Integrative analysis of<i>APOL3</i>gene CNV for adult cattle stature

Peng, Shujun; Cao, Xiukai; Dong, Dong; Liu, Mei; Hao, Dan; Shen, Xuemei; Huang, Yongzhen; Lei, Chuzhao; Ma, Yun; Bai, Yueyu; Hu, Linyong; Qi, Xinglei; Chaogetu, Buren; Chen, Hong

doi:10.1080/10495398.2019.1615933

Cited by 7 publications

(3 citation statements)

References 33 publications

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“…In this study, the most differentiated CNV loci between domestic goats and BI overlapped with APOL3-like, which might be a paralog of APOL3 and is adjacent to APOL3 in the goat genome. CNVs at the APOL3 locus have been reported in several cattle breeds [43,44] and found to be associated with adult cattle stature [45]. Furthermore, some genes overlapping with the highly divergent CNVs between domestic and wild goats were enriched in the immune system, which was consistent with the reports that some immunity-related CNV genes evolved rapidly between domestic and wild goats (Capra aegagrus) [16], and between domestic pigs and wild boars [46].…”

Section: Domestication-associated Cnvssupporting

confidence: 87%

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

et al. 2020

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Background Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) to public data for 26 individuals from three other breeds (two Moroccan and one Chinese) and 21samples from Bezoar ibexes. Results We obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~ 267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO terms and KEGG pathways, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the results from SNPs, agreeing with the geographical origins of these goats. Based on genome-wide FST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for several immunity-related pathways, whereas the genes overlapping with the highly differentiated CNVs between highland and lowland goats were mainly related to vitamin and lipid metabolism. Remarkably, a 507-bp deletion at ~ 14 kb downstream of FGF5 on chromosome 6 showed highly divergent (FST = 0.973) between the highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail. Conclusion We generated a comprehensive map of CNVs in goats. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds.

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Section: Domestication-associated Cnvssupporting

confidence: 87%

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

et al. 2020

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“…To date, many studies have revealed a correlation between indel variation and the growth traits, reproductive performance, and milk traits of livestock and poultry [ 9 , 10 , 11 , 12 ]. CNV as a format of structural variants has more significant impact on genetic diversity than SNP and indel [ 13 ]. Abnormally sized fragments of CNV are more than 50 bp and are usually caused by genomic deletion, insertion, recombination, and complicated variants of numerous chromosomal loci [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits

Chen

Bao

et al. 2022

Animals

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Copy number variation (CNV) is a structural variant with significant impact on genetic diversity. CNV has been widely used in breeding for growth traits, meat production or quality, and coat color. SRY-like box genes (SOXs) are a class of transcription factors that play a regulatory role in cell fate specification and differentiation. SOX5 and SOX8 belong to subgroups D and E of the SOXs, respectively. Previous studies have shown that SOX5 and SOX8 are essential in the development of bones. In this study, we explored the association between the growth traits and CNVs of SOX5 and SOX8 in 326 Ashidan yaks and detected mRNA expression levels in different tissues. Our results illustrated that CNVs of SOX5 and SOX8 were significantly associated with withers height at 18 months of age and chest girth at 30 months of age (p < 0.05). The CNV combination of SOX5 and SOX8 was significantly associated with withers height at 18 months of age (p < 0.01). SOX5 expression in the lung was significantly higher than in the heart, spleen, kidney, and muscle (p < 0.05). SOX8 expression in the lung was significantly higher than in the liver and muscle (p < 0.05). Our results provide evidence that the CNVs of SOX5 and SOX8 genes could be used as new markers for the selection of yak growth traits.

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“…The size of CNV is generally between 50 bp and 1 kb. Determination of CNV is recognised as an increasingly important factor for gene function, animal evolution and growth traits (Peng et al, 2020). In a small-scale insertion and deletion study of DNA fragments, Li et al (2019) found that the type of mutation in the CDKN3 gene of chickens is significantly related to individual growth traits.…”

Section: Introductionmentioning

confidence: 99%

Copy number variation of EIF4A2 loci related to phenotypic traits in Chinese cattle

Zhang

Peng

Wen

et al. 2022

Veterinary Medicine & Sci

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Background: Generally, copy number variation (CNV) is a large-scale structural variation between 50 bp and 1 kb of the genome. It can affect gene expression and is an important reason for genetic diversity and phenotypic trait diversity. Studies have shown that the eukaryotic translation initiation factor 4A2 (EIF4A2) gene plays an essential role in muscle development in both humans and pigs. However, the influence of bovine EIF4A2's copy number change on phenotypic traits has not been reported. Objectives:To detect the tissue expression profile of the EIF4A2 gene in adult cattle and individuals' CNV type of variation. Then, we explored the correlation between EIF4A2-CNV and growth traits in Chinese cattle breeds. Methods: Real-time fluorescent quantitative reverse transcription PCR (qRT-qPCR) was used to determine the expression profile of the EIF4A2 gene. Real-time fluorescent quantitative PCR (qPCR) was used to detect the CNV type of bovine populations. Then, SPSS 26.0 was used for association analysis. Results: In this study, a total of 513 individuals in four cattle breeds (Qinchuan cattle [QC], Yunling cattle [YL], Pinan cattle [PN] and Jiaxian cattle [JX]) were detected for EIF4A2 gene's CNV. The results showed that EIF4A2-CNV has an essential impact on hip width (HW) and rump length (RL) in QC, heart girth (HG), chest depth (CD) and RL in YL and HW in PN. However, it had no significant effect on JX. Conclusions:The above results suggest that EIF4A2 gene's CNV can be used as a molecular marker for cattle breeding, which is helpful to accelerate the breeding of superior beef cattle breeds.

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Integrative analysis ofAPOL3gene CNV for adult cattle stature

Cited by 7 publications

References 33 publications

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits

Copy number variation of EIF4A2 loci related to phenotypic traits in Chinese cattle

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