Genetic analysis of breeding-related traits in Brassica rapa

Brassica rapa is an important crop with a variety of forms, and a wide distribution in the world. It is used as oil seed and vegetable crop and a valuable source of diverse health-promoting metabolites. It also can serve as a model for genetic and molecular analysis in the Brassica genus, to which all rapes, kales and cabbages belong, as it has the smallest genome size and some genotypes with a rapid life cycle.
Insertional mutagenesis using heterologous maize transposons has been a valuable tool for the identification and isolation of genes in Arabidopsis. Transposon-based activation tagging systems use a construct with constitutive enhancer elements that can cause transcriptional activation of flanking plant genes, which can result in dominant mutant phenotypes and subsequent isolation of the genes involved. Chapter 2 describes the action of an En/I activation tagging construct in B. rapa through Agrobacterium rhizogenes–mediated hairy root transformation. Successful transformation of this construct to B. rapa ssp. by A. tumefaciens was not achieved, probably due to the combination of an inefficient plant transformation and regeneration system, the length of the construct and most importantly the presence of the SU1 gene in the construct that appears to inhibit the regeneration of transformed shoots.

As an alternative to the insertional mutagenesis approach to identify genetic loci that impact traits, there is a genetic approach based on quantitative trait locus (QTL) analysis. Segregating populations are needed to map QTLs for traits of interest. Chapter 3 describes the analysis of an F2 population derived from a cross between two distinct, but early flowering and self compatible, B. rapa genotypes, L58 and R-o-18. Amplified fragment length polymorphism (AFLP) markers together with simple sequence repeat (SSR) markers were used to genotype this F2 population and anchor the linkage map to the reference genetic map of B. rapa. Highly significant QTLs associated with the production of adventitious roots and the transformation competence to A. rhizogenes were detected, which will allow the selection of lines that are more efficient in transformation experiments. The analysis detected a strong QTL associated with seed coat color as well as QTLs for various morphological traits.

To fix the recombination events as much as possible and to obtain an “immortal” mapping population, a recombinant inbred line (RIL) population was developed from this F2 population. Chapter 4 describes development of this RIL population, for which a genetic linkage map was constructed using the Illumina® BeadXpressTM genotyping platform of Keygene NV and additional SSR markers. Analysis revealed an additional QTL for seed coat colour as well QTL for pod shattering, carpel number, cuticular wax and seed vivipary. Chapter 5 describes the detection of QTLs related to primary and secondary metabolites in this RIL population. The two parental lines show clear differences in metabolite profile, which allowed the finding of QTLs for glucosinolates, phenylpropanoids, glucose, glutamate and amino acids after analysis with H1- NMR. HPLC analysis of tocopherols revealed four QTLs controlling the levels of this important antioxidant.

The information on the genetic control of health related compounds indicates the potential to improve nutritional quality in classical crop breeding programs.