Breeding for growth and development

The group focuses on investigating the genetic regulation of phenotypic diversity. The two main crop species that we work on are Brassica oleracea and B. rapa on the one hand, and potato at the other hand. In Brassica a main topic is to understand the enormous phenotypic diversity, ranging from cabbages to tuber forming and oilseed crops, and the role of the recent genome triplication in this. In potato, the main goal is to understand tuber development. The cloning of the earliness gene was a major break-through and is continued, with special attention to the role of external factors on tuberization.

Brassica research

In Brassica a main team is to understand the enormous phenotypic diversity, with in B. oleracea cauliflowers, cabbages, kohlrabi’s, Brussels sprouts and kale and in B. rapa a similar diversity in crops, ranging from Chinese cabbage and pakchoi to turnips and rapeseed. We develop core collections and biparental populations from crosses between different morphotypes for (association) mapping and resequence inbred lines, landraces and modern hybrids to search marks of domestication. This illustrated that the genome triplication shared by these Brassica species facilitated diversification and showed that subgenome parallel selection is associated with convergent domestication of the different crops. Key traits for investigation are leafy head formation of cabbages and tuber formation of turnips and kohlrabi’s. In addition both flowering time and leaf development, which are strictly related to diverse morphotypes, are studied. We also studied seed quality and variation in glucosinolates, both in planta but also the variation in degradation kinetics during food processing in collaboration with Food Scientists.

Extreme morphological diversity in Brassica’s

Wide variation for morphological/developmental and nutritional traits exists in both B. rapa and B. oleracea and the genetic basis of this variation is largely unknown. Our goal is to unravel the genetic regulation of this extreme (morphological) diversity.

This generates fundamental knowledge on domestication traits and very important information for Plant Breeders to select desired phenotypes. We recently demonstrated that the triplicated nature of the Brassica genome facilitated domestication of this extreme variation. Analysis of genome resequencing data of B. rapa and B. oleracea resulted in the identification of domestication signals or selective sweeps for both leafy head formation of cabbages and tubers of turnips and kohlrabi’s. This illustrated that subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in the two species B. rapa and B. oleracea (turnips/kohlrabi and heading cabbages).

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This figure shows the genetic relationships between Asian and European Brassica vegetables. To the left B. rapa, with crops like Chinese cabbages, pakchoi’s, leafy vegetables, oil-types and turnips from Asia, but also with European turnips. To the right B. oleracea with vegetables domesticated mainly in Europe, like cauliflower, cabbages, broccoli and kohlrabi, but also Chinese kale, domesticated in China.

Glucosinates in Brassica's

Glucosinolates are a group of phytochemicals that are typical for Brassica species, with a role in the interaction with pathogens and pests.

Roles of Glucosinolates

Up to 120 different GLS gave been identified with a common core structure, with several that have anti-carcinogenic properties and are largely responsible for the typical flavor and odor of Brassica species.

Key research question

We study the genetic regulation of glucosinolate composition and content in B. rapa. Compared to B. rapa, B. oleracea contains several glucosinolates like glucoraphanin, that are well studied for their health promoting properties. Since various steps in the production chain (processing/preparation) affect the level of potential health-protective glucosinolates present in consumed vegetables of the Brassica genus, we decided to study the genetic regulation of glucosinolates in the chain, from farm to fork in an interdisciplinary collaboration with food scientists. The focus was on genetic regulation of thermal glucosinolate degradation.

Brassica seed quality

Brassica seeds are used both for consumer purposes (mainly vegetable oil) and propagation (vegetables and oil crops). High quality seeds are critical for both uses. However, the genetic variations that underlie seed quality traits and seedling vigour are complex and most are governed by multiple genetic loci that have quantitative effects.

Key research question

By targeting both seed quality, with particular emphasis on seed oil content, seed germination and seedling vigour in B. rapa, our aim is to establish the relationship between these traits and to identify major regulatory loci. The acquired information will be incorporated into strategies to breed for these important agronomic traits in both B. rapa and B. napus and will accelerate cloning of causative genes.

Research populations

Our approach to genetically dissect the regulation of seed quality is to collect seeds in the onset of oil deposition (seed-filling stage) from doubled haploid populations of B. rapa for gene expression analyses. Additionally mature seed from both populations will be collected for analysis of seed quality traits and seedling vigour under optimal conditions and under stress.

eQTL studies

All microarray data will be analyzed for eQTL, and regulatory networks will be constructed, using bioinformatics tools. The taken approach is innovative, since it not only identifies QTL and candidate genes underlying the QTL for important seed quality and seedling vigour traits, but also will establish the relationship between these traits.

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Lettuce

Lettuce (Lactuca sativa) is an economically important leafy crop that is consumed globally. Lettuce breeding faces numerous challenges to develop varieties that are resistant to climate change, emerging diseases, and adapted to new agricultural settings such as vertical farming. Lactuca sativa is a self-pollinating, annual, diploid plant with 2n = 2x = 18 chromosomes and a 2.5 Gb genome. Cultivars are thus highly homozygous inbred lines but can still be crossed with wild related species (interspecific cross-compatibility). High quality reference genomes of L. sativa and its wild relatives (L. saligna and L. serriola) have been released, plus publicly available resequencing data of hundreds of accessions. Given these characteristics, lettuce stands out as an excellent leafy crop for research, with the potential to become a model plant species for leafy greens.

In this project, we examine the phenotypic and genetic variation in cultivated (and non-cultivated) lettuce germplasm under different diel length conditions, light intensities and photoperiods. We aim to identify new breeding targets for vertical farming, study their molecular mechanisms and elucidate the regulatory role that the circadian clock plays in agronomical traits. Our goal is to identify candidate phenotypes and genes that harbour allelic variation that can be selected to breed tailored lettuce cultivars for VF: with an increased resource use efficiency, yield, and quality. Ultimately, we want to contribute to VF feasibility by providing a genomics toolkit for breeders, that can be used in the development of novel lettuce genotypes.

Potato research

Potato tuberisation and the moment it occurs are very important in determining the final size distribution, number of tubers and total yield. Following on from the identification of an important regulator of tuberisation controlling potato life cycle published in Nature in 2013 and also additional research into the important role of hormones in this process. The research focus is on the interaction between the regulation of flowering and tuber formation in potato and the effects of environmental stress on potato tuberisation.