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.
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.
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).
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.
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 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.
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.
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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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.
Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversificationBMC Biology 19 (2021)1. - ISSN 1741-7007
Genetic analysis of the “head top shape” quality trait of Chinese cabbage and its association with rosette leaf variationHorticulture Research 8 (2021)1. - ISSN 2052-7276
Extracting knowledge networks from plant scientific literature : potato tuber flesh color as an exemplary traitBMC Plant Biology 21 (2021)1. - ISSN 1471-2229
Potato CYCLING DOF FACTOR 1 and its lncRNA counterpart StFLORE link tuber development and drought responseThe Plant Journal 105 (2021)4. - ISSN 0960-7412 - p. 855 - 869.
Modelling the physiological relevance of sucrose export repression by an Flowering Time homolog in the long-distance phloem of potatoPlant, Cell & Environment 44 (2021)3. - ISSN 0140-7791 - p. 792 - 806.
Linked data platform for solanaceae speciesApplied Sciences 10 (2020)19. - ISSN 2076-3417
Haplotype-resolved genome analyses of a heterozygous diploid potatoNature Genetics 52 (2020)10. - ISSN 1061-4036 - p. 1018 - 1023.
Author Correction: Global status and conservation potential of reef sharksNature 585 (2020). - ISSN 0028-0836
Global status and conservation potential of reef sharksNature 583 (2020). - ISSN 0028-0836 - p. 801 - 806.
Synchronization of developmental, molecular and metabolic aspects of source–sink interactionsNature Plants 6 (2020). - ISSN 2055-026X - p. 55 - 66.
- Chengchneg Cai
- Lorena Ramirez Gonzalez
- Jorge Aleman Baez
- Li Shi
- Zihan Liu