Dataset Information

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.

SUBMITTER: Kim YH

PROVIDER: S-EPMC4229737 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Variation block-based genomics method for crop plants.

Kim Yul Ho YH Park Hyang Mi HM Hwang Tae-Young TY Lee Seuk Ki SK Choi Man Soo MS Jho Sungwoong S Hwang Seungwoo S Kim Hak-Min HM Lee Dongwoo D Kim Byoung-Chul BC Hong Chang Pyo CP Cho Yun Sung YS Kim Hyunmin H Jeong Kwang Ho KH Seo Min Jung MJ Yun Hong Tai HT Kim Sun Lim SL Kwon Young-Up YU Kim Wook Han WH Chun Hye Kyung HK Lim Sang Jong SJ Shin Young-Ah YA Choi Ik-Young IY Kim Young Sun YS Yoon Ho-Sung HS Lee Suk-Ha SH Lee Sunghoon S

BMC genomics 20140615

<h4>Background</h4>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.<h4>Results</h4>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 ...[more]

PMID: 24929792

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Project description:BackgroundCrop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored.ResultsWe performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary analysis reveals that the novel exons, comparing with their flanking annotated ones, are generally under weaker selection pressure at the protein level, but under stronger pressure at the RNA level, suggesting that most of the novel exons also represent novel alternatively spliced variants (ASVs). However, we also observed the consistency of evolutionary rates between certain novel exons and their flanking exons, which provided further evidence of their co-occurrence in the transcripts, suggesting that previously-annotated isoforms might be subject to erroneous predictions. Our validation showed that 54% of the tested genes expressed the newly-identified isoforms that contained the novel exons, rather than the previously-annotated isoforms that excluded them. The consistent results were steadily observed across cultivated (Oryza sativa and O. glaberrima) and wild (O. rufipogon and O. nivara) rice species, asserting the necessity of our curation of the crop genome annotations. Our comparative analyses also inferred the common ancestral transcriptome of grass plants and gain- and loss-of-ASV events.ConclusionsWe have reannotated the rice, maize, and sorghum genomes, and showed that evolutionary rates might serve as an indicator for determining whether the identified exons were alternatively spliced. This study not only presents an effective in silico strategy for the improvement of plant annotations, but also provides further insights into the role of AS events in the evolution and domestication of crop plants. ExonFinder and the novel exons/ASVs identified are publicly accessible at http://exonfinder.sourceforge.net/ .

Dataset Information

Variation block-based genomics method for crop plants.

Publications

Variation block-based genomics method for crop plants.

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