Whole-Genome Analyses of Korean Native and Holstein Cattle Breeds by Massively Parallel Sequencing

Abstract

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data

“…Despite the higher possibility, fewer amounts of CNVRs were detected in this study; the number of CNVs indicates that HAN may have a closer genetic relationship with YAN than the European-origin breeds. The CNVRs were unevenly distributed across the genome (Figure 1), which is consistent with the findings of previous studies on cattle (Fadista et al, 2010;Stothard et al, 2011;Bickhart et al, 2012;Hou et al, 2012;Choi et al, 2013;Jiang et al, 2013;Choi et al, 2014).…”

“…The CNVRs varied in size from 1,621 bp to 161,921 bp, and the average and median sizes corresponded to 6,147 bp and 5,085 bp, respectively (Table 2). These results further support that NGS-based CNV detection can significantly improve resolution of detected CNVs, even though we applied strict parameters to accurately detect CNVs, which produces a trade-off between resolution and specificity of CNVR detection (Bae et al, 2010;Fadista et al, 2010;Hou et al, 2011;Stothard et al, 2011;Hou et al, 2012;Choi et al, 2013;Choi et al, 2014 and 90.3%) were smaller than 10 kbp (Figure 2A). …”

“…ACCEPTED MANUSCRIPT 10 et al, 2013;Choi et al, 2014). Note that the number of individuals and sequence coverage used in this study is higher than those previous studies, producing a higher chance of detecting more CNVRs in the genome.…”

“…In particular, the array-based approaches granted the opportunity to detect genome-wide CNVs at a population scale using multiple cattle breeds (Fadista et al, 2010;Hou et al, 2011;Hou et al, 2012;Jiang et al, 2013). Furthermore, recent advances in NGS technologies have successfully been used to detect CNVs with higher resolution and accuracy in cattle genomes (Stothard et al, 2011;Bickhart et al, 2012;Choi et al, 2013;Choi et al, 2014); however, sequencing is still too expensive to perform genome-wide population-scale CNV analyses.…”

Genome-wide Copy Number Variation in a Korean Native Chicken Breed

“…SNP는 전장 유전체에 걸친 대표적 유전적 다형성으로 널리 사용되고 있지만, 최근 또 다른 주요 유전적 변이로서 유전체의 구조적 변이(structural variation) 중 하나인 복제수변이(copy number variation, CNV) 가 유전적 다형성 및 진화 과정에 기여한다는 것이 밝혀졌 다 (Richard and David, 1998;Daniel et al, 1999). 이러한 CNV 는 개 (Nicholas et al, 2009), 소 (Hou et al, 2011), 젖소 (Stothard et al, 2011), 한우 Choi et al, 2014), 닭(Croojimans et al, 2013;Jia et al, 2013) (Skinner et al, 2009;Volker et al, 2010;Jia et al, 2012;Luo et al, 2013 …”