2019
DOI: 10.1186/s12864-019-5687-0
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Abstract: Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pi… Show more

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Cited by 36 publications
(41 citation statements)
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“…Therefore, further development of bioinformatics algorithms and tools to generate high reliability CNVs is necessary for improving the quality of CNV studies. In the CNVs identified in this study, "deletion" events were far more frequent than "duplication" events, which concurred with the similar disequilibrium phenomenon found in studies of other species [8,27]. This may be because of the higher sensitivity of CNV calling algorithms to deletion events, as it is easier to identify a missing segment of the genome than an amplified one when there are limited numbers of sequence reads [20].…”
Section: Discussionsupporting
confidence: 89%
“…Therefore, further development of bioinformatics algorithms and tools to generate high reliability CNVs is necessary for improving the quality of CNV studies. In the CNVs identified in this study, "deletion" events were far more frequent than "duplication" events, which concurred with the similar disequilibrium phenomenon found in studies of other species [8,27]. This may be because of the higher sensitivity of CNV calling algorithms to deletion events, as it is easier to identify a missing segment of the genome than an amplified one when there are limited numbers of sequence reads [20].…”
Section: Discussionsupporting
confidence: 89%
“…We also compared our results with previous studies on CNVRs, which showed a low overlap rate [17,35,44,46,54,[57][58][59][60]. In brief, a total of 404 CNVRs entirely or partially overlapped with the previously reported CNVRs.…”
Section: Discussionsupporting
confidence: 52%
“…Accordingly, an association analysis was performed using CNVRs, with frequencies exceeding 0.5 percent [46].…”
Section: Cnvr Frequency In Two Populationsmentioning
confidence: 99%
“…The 312 CNVRs identified in this study exceeded those reported by using an SNP array in an Iberian × Landrace cross population (Ramayo-Caldas et al, 2010), Wang et al (63) in diverse populations including ten types of pig breeds , and Dong et al (105) in three Chinese pig breeds (Dong et al, 2015). As shown in Table 4, a total of 220 (70.5%) CNVRs with the length of 49.86 Mb completely or partially overlapped with CNVRs detected by other studies, with a maximum overlap of ~41.49 Mb (Stafuzza et al, 2019). In addition, the number of CNVRs overlapped with this studies varied greatly, ranging from 1 to 154, and this observation could be due to the different sample sizes and analysis platforms.…”
Section: Discussionmentioning
confidence: 84%
“…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%