goat, Longlin Yunshang Black 6). Through compared genomes non-dairy to analyze genetic diversity selection results show that eight could be divided into subgroups European, African, Chinese indigenous populations, also found Australian Alpine had highest linkage disequilibrium, lowest level nucleotide diversity, a higher inbreeding coefficient, indicating they were strongly artificially selected. addition, identified several candidate genes related specificity particularly associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction (TSHR, TSHB, PTGS2, ESR2), immunity (JAK1, POU2F2, LRRC66). Our provide not only insights evolutionary history breed but valuable information implementation improvement cross breeding program.

Language: Английский

---

Identification of genomic characteristics and selective signals in Guizhou black goat

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

Published: Feb. 9, 2024

Abstract Background Guizhou black goat is one of the indigenous breeds in southwest region Guizhou, China, which an ordinary for mutton production. They are characterized by moderate body size, coat, favorite meat quality with tender and lower odor, tolerance cold crude feed. However, little known about genetic characteristics or variations underlying their important economic traits. Results Here, we resequenced whole genome from 30 unrelated individuals breeding five core farms. A total 9,835,610 SNPs were detected, 2,178,818 identified specifically this breed. The population structure analysis revealed that shared a common ancestry Shaanbei white cashmere (0.146), Yunshang (0.103), Iran (0.054), Moroccan (0.002). showed relatively higher diversity level linkage disequilibrium than other seven nucleotide diversity, decay, runs homozygosity. Based on F ST θ π values, 645, 813, 804 selected regions between goat, goats. Combined results XP-EHH, there 286, 322, 359 candidate genes, respectively. Functional annotation these genes potentially responsible immune response (e.g., CD28 , CD274 IL1A TLR2 SLC25A31 ), humility-cold resistance HBEGF SOSTDC1 ARNT COL4A1/2 EP300 traits CHUK GAB2 PLAAT3 growth DPYD CSF1 fertility METTL15 MEI1 visual function PANK2 NMNAT2 ) goat. Conclusion Our indicated had high genomic low genome. Selection signatures detected mainly related to development, quality, reproduction, disease resistance, humidity-cold These would provide basis further resource protection improvement very local

Language: Английский

---

Trajectory of livestock genomics in South Asia: A comprehensive review

Gene, Journal Year: 2022, Volume and Issue: 843, P. 146808 - 146808

Published: Aug. 13, 2022

Language: Английский

---

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 20, 2024

Abstract A complete goat ( Capra hircus ) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats related species. Here, we assemble a telomere-to-telomere (T2T) gap-free (2.86 Gb) from cashmere (T2T-goat1.0), including Y chromosome 20.96 Mb. With base accuracy >99.999%, T2T-goat1.0 corrects numerous genome-wide structural errors previous assemblies adds 288.5 Mb previously unresolved regions 446 newly assembled genes to the genome. We sequence genomes five representative breeds for PacBio reads, use as identify total 63,417 variations (SVs) with up 4711 (7.42%) regions. was applied population global wild domestic goats, which revealed 32,419 SVs 25,397,794 SNPs, 870 545,026 SNPs Also, our reveal set selective variants associated (e.g., NKG2D ABCC4 traits ASIP ).

Language: Английский

---

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Animals, Journal Year: 2024, Volume and Issue: 14(2), P. 307 - 307

Published: Jan. 18, 2024

Goats belong to a group of animals called small ruminants and are critical sources livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity evolutionary processes that shape genomes functional genes/genomic regions. In this study, we exploited whole-genome data set analyze the genetic diversity, population structure selection signatures 44 individuals belonging 5 Ethiopian populations: 12 Aberegalle (AB), Afar (AF), 11 Begait (BG), Central highlands (CH) Meafure (MR) goats. Our results revealed highest in BG compared other populations. The pairwise differentiation (FST) among populations varied ranged 0.011 0.182, with closest value (0.003) observed between AB CH goats distant correlation (FST = 0.182) goats, indicating low moderate differentiation. Phylogenetic tree, ADMIXTURE principal component analyses classification five breeds accordance their geographic distribution. We also found three top genomic regions were detected under on chromosomes 2, 13. Moreover, study identified different candidate genes related milk characteristics (GLYCAM1 SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO MYOT) adaptive immune response (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 DEFB119). conclusion, could be helpful understanding scanning these important indigenous future improvement and/or as an intervention mechanism.

Language: Английский

---

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

Forensic Science International, Journal Year: 2025, Volume and Issue: 367, P. 112370 - 112370

Published: Jan. 12, 2025

Language: Английский

---

Whole-genome variants resource of 298 Saanen dairy goats

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: March 29, 2025

The Saanen breeds are often used as terminal sires for hybridization and play an important role in the global dairy food industry. However, there is still a lack of genomics information on goats. Whole-genome sequencing offers promising approach to identify genetic markers associated with economic traits discover new candidate genes. This can effectively utilize resources accelerate breeding processes improve lactation performance In this study, we present genomes 298 Through rigorous quality control, achieved average depth 14.6X, 92.3% high-quality (Q30 > 90%) data mapping ratio 99.9%, indicating reliable results. By comparing our reference genome goats, identified14.59 million single nucleotide polymorphisms (SNPs) 1.34 insertions-deletions (InDels). dataset significantly contributes enriching public databases goats provides valuable studying diversity, improving breeds, developing varieties.

Language: Английский

---

Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 15, 2025

In the genetic breeding research of dairy goats, traditional genotyping methods have limitations, and existing goat chips shortcomings in functional loci other aspects, which cannot meet precise analysis needs goats. Genotyping by Target Sequencing (GBTS) new generation sequencing technology provides possibility to solve these problems. A large number candidate SNP sites related important economic traits goats were identified through various screening methods. The chip ultimately retained 27,396 for probe design, can detect 46,459 SNPs. site distribution is uniform, data efficiency, base quality, alignment rate, indicators are good. detection rate high heterozygosity gene typing reasonable. GWAS was performed on 200 litter size birth weight traits, multiple genome-wide significantly SNPs genes (litter trait: SCAP, PTPN23, KIF9, ANTXRL, GRID1. NALCN, LRRN2, TMEM132D, COL5A2, HS3ST1) detected. 25 K multiplex liquid phase capture designed this study has excellent performance great value providing strong support development industry.

Language: Английский

---