Evolutionary origin of genomic structural variations in domestic yaks

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 19, 2023

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not distinguished previously. We constructed a graph-genome for 47 genomes 7 cross-fertile bovine species. This allowed detection 57,432 high-resolution structural (SVs) within across the species, which were genotyped in 386 individuals. evolutionary origins diverse SVs domestic yaks phylogenetic analyses. further identified 334 genes overlapping with that bore potential signals selection from wild yaks, plus an additional 686 introgressed cattle. Nearly 90% Introgression SV spanning KIT gene triggered breeding white yaks. validated significant association selected stratified expression, contributes phenotypic variations. Our results highlight different contribute diversity

Язык: Английский

---

Mapping conservation priorities for wild yak (Bos mutus) habitats on the Tibetan Plateau, China

The Science of The Total Environment, Год журнала: 2024, Номер 914, С. 169803 - 169803

Опубликована: Янв. 4, 2024

Язык: Английский

---

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Янв. 17, 2024

Abstract Background The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on plateau. Domestic yaks have been subjected to strong artificial selection environmental pressures over long-term. Understanding molecular mechanisms phenotypic differences in populations can reveal key functional genes involved domestication process improve genetic breeding. Material method Here, we re-sequenced 80 (Maiwa, Yushu, Huanhu populations) identify single-nucleotide polymorphisms (SNPs) as variants. After filtering quality control, remaining SNPs were kept genome-wide regions selective sweeps associated with domestic traits. four methods (π, XPEHH, iHS, XP-nSL) used detect population separation. Results By comparing stratification, linkage disequilibrium decay rate, characteristic sweep signals, identified 203 putative traits, 45 which mapped 27 known genes. They clustered into 4 major GO biological terms. All seven such dwarfism ( ANKRD28 ), milk HECW1 , HECW2 OSBPL2 meat SPATA5 GRHL2 fertility BTBD11 ARFIP1 adaptation NCKAP5 ANTXR1 LAMA5 AOC2 RYR2 growth GRID2 SMARCAL1 EPHB2 immune system INPP5D ADCYAP1R1 ). Conclusions We provided there an obvious different among progress these three populations. Our findings understanding switches processes

Язык: Английский

---

Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing

Animal Bioscience, Год журнала: 2023, Номер 36(7), С. 991 - 1002

Опубликована: Май 2, 2023

This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and discovery important genes encoding valuable traits.We used whole-genome resequencing explore genetic relationships, phylogenetic tree, population structure analysis. In addition, we identified 28 representative single-nucleotide polymorphisms (SNPs) genomic selective sweep with by fixation index (Fst) nucleotide diversity (θπ) ratio.The relationships analysis showed that each breed partitioned into its own clades had close relationships. We also many potential breed-specific regions, including associated hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), horn phenotypes (RXFP2). particular, a horn-related gene, RXFP2, four most significantly SNP loci (g. 29481646 A>G, g. 29469024 T>C, 29462010 C>T, 29461968 C>T) haplotypes.This finding demonstrates markers future molecular breeding programs improve selection phenotypes. The results will facilitate understanding basis production unique Chinese indigenous taxa offer reference sheep.

Язык: Английский

---

Single-cell analysis identifies critical regulators of spermatogonial development and differentiation in cattle-yak bulls

Journal of Dairy Science, Год журнала: 2024, Номер 107(9), С. 7317 - 7336

Опубликована: Апрель 19, 2024

Spermatogenesis is a continuous process in which functional sperm are produced through series of mitotic and meiotic divisions morphological changes germ cells. The aberrant development fate transitions spermatogenic cells cause hybrid sterility mammals. Cattle-yak, animal between taurine cattle (Bos taurus) yak grunniens), exhibits male-specific due to failure. In the present study, we performed single-cell RNA sequencing analysis identify differences testicular cell composition developmental trajectory cattle-yak. molecular signatures spermatogonial subtypes were dramatically different these 2 animals, expression genes associated with stem maintenance, differentiation entry was altered cattle-yak, indicating impairment undifferentiated decisions. Cell communication revealed that signaling within subpopulations weakened, progenitor spermatogonia unable or delayed receiving sending signals for transformation next stage Simultaneously, niche also abnormal. Collectively, obtained profiles transcriptome somatic populations at level identified critical regulators meiosis sterile findings this study shed light on genetic mechanisms lead speciation bovid species.

Язык: Английский

---

Advances in single-cell transcriptomics in animal research

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 2, 2024

Abstract Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of research, offering effective method study gene expression high-throughput single cells different tissues/organs animals. In unprecedented manner, researchers have identified cell types/subtypes their marker genes, inferred cellular fate trajectories, revealed cell‒cell interactions animals using transcriptomics. this paper, we introduce development technology review processes, advancements, applications research. We summarize recent efforts obtain a more profound understanding nutrition health, reproductive performance, genetics, disease models livestock species. Moreover, practical experience accumulated based on large number cases highlighted provide reference determining key factors (e.g., sample size, clustering, type annotation) analysis. also discuss limitations outlook current stage. This paper describes comprehensive progress novel insights sustainable advancements agricultural productivity health.

