Structural variations in livestock genomes and their associations with phenotypic traits: a review DOI Creative Commons
Yinghui Chen, Muhammad Zahoor Khan, Xinrui Wang

et al.

Frontiers in Veterinary Science, Journal Year: 2024, Volume and Issue: 11

Published: Nov. 12, 2024

Genomic structural variation (SV) refers to differences in gene sequences between individuals on a genomic scale. It is widely distributed the genome, primarily form of insertions, deletions, duplications, inversions, and translocations. Due its characterization by long segments large coverage, SVs significantly impact genetic characteristics production performance livestock, playing crucial role studying breed diversity, biological evolution, disease correlation. Research contributes an enhanced understanding chromosome function important for hereditary diseases mechanisms. In this article, we review concept, classification, main formation mechanisms, detection methods, advancement research genomes cattle, buffalo, equine, sheep, goats, aiming reveal basis phenotypic traits adaptive mechanisms through research, which will provide theoretical better utilizing resources herbivorous livestock.

Language: Английский

Relationship between the CUBN and the MIA3 gene copy number variation and growth traits in different cattle breeds DOI Creative Commons
Yue Han, Jiwei Liu, Congcong Zhang

et al.

Animal Biotechnology, Journal Year: 2025, Volume and Issue: 36(1)

Published: Jan. 28, 2025

Copy number variations (CNV) are important genetic variations. The endogenous factors cobalamin receptor (CUBN) and MIA SH3 domain ER-derived factor 3 (MIA3) associated with bone/muscle development intramuscular fat deposition. There have been no reports on the effects of CUBN MIA3 CNVs growth traits Chinese cattle. This study aimed to determine correlation between in qRT-PCR was used detect distribution CNV expression levels their mRNA, analysis conducted traits. differentially expressed different breeds cattle, correlated significantly body height, hip slanting length, width Grassland Red cattle (CYH); eye muscle area Yanbian (YB) Yan Yellow (YH). showed CYH YB only one deletion type occurred YH mRNA patterns tissues. In conclusion, is a novel molecular marker that could be exploited breeding.

Language: Английский

Citations

0
Copy Number Variations of the NSMF Gene and Their Associations with Growth Traits in Three Chinese Sheep Breeds DOI Open Access
Xiukai Cao, Yongqi Liu, Jie Cheng

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(2), P. 218 - 218

Published: Feb. 13, 2025

Copy number variations (CNVs) are a significant source of genetic variation and have been shown to influence growth traits in livestock. This study aimed validate previous CNV candidates within the NSMF gene (XM_015093798.1) identify novel markers for molecular breeding sheep. Using quantitative PCR (qPCR), we genotyped CNVs (chr3: 586,001-601,000) assessed their associations with three Chinese sheep breeds: Chaka (CKS, n = 312), Hu (HS, 67), Small-tailed Han (STHS, 70). Our results revealed differences genotype frequencies across breeds, highest proportion deletions observed STHS (98.44%) CKS (90.57%), while HS exhibited higher frequency duplications (14.06%). No were between (p-value > 0.05). However, could markedly affected cannon circumference 0.021), individuals carrying normal showing larger circumference. Additionally, marginally association was found body diagonal length 0.050). Future investigations employing cohorts warranted definitively establish utility as programs.

Language: Английский

Citations

0
Detection of Copy Number Variations in Woori-Heukdon Populations with the Illumina PorcineSNP60 Bead-Chip Array DOI Creative Commons
Yong‐Min Kim, Ha-Seung Seong,

Seok-Joo Ha

et al.

Animals, Journal Year: 2025, Volume and Issue: 15(6), P. 774 - 774

Published: March 9, 2025

This study investigated copy number variations (CNVs) in 2112 pigs from five populations: Korean Duroc (DUC), Native Pig (KNP), and their crossbred offspring (F1, F2, WRH). CNVs were detected using PennCNV QuantiSNP, with CNVRuler identifying 698 CNV regions (CNVRs), covering 109 Mb (4.83%) of the porcine genome. Comparison previous studies on swine revealed CNVR overlap rates ranging 31.12% (French Yorkshire) to 81.27% (Xiang), 9.06% newly identified CNVRs. DUC showed most CNVRs (n = 384), followed by WRH 225). Meanwhile, F1 F2 exhibited far fewer (five seven, respectively). Functional enrichment analysis highlighted various genes overlapping CNVRs, including 1236 572 WRH, linked biological processes. The quantitative trait loci (QTLs), particular traits such as average daily gain (4.24% QTLs DUC, 4.51% In contrast, KNP, F1, populations a higher frequency containing overlapped drip loss. These findings indicate that may inherit growth DUC. provides better understanding pigs, which can potentially be used improving genetic merits pig populations.

Language: Английский

Citations

0
Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions DOI Creative Commons

Jan Berghöfer,

Nadia Khaveh, Stefan Mundlos

et al.

