title: Variation block-based genomics method for crop plants.
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.
authors.affiliation: National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea. kimyuh77@korea.kr.
authors.forename: Yul Ho
authors.initials: YH
authors.lastname: Kim
authors.forename: Hyang Mi
authors.initials: HM
authors.lastname: Park
authors.forename: Tae-Young
authors.initials: TY
authors.lastname: Hwang
authors.forename: Seuk Ki
authors.initials: SK
authors.lastname: Lee
authors.forename: Man Soo
authors.initials: MS
authors.lastname: Choi
authors.forename: Sungwoong
authors.initials: S
authors.lastname: Jho
authors.forename: Seungwoo
authors.initials: S
authors.lastname: Hwang
authors.forename: Hak-Min
authors.initials: HM
authors.lastname: Kim
authors.forename: Dongwoo
authors.initials: D
authors.lastname: Lee
authors.forename: Byoung-Chul
authors.initials: BC
authors.lastname: Kim
authors.forename: Chang Pyo
authors.initials: CP
authors.lastname: Hong
authors.forename: Yun Sung
authors.initials: YS
authors.lastname: Cho
authors.forename: Hyunmin
authors.initials: H
authors.lastname: Kim
authors.forename: Kwang Ho
authors.initials: KH
authors.lastname: Jeong
authors.forename: Min Jung
authors.initials: MJ
authors.lastname: Seo
authors.forename: Hong Tai
authors.initials: HT
authors.lastname: Yun
authors.forename: Sun Lim
authors.initials: SL
authors.lastname: Kim
authors.forename: Young-Up
authors.initials: YU
authors.lastname: Kwon
authors.forename: Wook Han
authors.initials: WH
authors.lastname: Kim
authors.forename: Hye Kyung
authors.initials: HK
authors.lastname: Chun
authors.forename: Sang Jong
authors.initials: SJ
authors.lastname: Lim
authors.forename: Young-Ah
authors.initials: YA
authors.lastname: Shin
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Young Sun
authors.initials: YS
authors.lastname: Kim
authors.forename: Ho-Sung
authors.initials: HS
authors.lastname: Yoon
authors.forename: Suk-Ha
authors.initials: SH
authors.lastname: Lee
authors.forename: Sunghoon
authors.initials: S
authors.lastname: Lee
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D018556:Crops, Agricultural / Q000235:genetics*; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D010940:Plant Proteins