Язык: Английский

---

Gut microbiota and quantitative traits divergence at different altitude of long-tailed dwarf hamsters, Cricetulus longicaudatus

Frontiers in Microbiology, Год журнала: 2025, Номер 15

Опубликована: Янв. 24, 2025

To investigate the community structure and diversity of gut microflora their function in body mass regulation, as well effects various locations on microbiota Cricetulus longicaudatus regulation at elevations. We examined diversity, abundance, long-tailed dwarf hamsters from eight regions Shanxi province during summer using 16S rDNA sequencing technology analyzed relationships between these environmental variables morphological indicators. The results revealed Firmicutes Bacteroidetes dominant phyla phylum level, with Lactobacillus emerging predominant genus. observed differences different areas, this is affected by altitude. high-altitude areas individuals had lower β than low-altitude area. Moreover, skull indexes also changed result presented study indicated that size conforms to Bergmann's law. And Providencia significant correlation size. Finally, functional analysis showed changes metabolic depended elevation, collinear network how interacts each other. All suggest are depending altitude, altitude being main factor affecting both microbes way metabolism works. This shows has a big effect phenotypic traits hamsters. It species can adapt

Язык: Английский

---

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China

Frontiers in Genetics, Год журнала: 2023, Номер 13

Опубликована: Янв. 10, 2023

The Qinghai Province of China is located in the northeast region Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations archaeological records, mitochondrial DNA, Y chromosomal markers have suggested that was major center domestication. In present study, we examined genomic diversity, differentiation, selection signatures 113 yak, including 42 newly sequenced 71 publicly available individuals, from nine breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, Huzhu white) using high-depth whole-genome resequencing data. We observed most diversity based on four parameters (nucleotide inbreeding coefficients, linkage disequilibrium decay, runs homozygosity). Population structure analysis showed two lineages with ancestral origins are clustered into three distinct groups wild Geermu seven other domestic breeds/populations. FST values moderate differentiation between Positive signals were detected candidate genes associated disease resistance (CDK2AP2, PLEC, CYB5B), heat stress (NFAT5, HSF1, SLC25A48), pigmentation (MCAM, RNF26, BOP1), vision (C1QTNF5, MFRP, TAX1BP3), milk quality (OPLAH GRINA), neurodevelopment (SUSD4, INSYN1, PPP1CA), meat (ZRANB1), integrated PI, composite likelihood ratio (CLR), methods. These findings offer new insights mechanisms underlying target traits provide important information for understanding characteristics Qinghai.

Язык: Английский

---

The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates

BMC Genomics, Год журнала: 2023, Номер 24(1)

Опубликована: Сен. 6, 2023

The harsh conditions of high-altitude environments are known to drive the evolution physiological and morphological traits in endothermic animals. These expected result adaptive protein coding genes encoded mitochondrial genomes that vital for oxidative phosphorylation pathway. In this study, we formally tested signatures on Tapirus pinchaque other odd-toed ungulates inhabiting high-elevation environments.The AT-rich genome T. is 16,750 bp long. A phylomitogenomic analysis supports monophyly genus families Perissodactyla. ratio non-synonymous synonymous substitutions demonstrated all undergo purifying selection odd living at high elevations. Over negative background selection, Branch Models suggested cox3 nad6 might be undergoing stronger than genes. Furthermore, Site one four sites nad2 nad5, respectively, could experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation strength nad6, evidence episodic diversifying cob, revealed positive/diversifying two nad1, site each nad4.The an important genomic resource conservation species study contributes understanding environments.

Язык: Английский

---

Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Апрель 25, 2024

Abstract Background Jasmine ( Jasminum ), renowned for its ornamental value and captivating fragrance, has given rise to numerous species accessions. However, limited knowledge exists regarding the evolutionary relationships among various species. Results In present study, we sequenced seven distinct species, resulting in assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that size 12 cp genomes ranged from 159 165 kb encoded 134–135 genes, including 86–88 protein-coding 38–40 tRNA 8 rRNA genes. J. nudiflorum exhibited a larger genome compared other mainly attributed elevated number forward repeats (FRs). Despite typically conservative nature chloroplasts, variations presence or absence acc D have been observed within sambac . The calculation nucleotide diversity Pi ) values 19 indicated potential mutation hotspots were more likely be located LSC regions than regions, particularly genes ycf 2, rbc L, atp E, ndh K, C > 0.2). Ka/Ks strong selection pressure on rps A, rpo C1, rpl 33 when comparing with three most closely related auriculatum , multiflorum dichotomum ). Additionally, SNP identification, along results Structure, PCA, phylogenetic tree analyses, divided into six groups. Notably, polyanthum showed gene flow signals both G5 group G3 tortuosum fluminense Phylogenetic analysis reflected same genus clustered together robust support Oleaceae, strongly supporting monophyletic Conclusion Overall, this study provides comprehensive insights genomic composition, variation, These enhance our understanding genetic history

Язык: Английский

---