Mapping of QTLs controlling root shape and red pigmentation in radish, Raphanus sativus L.

Abstract

Genetic factors controlling root shape and red pigmentation on the surface of the hypocotyl (upper part of root) were investigated using a molecular linkage map based on an F₂ population derived from a cross between two radish cultivars, ‘Huang-he hong-wan’ and ‘Utsugi-gensuke’. One hundred and ninety-eight segregating markers (169 AFLPs, 28 Brassica SSRs and one SLG-CAPS) were located on 14 linkage groups (LGs) at a LOD threshold value of 5.0. The mapping position of Brassica SSRs revealed that frequent genomic rearrangements occurred between the Brassica and Raphanus genomes. Three quantitative trait loci (QTLs) for root shape with LOD values of 2.42, 3.22 and 2.88 were identified on LGs 3, 8 and 9, respectively. These three QTLs accounted for 42.4% of the phenotypic variance when joined together. Analysis of QTL(s) for root diameter revealed the presence of two QTLs on LG4 and LG8. The QTL on LG8 was considered to control root thickening and to affect the root shape. For hypocotyl pigmentation, a QTL which exerted a large genetic effect with a LOD value of 9.58, was recognized on LG 11 and accounted for 43.8% of the phenotypic variance.