A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

Revilla, Manuel; Puig-Oliveras, Anna; Castelló, Anna; Crespo-Piazuelo, Daniel; Paludo, E.; Fernández, Ana; Ballester, María; Folch, Josep María

doi:10.1371/journal.pone.0177014

Cited by 38 publications

(43 citation statements)

References 60 publications

(77 reference statements)

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“…The average frequency of duplications was higher than that of deletions in both Duroc and Meishan pigs in the present study. Revilla et al also found duplications showed a higher average frequency than did deletions (106 vs. 77) in a global analysis of CNVs in swine [12]. Similar pattern was also observed in another CNV study in porcine using a 60 k SNP BeadChip, the predicted status for the CNVRs in this study was 38.7% for gain, and 16.3% for loss [44].…”

Section: Characteristic and Functional Analysis Of The Cnvrssupporting

confidence: 89%

“…Besides the OR gene family, we also found some genes involved in immunity and cytochrome P450, such as CYP4A24, CYP2C42 and CYP3A29. These results were observed in previous swine CNV studies [12,14], and together with ORs, CNV in CYP450 genes suggests a relevant role of these genes in the organism's adaptation to rapid changes in the environment [14]. Among KEGG pathways, we found the Ras signaling pathway and MAPK signaling pathway were included.…”

Section: Characteristic and Functional Analysis Of The Cnvrssupporting

confidence: 84%

“…For instance, Chen et al identified 1,315 putative CNVs belonging to 565 CNVRs in 1,693 pigs from 18 diverse populations using Porcine SNP60 BeadChip and PennCNV algorithm and revealed 7 copy number variable genes as candidate genes related to carcass length, backfat thickness, abdominal fat weight, length of scapular [11]. Revilla et al [12] identified 1,279 CNVs and 540 CNVRs using whole genome data and they provided candidate genes for fatty acid composition and growth traits. Jiang et al [13] indicated the total CNVRs amounted to 4.0% based on the porcine genome (Sus scrofa build10.2) and most CNVRs fell into the interval between 10 kb and 20 kb.…”

Section: Introductionmentioning

confidence: 99%

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CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

Zheng

Zhao

Yang

et al. 2020

J Animal Sci Biotechnol

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Background: Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood. Results: In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by nextgeneration sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight. Conclusions: The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

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Section: Characteristic and Functional Analysis Of The Cnvrssupporting

confidence: 89%

Section: Characteristic and Functional Analysis Of The Cnvrssupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

Zheng

Zhao

Yang

et al. 2020

J Animal Sci Biotechnol

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“…Currently, there are three main platforms, including comparative genomic hybridization (CGH;De Smith et al, 2007;Li et al, 2012), SNP arrays (Dong et al, 2015;Ma et al, 2017;Stafuzza et al, 2019) and next-generation sequencing (NGS; Jiang et al, 2014;Paudel et al, 2013;Revilla et al, 2017), which have been used extensively to detect CNVs in humans and animals. Compared to the CGH and NGS, SNP arrays have an advantage in large-scale CNV detections due to their lower cost, particular at the genome-wide scale (Dong et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip

Wang

Zhang

Wang

2019

J Animal Breeding Genetics

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Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome‐wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.

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“…Recently, CNV maps in cattle [35], sheep [43] and pigs [44] have been constructed, indicating that structural polymorphisms within them constitute an important proportion of their genomes. Furthermore, CNVs have been associated with various growth traits, such as body length in cattle [45] and pigs [46] and pigmentation traits in goats [47] and horses [48], in addition to reduced immunological resistance to diseases [49]. Consistent with these results, it is widely believed that this form of genetic variation in livestock is of great importance to phenotypic traits.…”

Section: Discussionmentioning

confidence: 77%

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Chen

et al. 2019

Animals

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Simple Summary: Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss-or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects.Abstract: Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.Animals 2019, 9, 1008 2 of 11 polymorphisms (RFLP), single nucleotide polymorphisms (SNP), indels (Insertion/Deletion) and structural variations, such as inversions, duplications and deletions. To date, SNPs are used extensively for complex economic disease traits in livestock [2][3][4][5]. More than 99% of indels are less than 50 bp in length [6,7], and some long insertions and deletions are returned into the concept of structural variation [8]. As a genetic marker, indels have great potential whether in growth and reproduction...

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A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

Cited by 38 publications

References 60 publications

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

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