A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats

Yuan, Ying; Zhang, Weiyi; Yang, Bo; Zhou, Dong‐Ke; Xu, Lu; He, Yongmeng; Zhang, Haoyuan; Liu, Chengli; Ma, Yuehui; Chu, Mingxing; Zhang, Wenguang; Gao, Huijiang; Jiang, Lin; Zhao, Fuping; Zhang, Lupei; Na, Risu; Oyungerel, Baatarchogt; Han, Yilin; Zeng, Yan; Wang, Shizhi; Huai-zhi, Jiang; Zhang, Hongping; Jiang, Xunping; He, Jianning; Liang, Hao; Kaushalendra, Kaushalendra; Sun, Yawang; Huang, Yongfu; Zhao, Yong; Zhao, Zhongquan; Guang‐Xin, E

doi:10.24272/j.issn.2095-8137.2022.384

Cited by 4 publications

(2 citation statements)

References 80 publications

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“…All of these proteins are closely related to the known function of the PLEC. CNVs may potentially affect gene expression by altering gene dose and transcriptional structure [41]. Alterations in the copy number of this extensive coding sequence suggest that, irrespective of the copy number itself, the presence of multiple copies may lead to the deterioration of the gene.…”

Section: Discussionmentioning

confidence: 99%

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Wang,

Zhang,

Han

et al. 2023

Animals

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The plectin (PLEC) gene is crucial in regulating muscle development and maintaining the cytoskeleton. An abnormal expression of PLEC can lead to muscle atrophy and muscular dystrophy. In a previous study, we found that Leizhou black goats exhibit abundant structural variations in the PLEC gene. However, the genetic effects of these variations on growth traits and meat quality in goats are not fully understood. In this study, three PLEC copy number variations (CNVs) were identified in a population of 417 Leizhou black goats, using quantitative polymerase chain reaction (qPCR) technology. Population distribution analysis revealed a high abundance of various types of these three CNVs. PLEC mRNA was found to be highly expressed in muscle tissue and remained consistently high from 1 month to 24 months after birth. Specifically, the gain type of CNV-1 (chr14: 81056401-81064800) showed a significant association with PLEC mRNA expression in muscle tissue (p < 0.01). The sequence of CNV-1 in PLEC shares similarities with three domain superfamilies associated with muscle development and skin disease. Furthermore, there were significant differences in chest circumference, body weight, carcass weight, the cross-sectional area of the longissimus dorsi lumbar muscle, and shear stress between different types of CNV-1 (p < 0.05). Notably, goats with the CNV-1 gain type demonstrated better phenotypic values compared to those with loss and normal types. These findings suggest that PLEC CNV-1 could play a crucial role in the growth and muscle development of Leizhou black goats, making it a potential marker for assisted selection in goat breeding.

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Section: Discussionmentioning

confidence: 99%

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Wang,

Zhang,

Han

et al. 2023

Animals

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“…In general, SVs can be divided into two types based on changes in the DNA content of the genome: 1) unbalanced copy number variants (CNVs), including deletions (DELs), duplications (DUPs), insertions (INSs), and mobile element insertions (MEIs); and 2) balanced rearrangements, including inversions (INVs) and translocations (TRAs) [ 3 ]. In livestock research, SVs have been shown to be associated with adaptability and production traits [ 4 , 5 ]. Compared to SNPs, SVs contribute to a higher proportion of complex phenotypes [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Zong,

Wang,

Zhao

et al. 2023

J Animal Sci Biotechnol

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Background During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. Results Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

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One Copy Number Variation within the Angiopoietin-1 Gene Is Associated with Leizhou Black Goat Meat Quality

Wu,

Han,

Zhang

et al. 2024

Animals

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The ANGPT1 gene plays a crucial role in the regulation of angiogenesis and muscle growth, with previous studies identifying copy number variations (CNVs) within this gene among Leizhou black goats. In this study, we investigated three ANGPT1 CNVs in 417 individuals of LZBG using quantitative PCR (qPCR), examining the impact of different CNV types on the ANGPT1 gene expression and their associations with growth and meat quality traits. Notably, the ANGPT1 CNV-1 (ARS1_chr14:24950001-24953600) overlaps with protein-coding regions and conserved domains; its gain-of-copies genotype (copies ≥ 3) was significantly correlated with ANGPT1 mRNA expression in muscle tissue (p < 0.01). Furthermore, the gain-of-copies genotype of CNV-1 demonstrated significant correlations with various phenotypic traits, including carcass weight, body weight, shear stress, chest circumference, and cross-sectional area of longissimus dorsi muscle. These findings indicate that the CNV-1 gain-of-copies genotype in the ANGPT1 gene may serve as a valuable marker for selecting Leizhou black goats exhibiting enhanced growth and muscular development characteristics, thereby holding potential applications in targeted breeding programs aimed at improving meat quality.

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A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats

Cited by 4 publications

References 80 publications

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

One Copy Number Variation within the Angiopoietin-1 Gene Is Associated with Leizhou Black Goat Meat Quality

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