Journal Article

Quantitative Trait Loci Mapping in <i>Brassica rapa</i> Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of <i>Brassica</i> Species

Xiaonan Li, Nirala Ramchiary, Vignesh Dhandapani, Su Ryun Choi, Yoonkang Hur, Ill-Sup Nou, Moo Kyoung Yoon and Yong Pyo Lim

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 20, issue 1, pages 1-16
Published in print February 2013 | ISSN: 1340-2838
Published online December 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss029

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Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species.

Keywords: Brassica rapa; quantitative trait loci (QTL); morphological traits; single nucleotide polymorphism (SNP); conserved genome blocks

Journal Article.  7948 words.  Illustrated.

Subjects: Genetics and Genomics

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