Orphan no more: Ethnobotany and genetic analysis of leaf yield and secondary metabolites content in Gynandropsis gynandra (Cleomaceae)

Orphan crops have been used for centuries around the world as food, medicines and as sources of income. They also have ensured diversified and nutritious diets to local communities. However, these species have been largely absent from agricultural research agendas compared to the only a handful of commercial crops which cover 90% of human food demand. Reducing malnutrition and food insecurity in the world requires promoting novel and orphan crops. This thesis focused on developing a breeding strategy in the orphan leafy vegetable spider plant (Gynandropsis gynandra) for improved leaf yield and nutrient content.

The thesis starts with a reflection on the appropriate strategies for orphan leafy vegetable breeding using spider plant as a model (Chapter 2). G. gynandra belongs to the Cleomaceae family, the sister family of the Brassicaceae and is used as a vegetable and medicinal plant in Africa and Asia. A breeding program for the species should take into account the following components: (1) investigation of end-users preferences for the definition of breeding goals; (2) germplasm assembly, characterisation, and management; (3) the definition of product targets; (4) characterisation of the genetic control of key traits; (5) design of the process of cultivar development; (6) integration of genomics data to optimize that process; (7) multi-environment participatory trials and end-user evaluation; and (8) crop value chain development.

During germplasm collection in West Africa, observations of striking differences in the management systems of spiderplant, wild in some areas and cultivated all-year round under irrigated systems/fields/plots in others, led to an investigation of the variation in knowledge and management in seven communities in Benin and Togo (Chapter 3). Semi-structured interviews conducted with 428 respondents using cultural significance and management indices revealed that in addition to food uses, G. gynandra was used to cure 42 different diseases. The cultural importance and level of management of the species were strongly associated with ethnicity and gender. Socio-linguistic groups with similar cultural background had comparable perceptions of the cultural importance of the species and described similar management practices. An analysis of farmers’ willingness to change their current management practices revealed that migration, market opportunities, and external intervention might significantly affect future management decision-making processes. The study highlighted how understanding socio-economic and cultural context can contribute to efficient design of research for development strategies aiming at inducing changes in local communities’ management practices. Furthermore, the documented traditional knowledge on the species in surveyed areas will substantially contribute to promoting the species among potential consumers in urban areas.

Breeding programs require a good knowledge in the natural variation in traits of interest. Therefore, in Chapter 4 variation in carotenoids, tocopherols and ascorbic acid as well as morphological traits in a worldwide germplasm of 76 accessions were investigated under greenhouse conditions. The levels of carotenoids and tocopherols accumulating in the leaves varied significantly across accessions and were linked with geographical origin and morphological variation. The main carotenoids included lutein, β-carotene, α-carotene and violaxanthin. A two-fold to three-fold variation was observed for these compounds. The main tocopherols detected were α-tocopherol and γ-tocopherol with a 20-fold variation. A nine-fold variation in vitamin C concentration and independent of geographical origin was observed. Overall, the accessions were grouped into three clusters based on variation in nutrient content and morphology. West African accessions were short plants with small leaves and with high tocopherol contents and relatively low carotenoid contents; Asian accessions were short plants with broad leaves and with relatively low carotenoid and high tocopherol contents; while East/ Southern African plants were tall with high contents of both carotenoids and chlorophylls and low tocopherol contents. Carotenoids were positively correlated with plant height as well as foliar and floral traits but negatively correlated with tocopherols. The absence of a significant correlation between vitamin C and other traits indicated that breeding for high carotenoids or tocopherols content may be coupled with improved leaf yield and vitamin C content.

To further investigate the variation in secondary metabolites in the species, metabolite profiling was performed on 48 accessions using liquid-chromatography mass spectrometry to detect semi-polar metabolites and gas-chromatography mass spectrometry for volatile compounds (Chapter 5). Results revealed large variation in 936 semi-polar compounds including flavonoids, terpenoids, glucosinolates and hydroxycinnamic acid derivatives. The variation in relative levels of semi-polar metabolite profiles was mainly driven by geography, suggesting incipient speciation, with the accessions from both West Africa and Asia forming a group clearly separated from the East/Southern African accessions. Volatile organic compounds detected included different sesquiterpenes, aldehydes, ketones, and sulphur-containing isothiocyanates. The variation in these volatiles was however not geography-specific, but likely linked to the taste and odour of the accessions. The relative abundance in glucosinolates and associated volatile sulphur compounds in the leaves allowed to cluster the accessions in three main groups that could be used for future plant-herbivore interaction studies.

Chapter 6 presents the current draft genome of G. gynandra coupled with ancient polyploidy event detection and the whole-genome re-sequencing of 53 accessions from East/Southern Africa, West Africa and Asia. The genome was assembled into 1693 scaffolds and SNP calling based on the resequenced diversity panel yielded 10.8 million SNPs. Genetic diversity analyses showed that variation at the genome level was associated with geographic origin of the accessions, and identified a strong differentiation between populations, consistent with morphological characterisation and metabolome profiling. Accessions from West Africa and Asia exhibited a higher level of linkage disequilibrium suggesting that these populations diverged more recently than East/Southern African ones. Thus, the results suggest an African origin for the species, a hypothesis that needs to be further investigated with a more  comprehensive set of accessions.

In Chapter 7, SNPs called between two accessions with contrasting morphological and metabolic profiles re-sequenced in Chapter 6 allowed genotyping of 219 F2 individuals using a targeted genotyping-by-sequencing approach. The high level of segregation distortion reduced considerably the number of SNPs effectively used to build the genetic map. However, twelve quantitative trait loci were identified for leaf area, plant height, flowering time, lutein content, tocopherol content and ascorbic acid content. QTLs with pleiotropic effects were identified on linkage groups 3, 7, 9 and 16. Candidate genes identified based on homology with Arabidopsis included flowering time (FTIP1, CDKG2, MRF1), carotenoid biosynthesis (CRTISO, CYP97B3), tocopherol biosynthesis (ABC1K1, CHLP, TAT1, VTE2), leaf area (DOT3) and plant height (AGL24). No obvious candidate gene for ascorbic acid content was identified. Further validation of the QTLs is required for marker-assisted breeding for higher leaf-yield and nutrient content in the species. Finally, Chapter 8 discussed the main findings in this thesis putting them in the broader context of orphan crops breeding, presented an overview of on-going collaborative research on G. gynandra by different institutions and defined research avenues for G. gynandra breeding. This thesis is expected to be a starting point for omics-assisted breeding in G. gynandra and promotion of the species in Africa and beyond.