title: Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus.
abstract: Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Xiaona
authors.initials: X
authors.lastname: Yu
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Vignesh
authors.initials: V
authors.lastname: Dhandapani
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Jana Jeevan
authors.initials: JJ
authors.lastname: Rameneni
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Xiaonan
authors.initials: X
authors.lastname: Li
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Wenxing
authors.initials: W
authors.lastname: Pang
authors.affiliation: School of Biological Sciences, College of Natural Science, Seoul National University Seoul, South Korea.
authors.forename: Ji-Young
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University Daejeon, South Korea.
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
keywords: candidate gene; comparative mapping; morphological trait; quantitative trait loci (QTLs)