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Title 

Variation block-based genomics method for crop plants

 

변이 블록 기반의 농작물 유전체 분석 방법론

Authors 

Y H KimH M ParkT Y HwangS K LeeM S ChoiS JhoSeungwoo HwangH M KimD LeeB C KimC P HongY S ChoH KimK H JeongM J SeoH T YunS L KimY U KwonW H KimH K ChunS J LimY A ShinI Y ChoiY S KimH S YoonS H LeeS Lee

Publisher 

BioMed Central

Issue Date 

2014

Citation 

BMC Genomics, vol. 15, no. 0, pp. 477-477

Keywords 

Comparative genomicsCrop plantsRecombinationSoybeanWhole-genome sequencing

Abstract 

Background: In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits.Results: We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color.Conclusions: We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.

ISSN 

1471-2164

Link 

http://dx.doi.org/10.1186/1471-2164-15-477

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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