Relationship between the CUBN and the MIA3 gene copy number variation and growth traits in different cattle breeds

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

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A Comprehensive Review: Molecular and Genealogical Methods for Preserving the Genetic Diversity of Pigs

Applied Sciences, Journal Year: 2025, Volume and Issue: 15(6), P. 3394 - 3394

Published: March 20, 2025

Anthropogenic activities and rapidly increasing climate change have led to a significant loss of genetic diversity in domestic animals. Genealogical data traditionally been used monitor diversity. However, due dependency on pedigree completeness errors that can occur genealogical records, inaccurate estimation population parameters, such as the inbreeding coefficient or effective size, might occur. To reduce possible errors, it is necessary combine with molecular data. An integrated approach using leads optimization breeding programs while controlling within Molecular techniques single nucleotide polymorphism (SNP) genotyping, whole-genome sequencing (WGS), genome-wide association studies (GWASs) enable detailed understanding breed-specific profiles their use conservation programs. In addition, methods structural variation (SV) analysis pangenome epigenomic profiling provide more comprehensive insight into The particular importance for an autochthonous breed its resilience unfavorable climatic conditions, specific productive traits, disease resistance. A combined helps maintain sustainable agricultural systems under evolving environmental challenges.

Language: Английский

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

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

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Genome-wide CNV analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis)

Journal of Dairy Science, Journal Year: 2024, Volume and Issue: 107(9), P. 7022 - 7037

Published: May 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.

Language: Английский

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The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs

Animals, Journal Year: 2024, Volume and Issue: 14(1), P. 174 - 174

Published: Jan. 4, 2024

Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, characterized by strong resistance extreme hot temperatures and humidity. The relationship between their immune response growth still needs be clarified. In this study, we used whole genome sequencing (WGS) detect variations within 37 WZS 32 Large White (LW) 22 Xiangxi black (XXB) ~2.49 GB of SNPs were obtained. These data combined with those two other pig breeds, it was found that most the genes detected (354) located distinct genetic regions pigs LW pigs. network constructed using these represented a center including 12 hub genes, five had structural (SVs) regulatory regions. Furthermore, RNA-seq RT-qPCR for primarily consistent liver, spleen, LDM tissues. Notably, expression HSPs (HSPD1 HSPE1) higher while involved JAK3-STAT pathway lower liver tissue compared This likely not only reduced inflammation-related but also impaired growth. Our findings demonstrated role connection inflammation rate, providing fundamental selection adaptability

Language: Английский

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Genomic signatures reveal selection in Chinese and European domesticated geese

Animal Genetics, Journal Year: 2023, Volume and Issue: 54(6), P. 763 - 771

Published: Sept. 19, 2023

The Swan goose and Greylag are species of geese native to East Asia Europe, respectively, widely believed be the ancestors Chinese European domesticated geese. Yili (YL) domestic originated from goose, but history domestication is unclear. In this study, we sequenced analyzed genome YL Hortobagy combine with other previously populations for in-depth analysis. population genetic variations in Stone geese, Zhejiang White Geese, Taihu Zi were also identified compared. results showed that admixture gene flow existed population, which was introgressed by suggesting events frequent widespread among Further selected sweep analysis candidate genes metabolic pathways may related differences morphology. Several such as TGFBR3L, CMYA5, FOXD1, ARHGEF28 SUCLG2 associated growth, reproduction fertility traits. study will help understand characteristics affecting important traits provide a basis improved breed

Language: Английский

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SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds

Foods and raw materials, Journal Year: 2023, Volume and Issue: 12(2), P. 283 - 307

Published: Nov. 17, 2023

Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc than Landrace and Large White breeds, which participated in creation. The aim study to determine SNP-based genetic signatures fat-type shared with commercial ones are affected by putative selection. genome-wide SNP genotyping carried out using Porcine GGP HD BeadChip, contains ~ 80 000 SNPs. Obtained relationship admixture results indicated insignificant participation breeds formation modern allelofund pigs. 238 candidate genes were found genomic regions selection signatures, 182 described functions identified. In 35 common detected formed cluster enrichment coefficient = 4.94 predominant HOXD genes. largest amounts (62 average), two clusters. Cluster 1, 2.11, characterized involved glucose metabolism. 2, 1.60, demonstrated helicase Annotated clusters not determined for breed. However, 50 specific pigs associated various growth, carcass reproductive traits, essential thermoregulation. Results revealed breeding effects indigenous compared

Language: Английский

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