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

Published: March 22, 2025

Copy number variations (CNVs) represent a common and highly specific type of variation in the genome, potentially influencing genetic diversity mammalian phenotypic development. Structural variants, such as deletions, duplications, insertions, have frequently been highlighted key factors traits high-production pigs. However, comprehensive CNV analyses miniature pig breeds are limited despite their value biomedical research. This study performed whole-genome sequencing 36 pigs from nine America, Asia Oceania, Europe. By employing multi-tool approach (CNVpytor, Delly, GATK gCNV, Smoove), accuracy identification was improved. In total, 34 homozygous CNVs overlapped with exonic regions all samples, suggesting role expressing phenotypes uniform growth patterns, fertility, or metabolic function. addition, 386 copy (CNVRs) shared by were detected, covering 33.6 Mb (1.48% autosomal genome). Further, 132 exclusive CNVRs identified for American breeds, 47 Asian Oceanian 114 European breeds. Functional enrichment analysis revealed genes within involved body height determination other growth-related parameters. Exclusive located region enriched lipid metabolism minipigs, reproductive cardiovascular features selected groups, quantitative trait loci associated size, meat quality, reproduction, disease susceptibility highlighted. investigation landscape minipigs underlines impact selective breeding on structural variants its development breed across geographical areas. The provides valuable resource future studies effects artificial selection livestock genomes.

Language: Английский

Citations

0
Genome wide copy number diversity in Indian goat breeds scaled to world-wide breeds DOI
Nidhi Sukhija, Indrajit Ganguly,

K K Kanaka

et al.

Small Ruminant Research, Journal Year: 2025, Volume and Issue: unknown, P. 107525 - 107525

Published: May 1, 2025

Language: Английский

Citations

0
Application of Omics in Donkey Meat Research: A Review DOI Creative Commons

Qiying Zhu,

Yongdong Peng,

Xiaotong Liu

et al.

Animals, Journal Year: 2025, Volume and Issue: 15(7), P. 991 - 991

Published: March 29, 2025

This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. study nutritional profile meat, which is rich in protein, essential amino acids, unsaturated fatty acids. Through a systematic literature search across Web Science, Google Scholar, PubMed, Scopus databases (2000-2024), we collected analyzed data 400 research articles using predefined inclusion criteria focused on composition, approaches, quality parameters populations. The also evaluates various factors affecting quality, including breed differences, age, feeding management, storage conditions. Advanced genomic transcriptomic analyses have revealed numerous candidate such as ACTN3, BMP7, NR6A1, Wnt7a, HOXC8, LCORL, TPM2, TPM3, associated with growth traits characteristics, providing valuable insights for genetic improvement programs. Furthermore, discusses authentication methods ensuring preventing adulteration, highlighting integration traditional modern analytical

Language: Английский

Citations

0
Comparative Study on the Sperm Proteomes of Horses and Donkeys DOI Creative Commons

Hong Ren,

Xin Wen, Qianqian He

et al.

Animals, Journal Year: 2024, Volume and Issue: 14(15), P. 2237 - 2237

Published: July 31, 2024

The reproductive performance of horse sperm and donkey has been reported to differ. Sperm proteins play a crucial role in viability fertility. Although differences between species are known, no prior study investigated disparities the proteome horses donkeys. Therefore, this characterized compared proteomes donkeys using 4D-DIA mass spectrometry technology. We identified 3436 3404 sperm. Of these, 3363 were expressed both sperm, with 73 being specifically 41 According data analysis, exhibited greater percentage motility progressive movement straight-line than horses, as well lower percentages static slow horses. Joint analysis results from their CEROS II-read parameters demonstrated possible association patterns. These findings suggest that there discrepancies expression levels protein compositions certain specific may be responsible for these two species.

Language: Английский

Citations

1
Deciphering new insights into copy number variations as drivers of genomic diversity and adaptation in farm animal species DOI

C. S. Celus,

Sheikh Firdous Ahmad,

Munish Gangwar

et al.

Gene, Journal Year: 2024, Volume and Issue: 939, P. 149159 - 149159

Published: Dec. 11, 2024

Language: Английский

Citations

1
Structural variations in livestock genomes and their associations with phenotypic traits: a review DOI Creative Commons
Yinghui Chen, Muhammad Zahoor Khan, Xinrui Wang

et al.

Frontiers in Veterinary Science, Journal Year: 2024, Volume and Issue: 11

Published: Nov. 12, 2024

Genomic structural variation (SV) refers to differences in gene sequences between individuals on a genomic scale. It is widely distributed the genome, primarily form of insertions, deletions, duplications, inversions, and translocations. Due its characterization by long segments large coverage, SVs significantly impact genetic characteristics production performance livestock, playing crucial role studying breed diversity, biological evolution, disease correlation. Research contributes an enhanced understanding chromosome function important for hereditary diseases mechanisms. In this article, we review concept, classification, main formation mechanisms, detection methods, advancement research genomes cattle, buffalo, equine, sheep, goats, aiming reveal basis phenotypic traits adaptive mechanisms through research, which will provide theoretical better utilizing resources herbivorous livestock.

Language: Английский

Citations

0