Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Silva, Joaquim Manoel da; Giachetto, P. F.; Silva, Luiz Otávio da; Cintra, Luiz Cálice; Paiva, Samuel Rezende; Yamagishi, M. E. B.; Caetano, Alexandre Rodrigues

doi:10.1186/s12864-016-2752-9

Cited by 40 publications

(33 citation statements)

References 95 publications

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“…Compared with SNP, CNVs are longer fragments of variation with more significant effects on the growth traits of sheep. More and more copy number variation studies have been performed on different species, such as human [24], mouse [25], cattle [26,27], chicken [28], monkey [29], and sheep [30,31]. In recent years, with increasing consumer requirements for sheep quality and the development of molecular breeding, there is a need to exploit CNV molecular genetic variation for economic trait selection and disease prevention.…”

Section: Discussionmentioning

confidence: 99%

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Feng

Cheng

et al. 2020

Animals

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Simple Summary:The PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) gene is a member of the PIG gene family and encodes the glycosylphosphatidylinositol-Nacetylglucosaminyltransferase (GPI-GnT) complex. It initiates the biosynthesis of GPI and plays an important role in cell-cell interactions. Sequencing has revealed a 3600 bp copy number variation (CNV) in exon 2 of the PIGY gene in sheep, potentially altering a functional part of the protein. The CNV overlaps 28 quantitative trait loci that are relevant to some economic traits like muscle density and carcass weight. We screened for this CNV of the PIGY gene in 569 individuals, namely, 240 Chaka sheep (CKS), 168 Hu sheep (HS), and 161 small-tailed Han sheep (STHS), and analyzed the association between the presence of this CNV and sheep body size traits. The results showed that the loss-type CNV was more prevalent than other types in these three breeds, and there were significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of cannon bone of sheep. The results showed that sheep with gain-type CNV had better growth traits than those with other types. The findings reveal the relationship between the CNV of the PIGY gene and growth traits of sheep, suggesting that CNV could be utilized for improved molecular breeding of sheep.Abstract: Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601-36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

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Section: Discussionmentioning

confidence: 99%

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Feng

Cheng

et al. 2020

Animals

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“…CNV research has been extended to all types of livestock, including chicken [7,8], pig [9,10], goat [11], and sheep [12]. At the same time, more and more people are paying attention to the link between CNV and cattle health and production performance [13,14].…”

Section: Introductionmentioning

confidence: 99%

The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle

Yang

Zhang

et al. 2020

Animals

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Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.

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“…Single copy duplications (58.9 %) followed by single copy deletions (37.5 %) were the most frequent events in this Nelore population (Table 2). Similarly, Silva et al, [28] observed these two events as the most commons in 1,717 commercially available Nelore semen samples, accounting together for 97.3 % of the CNV calls identified. The distribution of the 2,119 CNVs across the bovine chromosomes is shown in Fig 1. The highest percentage of the CNV calls is located on BTA12 (10.4 %), followed by BTA15 (7.8 %), BTA7 (6.8 %) and BTA10 (6.3 %), harboring together 663 CNVs.…”

Section: Genome-wide Cnv Detectionmentioning

confidence: 68%

“…Presence of both types was observed in 14 regions. Likewise, Santana et al [27] and Silva et al [29] reported more losses than gain and mixed regions, opposing to Silva et al [28] that observed more mixed regions. CNVRs length varied from 7.2 to 2,910.2 kb, with an average of 121.3 kb.…”

Section: Cnv Regions Mapping and Association Analysismentioning

confidence: 90%

“…Therefore, many studies have been successfully performed to identify CNVs in regions containing genes affecting complex traits in livestock animals [17][18][19][20][21][22][23][24][25]. In Nelore cattle, copy number variable genes affecting growth, production, feed efficiency, environmental adaptation and meat quality traits have been reported [26][27][28][29][30][31][32]. Several factors, such as technology, array platform, array density, calling algorithm and population genetic background, influence the performance of CNV screening [33][34][35].…”

Section: Introductionmentioning

confidence: 99%

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Identificação de CNVR associadas à qualidade de carcaça e carne em bovinos da raça Nelore

Andrade¹

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The proposal of the study was to identify structural variants in the genome, named as CNVs (copy number variations), and investigate the association of CNVRs (copy number variation regions) with carcass and meat quality traits in 658 Nellore bulls with evaluation of hot carcass weight (HCW), rib-eye area (REA), subcutaneous backfat thickness (SBT), meat tenderness (TD) after 7, 14 and 21 days of aging, intramuscular fat content (IFC) and intramuscular cholesterol content (ICC). Among those, 407 animals were genotyped with the Illumina Bovine beadchip HD ® (777,962 SNPs). The PennCNV software was used to identify CNVs, which were concatenated and associated with the traits of interest by the CNVRuler program. Finally, genes overlapping total or partially the significant CNVRs (p<0.05) were identified by the BioMart package from R software using the UMD3.1 version of the bovine genome. In total, 2,119 distinct CNVs, representing 1,248 single duplications, 5 double replications, 794 single deletions and 72 double deletions, were identified. The CNVs were condensed into 475 CNVRs, covering 2.29% of the bovine genome. Of those, 59 CNVRs were significantly associated with the analyzed traits. Some genes identified in the significant CNV regions showed putative pleiotropic effect on carcass and meat quality traits, being involved in biological processes related to the immune system, cellular membrane structure, ATP binding and olfactory receptors. The identification of CNVs along the bovine genome and the association of CNVRs with carcass and meat quality traits in Nellore cattle may improve our knowledge on the biological architecture of these complex traits. In addition to enabling the development of novel selection strategies.

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Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Cited by 40 publications

References 95 publications

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle

Identificação de CNVR associadas à qualidade de carcaça e carne em bovinos da raça Nelore

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