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A variant block-based comparative genomics method for the detection of functional loci in soybeans

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  • URLhttps://db.koreascholar.com/Article/Detail/294497
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한국육종학회 (The Korean Breeding Society)
초록

Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.

저자
  • Yul Ho Kim(National Institute of Crop Science, Rural Development Administration) Corresponding Author
  • Tae-Young Hwang(National Institute of Crop Science, Rural Development Administration)
  • Hyang Mi Park(National Institute of Crop Science, Rural Development Administration)
  • Seuk Ki Lee(National Institute of Crop Science, Rural Development Administration)
  • Man Soo Choi(National Institute of Crop Science, Rural Development Administration)
  • Seung woo Hwang(Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
  • Kwang Ho Jeong(National Institute of Crop Science, Rural Development Administration)
  • Min Jung Seo(National Institute of Crop Science, Rural Development Administration)
  • Hong Tai Yun(National Institute of Crop Science, Rural Development Administration)
  • Sun Lim Kim(National Institute of Crop Science, Rural Development Administration)
  • Young-Up Kwon(National Institute of Crop Science, Rural Development Administration)
  • Ho-Sung Yoon(Department of Biology, Kyungpook National University)
  • Suk-Ha Lee(Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University)
  • JongBhak(Theragen Bio Institute, TheragenEtex, Personal Genomics Institute, Genome Research Foundation)
  • Sunghoon Lee(Theragen Bio Institute, TheragenEtex, Personal Genomics Institute, Genome Research Foundation)