title: Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes.
abstract: This study provides high-quality variation data of diverse radish genotypes. Genome-wide SNP comparison along with RNA-seq analysis identified candidate genes related to domestication that have potential as trait-related markers for genetics and breeding of radish. Radish (Raphanus sativus L.) is an annual root vegetable crop that also encompasses diverse wild species. Radish has a long history of domestication, but the origins and selective sweep of cultivated radishes remain controversial. Here, we present comprehensive whole-genome resequencing analysis of radish to explore genomic variation between the radish genotypes and to identify genetic bottlenecks due to domestication in Asian cultivars. High-depth resequencing and multi-sample genotyping analysis of ten cultivated and seven wild accessions obtained 4.0 million high-quality homozygous single-nucleotide polymorphisms (SNPs)/insertions or deletions. Variation analysis revealed that Asian cultivated radish types are closely related to wild Asian accessions, but are distinct from European/American cultivated radishes, supporting the notion that Asian cultivars were domesticated from wild Asian genotypes. SNP comparison between Asian genotypes identified 153 candidate domestication regions (CDRs) containing 512 genes. Network analysis of the genes in CDRs functioning in plant signaling pathways and biochemical processes identified group of genes related to root architecture, cell wall, sugar metabolism, and glucosinolate biosynthesis. Expression profiling of the genes during root development suggested that domestication-related selective advantages included a main taproot with few branched lateral roots, reduced cell wall rigidity and favorable taste. Overall, this study provides evolutionary insights into domestication-related genetic selection in radish as well as identification of gene candidates with the potential to act as trait-related markers for background selection of elite lines in molecular breeding.
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea.
authors.forename: Young-Min
authors.initials: YM
authors.lastname: Jeong
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.
authors.forename: Seongmun
authors.initials: S
authors.lastname: Jeong
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
authors.forename: Goon-Bo
authors.initials: GB
authors.lastname: Kim
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
authors.forename: Seunghoon
authors.initials: S
authors.lastname: Baek
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
authors.forename: Young-Eun
authors.initials: YE
authors.lastname: Kwon
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
authors.forename: Ara
authors.initials: A
authors.lastname: Cho
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.
authors.forename: Sang-Bong
authors.initials: SB
authors.lastname: Choi
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.
authors.forename: Jiwoong
authors.initials: J
authors.lastname: Kim
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea.
authors.forename: Won-Jun
authors.initials: WJ
authors.lastname: Lim
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea.
authors.forename: Kyoung Hyoun
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea.
authors.forename: Won
authors.initials: W
authors.lastname: Park
authors.affiliation: Epigenomics Research Center of Genome Institute, Daejeon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon, 34141, Korea.
authors.forename: Jae-Yoon
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Department of Genetic Engineering, Dong-A University, Busan, 49315, Korea.
authors.forename: Jin-Hyun
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea.
authors.forename: Bomi
authors.initials: B
authors.lastname: Yim
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea.
authors.forename: Young Joon
authors.initials: YJ
authors.lastname: Lee
authors.affiliation: Breeding Research Institute, Dongbu Farm Hannong Co. Ltd., Ansung, 17503, Korea.
authors.forename: Byung-Moon
authors.initials: BM
authors.lastname: Chun
authors.affiliation: Breeding Research Institute, Dongbu Farm Hannong Co. Ltd., Ansung, 17503, Korea.
authors.forename: Young-Pyo
authors.initials: YP
authors.lastname: Lee
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 54874, Korea.
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea. yuheeju@catholic.ac.kr.
authors.forename: Hee-Ju
authors.initials: HJ
authors.lastname: Yu
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea. munjh@mju.ac.kr.
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
mesh_terms: D000071278:Domestication; D019143:Evolution, Molecular; D018745:Genome, Plant; D005838:Genotype; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D031224:Raphanus / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D018749:RNA, Plant