Livestock Science, Год журнала: 2024, Номер 289, С. 105587 - 105587
Опубликована: Окт. 24, 2024
Язык: Английский
Gene, Год журнала: 2023, Номер 886, С. 147719 - 147719
Опубликована: Авг. 18, 2023
Язык: Английский
Процитировано
16
Genome biology, Год журнала: 2024, Номер 25(1)
Опубликована: Июнь 6, 2024
Abstract Background Sheep and goats have undergone domestication improvement to produce similar phenotypes, which been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, implement comprehensive analysis SVs in 897 genomes worldwide wild domestic populations sheep reveal genetic signatures underlying convergent evolution. Results We characterize the SV landscapes terms diversity, chromosomal distribution their links with genes, QTLs transposable elements, examine impacts on regulatory elements. identify several novel annotate corresponding genes (e.g., BMPR1B , BMPR2 RALYL COL21A1 LRP1B ) associated important production traits such as fertility, meat milk production, wool/hair fineness. detect selection involving parallel evolution orthologous SV-associated during domestication, local environmental adaptation, improvement. In particular, find that fecundity experienced targeting gene DEL00067921 deletion explaining ~10.4% phenotypic variation observed goats. Conclusions Our results provide new insights into serve rich resource for future sheep, goats, related livestock.
Язык: Английский
Процитировано
7
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Март 28, 2025
The hypothalamus is a critical organ that regulates sexual development in animals. However, current research on the hypothalamic regulation of maturation female goats remains limited. In this study, we conducted metabolomic and transcriptomic analyses tissues Jining grey at different stages (1 day old (neonatal, D1, n = 5), 2 months (prepuberty, M2, 4 (sexual maturity, M4, 6 (breeding period, M6, 5)). A total 418 differential metabolites (DAMs) were identified among which abundance such as anserine, L-histidine, carnosine, taurine, 4-aminobutyric gradually increased with progression development. These may regulate neuronal hormone secretion processes by influencing metabolism histidine phenylalanine. Through combined analyses, differentially expressed genes mitogen-activated protein kinase 9 (MAP3K9), prune homolog BCH domain (PRUNE2), potassium voltage-gated channel interacting 4(KCNIP4) jointly energy Gonadotropin-releasing neurons conjunction DAMs, including LPC22:5, 2-Arachidonyl Glycerol ether, LPE22:5, Lysops22:5. Additionally, elucidated molecular mechanism through glutathione goats. summary, study illustrates dynamic changes mRNA within tissue during postnatal This provide significant scientific insights for future animal breeding.
Язык: Английский
Процитировано
0
BMC Genomics, Год журнала: 2023, Номер 24(1)
Опубликована: Окт. 16, 2023
Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution genetic diversity and association with important pathophysiological states. The present study aimed elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X 30X). Post-quality control, sequence reads were aligned latest draft release Bubaline genome. CNVs elucidated a read-depth approach CNVnator bin sizes. Adjacent concatenated into variation regions (CNVRs) genomic coverage was elucidated.Overall, average size CNVR lower 30X coverage, providing finer details. Most CNVRs either deletion or duplication type while occurrence mixed events lesser on comparative basis all breeds. (0.201 Mb) as compared 10X (0.013 finest Banni buffaloes. maximum observed Murrah (2627) Pandharpuri (25,688) coverages, respectively. Whereas minimum scored Surti both (2092 17,373). On other hand, highest lowest Jaffarabadi (833 10,179 events) (783 7553 coverages. Deletion overnumbered duplications Gene profiling common overlapped genes longest provided insights evolutionary history these indicate under selection respective breeds.The is first its kind major populations data. results revealed divergence along timescale.
