ArticleBMC genomics2014
Variation block-based genomics method for crop plants.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat.Plant physiology · 2022Article
- Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.PloS one · 2021Article
- A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis.PloS one · 2017Article
- Barcode System for Genetic Identification of Soybean [Frontiers in plant science · 2017Article
- Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.).Scientific reports · 2016Article
- InDel marker detection by integration of multiple softwares using machine learning techniques.BMC bioinformatics · 2016Article
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27 authors.
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Abstract
backgroundIn 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.
resultsWe 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.
conclusionsWe 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.
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