Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats

Li, Lijuan; Yang, Peng; Shi, Shu-Yue; Zhang, Zijing; Shi, Qiaoting; Xu, Jie; He, Hongbin; Lei, Chuzhao; Wang, ErYao; Chen, Hong; Huang, Yongzhen

doi:10.3390/ani10030441

Cited by 5 publications

(5 citation statements)

References 23 publications

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“…Association analysis has been widely used for analyzing the effect of gene polym phism on quantitative traits in animals [34][35][36]. Target sequence and reference sequ primers were used to amplify each sample by qPCR (each group has three replicatio Then, we analyzed the qPCR results by referring to previous studies in our labora [37].…”

Section: Discussionmentioning

confidence: 99%

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Yang

Yue

et al. 2022

Biology

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Currently, studies of the SYT11 gene mainly focus on neurological diseases such as schizophrenia and Parkinson’s disease. However, some studies have shown that the C2B domain of SYT11 can interact with RISC components and affect the gene regulation of miRNA, which is important for cell differentiation, proliferation, and apoptosis, and therefore has an impact on muscle growth and development in animals. The whole-genome resequencing data detected a CNV in the SYT11 gene, and this may affect cattle growth traits. In this study, CNV distribution of 672 individuals from four cattle breeds, Yunling, Pinan, Xianan, and Qinchuan, were detected by qPCR. The relationship between CNV, gene expression and growth traits was further investigated. The results showed that the proportion of multiple copy types was the largest in all cattle breeds, but there were some differences among different breeds. The normal type had higher gene expression than the abnormal copy type. The CNVs of the SYT11 gene were significantly correlated with body length, cannon circumference, chest depth, rump length, and forehead size of Yunling cattle, and was significantly correlated with the bodyweight of Xianan cattle, respectively. These data improve our understanding of the effects of CNV on cattle growth traits. Our results suggest that the CNV of SYT11 gene is a protentional molecular marker, which may be used to improve growth traits in Chinese cattle.

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Section: Discussionmentioning

confidence: 99%

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Yang

Yue

et al. 2022

Biology

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“…The quantitative PCR primer pairs (CNV1, CNV2 and CNV3) were used to detect the copy number variations of the PPP3CA gene in different individuals, and they were designed using Primer Blast ( accessed on 12 September 2021). Following a previous study, the MC1R gene was used as internal control [ 20 ]. Additionally, all primers’ pair sequence information is shown in Table 2 .…”

Section: Methodsmentioning

confidence: 99%

“…Subsequently, the qPCR results of the copy number of the PPP3CA gene were analyzed using the 2*2 − ∆CT method, where ∆CT = Ct target − Ct internal , Ct target is the number of cycles when the target gene amplification reaches the threshold and Ct internal is the cycle number when the internal reference gene amplification reaches the threshold. The CNVs were divided into three types, Gain (2 × 2 − ∆CT ≥ 3), Loss (2 × 2 − ∆CT < 2), and Medium (2 × 2 − ∆CT = 2) [ 20 , 23 ].…”

Section: Methodsmentioning

confidence: 99%

“…In terms of the number of mutated nucleotides and the impact on the individual traits of organisms, CNV may be more important for the genetic variation and diversity of organisms than SNPs and InDels. Since CNV has a greater impact on gene regulation and expression, more studies are being conducted on CNV in important livestock and poultry species [ 18 , 19 , 20 ]. As a critical reproductive trait, litter size and semen quality affect the economic benefits of the goat industry.…”

Section: Introductionmentioning

confidence: 99%

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Investigation of Copy Number Variations (CNVs) of the Goat PPP3CA Gene and Their Effect on Litter Size and Semen Quality

Bai

Zhang

Liu

et al. 2022

Animals

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Copy number variations (CNVs) have many forms of variation structure, and they play an important role in the research of variety diversity, biological evolution and disease correlation. Since CNVs have a greater impact on gene regulation and expression, more studies are being finalized on CNVs in important livestock and poultry species. The protein phosphatase 3 catalytic subunit alpha (PPP3CA) is a key candidate gene involved in the goat fecundity trait, and has important effects on precocious puberty, estrogen signal transduction pathways and oocyte meiosis. Additionally, PPP3CA also has a dephosphorylation effect in the process of spermatogonial stem cell meiosis and spermatogenesis. So far, there is no research on the relationship between the copy number variations of the PPP3CA gene and reproduction traits. Therefore, the purpose of this study was to determine the association between copy number variations in the goat PPP3CA gene and litter size and semen quality in Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima goats (n = 64). Based on the association analysis, the results showed that only CNV1 and CNV2 within the PPP3CA gene were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10−11; p = 5.0895 × 10−9, respectively) and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). In addition, individuals with Loss genotypes demonstrated better phenotypic performance compared to those with other types. Therefore, CNV1 and CNV2 of the PPP3CA gene are potentially useful for breeding, as they are linked to important goat reproduction traits.

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“…CNVs can directly modulate phenotype by changing gene copy number (CN) and gene structure or disturbing gene regulatory sequence. Previous studies have shown that SH3RF2 -CNV was significantly associated with growth and carcase traits in chickens (Jing et al ., 2020), Opn4 -CNV were significantly associated with body weight traits (Li et al ., 2020). Numerous studies have reported the association between gene-CNV and growth traits (Feng et al ., 2020; Shi et al ., 2020; Zhang et al ., 2021).…”

Section: Introductionmentioning

confidence: 99%

Prediction and copy number variation identification of ZNF146 gene related to growth traits in Chinese cattle

Ding

Liu²,

et al. 2022

J. Agric. Sci.

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The great demographic pressure brings tremendous volume of beef demand. The key to solve this problem is the growth and development of Chinese cattle. In order to find molecular markers conducive to the growth and development of Chinese cattle, sequencing was used to determine the position of copy number variations (CNVs), bioinformatics analysis was used to predict the function of ZNF146 gene, real-time fluorescent quantitative polymerase chain reaction (qPCR) was used for CNV genotyping and one-way analysis of variance was used for association analysis. The results showed that there exists CNV in Chr 18: 47225201-47229600 (5.0.1 version) of ZNF146 gene through the early sequencing results in the laboratory and predicted ZNF146 gene was expressed in liver, skeletal muscle and breast cells, and was amplified or overexpressed in pancreatic cancer, which promoted the development of tumour through bioinformatics. Therefore, it is predicted that ZNF146 gene affects the proliferation of muscle cells, and then affects the growth and development of cattle. Furthermore, CNV genotyping of ZNF146 gene was three types (deletion type, normal type and duplication type) by Real-time fluorescent quantitative PCR (qPCR). The association analysis results showed that ZNF146-CNV was significantly correlated with rump length of Qinchuan cattle, hucklebone width of Jiaxian red cattle and heart girth of Yunling cattle. From the above results, ZNF146-CNV had a significant effect on growth traits, which provided an important candidate molecular marker for growth and development of Chinese cattle.

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Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats

Cited by 5 publications

References 23 publications

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Investigation of Copy Number Variations (CNVs) of the Goat PPP3CA Gene and Their Effect on Litter Size and Semen Quality

Prediction and copy number variation identification of ZNF146 gene related to growth traits in Chinese cattle

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