Wide variation for morphological traits exists in Brassica rapa and the genetic basis of this morphological variation is largely unknown. Here is a report on quantitative trait loci (QTL) analysis of flowering time, seed and pod traits, growth-related traits, leaf morphology, and turnip formation in B. rapa using multiple populations. The populations resulted from crosses between the following accessions: Rapid cycling, Chinese cabbage, Yellow sarson, Pak choi, and a Japanese vegetable turnip variety. A total of 27 QTL affecting 20 morphological traits were detected, including eight QTL for flowering time, six for seed traits, three for growth-related traits and 10 for leaf traits. One major QTL was found for turnip formation. Principal component analysis and co-localization of QTL indicated that some loci controlling leaf and seed-related traits and those for flowering time and turnip formation might be the same. The major flowering time QTL detected in all populations on linkage group R02 co-localized with BrFLC2. One major QTL, controlling turnip formation, was also mapped at this locus. The genes that may underly this QTL and comparative analyses between the four populations and with Arabidopsis thaliana are discussed.

Flowering time is an important agronomic trait, and wide variation exists among Brassica rapa. In Arabidopsis, FLOWERING LOCUS C (FLC) plays an important role in modulating flowering time and the response to vernalization. Brassica rapa contains several paralogues of FLC at syntenic regions. BrFLC2 maps under a major flowering time and vernalization response quantitative trait locus (QTL) at the top of A02. Here the effects of vernalization on flowering time in a double haploid (DH) population and on BrFLC2 expression in selected lines of a DH population in B. rapa are descibed. The effect of the major flowering time QTL on the top of A02 where BrFLC2 maps clearly decreases upon vernalization, which points to a role for BrFLC2 underlying the QTL. In all developmental stages and tissues (seedlings, cotyledons, and leaves), BrFLC2 transcript levels are higher in late flowering pools of DH lines than in pools of early flowering DH lines. BrFLC2 expression diminished after different durations of seedling vernalization in both early and late DH lines. The reduction of BrFLC2 expression upon seedling vernalization of both early and late flowering DH lines was strongest at the seedling stage and diminished in subsequent growth stages, which suggests that the commitment to flowering is already set at very early developmental stages. Taken together, these data support the hypothesis that BrFLC2 is a candidate gene for the flowering time and vernalization response QTL in B. rapa.