Язык: Английский
Процитировано
9
Animals, Год журнала: 2024, Номер 14(2), С. 236 - 236
Опубликована: Янв. 12, 2024
South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well indigenous and village pigs reared under low-input production systems. The aim this study was to investigate how natural artificial selection have shaped the genomic landscape African populations sampled from different genetic backgrounds For purpose, integrated haplotype score (iHS), cross population extended homozygosity (XP-EHH) Lewontin Krakauer’s extension Fst statistic based on information (HapFLK) were utilised. Our results revealed several population-specific signatures associated with importance in highlighted, majority regions identified these populations. Regions causing distinct footprints also allow for identification genes pathways that may influence adaptation. In context breeds (Large White, Kolbroek, Windsnyer), included quantitative loci (QTLs) economically important traits. example, meat carcass QTLs prevalent all showing potential populations’ ability be managed improved such Results therefore increase our understanding intricate interplay between pressures, adaptations, desirable traits within
Язык: Английский
Процитировано
2
Genes, Год журнала: 2024, Номер 15(11), С. 1450 - 1450
Опубликована: Ноя. 10, 2024
(1) Background: Buffaloes are crucial livestock species for food and service in tropical subtropical regions. Buffalo genetics, particularly indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits regional significance. (2) Methods: This investigation utilized whole-genome sequences twenty XWBs (newly sequenced), along with eighty published other (including Guizhou buffalo, river Yangtze River). Using sequencing analysis technology, population structure, genomic diversity, selection signatures XWB were determined. (3) Results: revealed that XWB, being phylogenetically positioned middle lower reaches River, exhibited substantial diversity. Employing four sweep detection methods (CLR, iHS, π-ratio,
Язык: Английский
Процитировано
2
Journal of Dairy Science, Год журнала: 2024, Номер 107(9), С. 7022 - 7037
Опубликована: Май 17, 2024
Buffaloes are vital contributors to the global dairy industry. Understanding genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp 126 crossbred buffaloes. We identified 36,548 copy number variant (CNVs) spanning 133.29 Mb genome, resulting 2,100 regions (CNVRs), with 1,993 shared CNVRs being found within studied types. Analyzing highlighted distinct differentiation between subspecies, verified by evolutionary tree principal component analyses. Admixture analysis grouped buffaloes into categories, displaying mixed ancestry. To identify candidate genes associated traits, employed 3 approaches. First, used Vst-based population differentiation, revealing 11 that exhibited significant divergence different linked traits. Second, expression quantitative loci (eQTL) revealed differential CNVR-driven (DECGs) Notably, known production-related were among these DECGs, validating their relevance. Last, a genome-wide association study (GWAS) significantly peak yield. Our provides comprehensive genomic insights identifies These findings facilitate aimed at increasing yield quality economically important livestock species.
Язык: Английский
Процитировано
1
Animals, Год журнала: 2024, Номер 14(19), С. 2784 - 2784
Опубликована: Сен. 26, 2024
This research is designed to examine the genetic diversity and kinship among Hu sheep, as well discover genes associated with crucial economic traits. A selection of 50 unrelated adult male sheep underwent genotyping SNP50K BeadChip. Seven indicators were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), marker ratio (PN), expected heterozygosity (He), observed (Ho), number alleles, minor allele frequency (MAF). Plink software was employed compute IBS distance matrix detect runs homozygosity (ROHs), while G principal component analysis performed using GCTA software. Selective sweep carried out ROH, Pi, Tajima’s D methodologies. study identified a total 64,734 SNPs, which 56,522 SNPs remained for downstream after quality control. The displayed relatively high diversity. ultimately grouped into 12 distinct families, families 6, 8, 10 having highest numbers individuals, each consisting 6 sheep. Furthermore, 294 ROHs detected, majority lengths between 1 5 Mb, inbreeding coefficient FROH 0.01. In addition, 41, 440, 994 candidate by methods, respectively, 3 overlapping (BMPR1B, KCNIP4, FAM13A). These results offer valuable insights future breeding, assessment, management.
Язык: Английский
Процитировано
1
Conservation Genetics, Год журнала: 2024, Номер 26(1), С. 49 - 62
Опубликована: Окт. 25, 2024
Язык: Английский
Процитировано
1
BMC Genomics, Год журнала: 2024, Номер 25(1)
Опубликована: Ноя. 14, 2024
Indigenous buffaloes, as the important livestock species contributing to economy of country, are lifeline livelihood in Nepal. They distributed across diverse geographical regions country and have adapted various feeding, breeding, management conditions. The larger group these native buffalo breeds present narrow stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for conservation breeds. We utilized whole-genome sequencing (WGS) investigate genetic diversity, population structure, selection signatures Nepalese indigenous buffaloes. compared 66 sequences with 118 publicly available from six river five swamp Genomic diversity parameters indicated variability level buffaloes comparable those Indian breeds, structure revealed distinct geography-mediated differentiation among used locus-specific branch length analysis (LSBL) genome-wide scan, list potentially selected genes Lime Parkote that inhabit region. A gene ontology (GO) discovered many GO terms were associated cardiac function regulation. Furthermore, complementary analyses local signatures, tissue expression profiles, haplotype differences identified candidate genes, including KCNE1, CSF1R, PDGFRB, related regulation pulmonary functions. This study comprehensive WGS-based Our suggested "hilly" especially undergone some characteristic changes evolved increased their steep terrains country.
Язык: Английский
Процитировано
1