Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica

• Published in: Theoretical and applied genetics Vol. 127; no. 9; pp. 1975 - 1989
• Main Authors: Jeong, Young-Min, Chung, Won-Hyong, Chung, Hee, Kim, Namshin, Park, Beom-Seok, Lim, Ki-Byung, Yu, Hee-Ju, Mun, Jeong-Hwan
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.09.2014; Springer Berlin Heidelberg; Springer; Springer Nature B.V
• Subjects: Agriculture; Arabidopsis thaliana; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Biotechnology; Brassica; Brassica - genetics; Brassica rapa; Brassicaceae; breeding; Chromosome Mapping; Comparative analysis; Comparative genomic hybridization; Condiments; Conserved Sequence; correlation; Crops; cultivars; Daikon; DNA, Plant - genetics; Genes; Genetic aspects; Genetic research; Genome, Plant; Genomes; genomics; Life Sciences; Original Paper; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; proteins; proteome; Radishes; Raphanus - genetics; Raphanus sativus; Sequence Analysis, DNA; Synteny; South Korea; Restriction Fragment Length Polymorphism Marker; Ancestral Karyotype; Polyploidy Event; Comparative Genome Mapping; Brassica Species
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-014-2354-3

KEY MESSAGE : This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9–92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F₂ population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.