Open Access Methodology article

Variation block-based genomics method for crop plants

Yul Ho Kim1*, Hyang Mi Park1, Tae-Young Hwang1, Seuk Ki Lee1, Man Soo Choi1, Sungwoong Jho2, Seungwoo Hwang3, Hak-Min Kim2, Dongwoo Lee2, Byoung-Chul Kim2, Chang Pyo Hong4, Yun Sung Cho2, Hyunmin Kim4, Kwang Ho Jeong1, Min Jung Seo1, Hong Tai Yun1, Sun Lim Kim1, Young-Up Kwon1, Wook Han Kim1, Hye Kyung Chun1, Sang Jong Lim1, Young-Ah Shin2, Ik-Young Choi5, Young Sun Kim6, Ho-Sung Yoon6, Suk-Ha Lee7 and Sunghoon Lee24*

Author Affiliations

1 National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea

2 Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea

3 Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 306-809, Republic of Korea

4 Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea

5 National Instrumentation Center for Environmental Management, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Republic of Korea

6 Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea

7 Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea

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BMC Genomics 2014, 15:477  doi:10.1186/1471-2164-15-477

Published: 15 June 2014

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.

Keywords:
Comparative genomics; Recombination; Whole-genome sequencing; Soybean; Crop plants