Biology subjects

van Zonneveld, M.

Publications and source records attributed to van Zonneveld, M..

5 recordsLinked to original sources

bioRxiv2025

Assessment of Genetic Resources to Major Tomato Diseases: Insights from wild germplasm and public S. lycopersicum collections

Tomato (Solanum lycopersicum L.) production is severely impacted by biotic stresses, leading to significant yield losses. Developing genetically resistant cultivars presents a sustainable alternative to chemical control, which is often costly and ineffective against evolving pathogens. This study utilized molecular markers to assess genetic resistance to key tomato diseases, including Fusarium wilt, late blight, bacterial wilt, root-knot nematode, Tomato Mosaic Virus (ToMV), and Tomato Yellow Leaf Curl Virus (TYLCV), across 964 tomato accessions comprising both wild germplasm and cultivated varieties. Wild germplasm exhibited the highest frequencies, with S. peruvianum identified as a rich reservoir of resistance loci. Markers associated with TYLCV (Ty-1/3, Ty2) and Fusarium wilt (I2(OH)) were particularly prevalent in wild species. The potential for gene pyramiding potential was evident, with some wild accessions carrying up to six resistance loci. In contrast, resistance loci were limited in Solanum lycopersicum. Two S. lycopersicum germplasm collections were screened: a geographically representative collection from four Southeast Asian national genebanks and a genetically representative core collection from global public genebanks. The highest resistance frequencies in S. lycopersicum were observed for bacterial wilt-associated markers SLM12-2 and SLM12-10. However, the overall scarcity of resistance alleles in S. lycopersicum emphasizes the need for further introgression of resistance genes from wild relatives. This study provides valuable genetic insights into tomato germplasm for combating biotic stress, forming a foundation for sustainable breeding strategies to enhance disease resistance and safeguard global tomato production.

plant biology↗

bioRxiv2024

Association analyses reveal both anthropic and environmental selective events during eggplant domestication

Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the Genome-wide association (GWA) of historical genebank phenotypic data on a genotyped worldwide collection of 3,449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a Genotype-Environment Association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association (OA) identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.

genomics↗

bioRxiv2024

Citizen science informs demand-driven breeding of opportunity crops

CONTEXTOpportunity crops, also known as neglected and underutilized species (NUS), offer benefits to diversify food systems with nutritious and climate-resilient foods. A major limitation to incorporate these crops in farming systems is the lack of improved varieties impedes farmers accessing quality planting material of these crops. OBJECTIVESThe study explored how citizen science methods can support demand-driven breeding and seed production of opportunity crops using leafy amaranth - a nutritious and hardy vegetable- as a case study. The study identified farmer preferences and market segments, with particular attention to gender and social differentiation. METHODSWe used the tricot approach to conduct participatory on-farm trials of 14 varieties with 2,063 farmers from Benin, Mali, and Tanzania. We then analyzed farmer trait and varietal preferences in aggregate and among segments of farmers, generated using cluster analysis. RESULTSFarmers overall preferences for amaranth varieties was driven principally by plant survival, yield, leaf size, taste, and marketability. Distinct farmer segments (older women generalists, young women specialists, older men generalists, and young men specialists) preferred different varieties depending on gender, business-orientation. DISCUSSION AND CONCLUSIONThe farmer segments identified here, along with their unique variety preferences provide valuable information for breeders and seed enterprises, and support demand-driven amaranth breeding and seed system development. We specifically noted the need for breeding programs to understand the preferences of young amaranth specialists, both men and women, and to explore organoleptic and market-related properties of amaranth. SIGNIFICANCEOur findings on differentiated producer preferences will support scaling seed supply of amaranth in Africa to diversify farming systems with a climate-resilient and nutritious crop. The methods used and lessons learned from our citizen science exercise can be applied to enhance breeding and seed supply of other opportunity crops that are underutilized in Africa or other continents. HighlightsO_LIFarmer citizen science methods reveal seed market insights for opportunity crops C_LIO_LIAmaranth variety preferences vary widely across gender, age, and countries C_LIO_LIYoung amaranth producers focus on market and sensory traits compared to old producers C_LIO_LILarge-scale farmer feedback guides opportunity crop breeding for diverse segments C_LI

plant biology↗

bioRxiv2021

De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

Amaranths serve as pseudo cereals and also as traditional leafy vegetables worldwide. In addition to high vigor and richness in nutrients, drought and salinity tolerance of amaranth makes it a promising vegetable to acclimatize to the effects of global climate change. The World Vegetable Center genebank conserves about 1,000 amaranth accessions and various agronomic properties of these accessions were recorded during seed regeneration over decades. In this study, we verified the taxonomic annotation of the germplasm based on a 15K SNP set. Besides, in the assumption that the yield components of grain amaranths are different from those of leaf amaranths, we observed that grain amaranths presented larger inflorescences and earlier flowering than leaf amaranths. Dual-purpose amaranth showed larger leaves than leaf amaranths and later flowering than grain amaranths, which seemed reasonable because farmers can harvest more leaves during the prolonged vegetable stage, which also provides recovery time to enrich grain production. Considering frequent interspecies hybridization among grain amaranth complex, we proposed an interspecies GWAS for days to flowering, identifying a AGL20/SOC1 homolog. Meanwhile, another GWAS using only A. tricolor accessions revealed six candidate genes homologous to lba1, bri1, sgs1 and fca. These homologous genes were involved in the regulation of flowering time in Arabidopsis. This study revealed the usefulness of genotypes for species demarcation in the genus Amaranthus and the potential of interspecies GWAS to detect QTLs across different species, opening up the possibility of targeted introduction of specific genetic variants into different Amaranthus species.

genomics↗

bioRxiv2019

Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding

Although new varieties are urgently needed for climate-smart legume production, legume breeding lags behind with cereals and underutilizes wild relatives. This paper provides insights in patterns of abiotic and biotic stress resilience of legume crops and wild relatives to enhance the use and conservation of these genetic resources for climate-smart legume breeding. We focus on Vigna, a pantropical genus with more than 88 taxa including important crops such as cowpea and mung bean. Sources of pest and disease resistance occur in more than 50 percent of the Vigna taxa, which were screened while sources of abiotic stress resilience occur in less than 20 percent of the taxa, which were screened. This difference suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses or tolerate salinity. These rare Vigna taxa should be prioritized for conservation and screening for multifunctional traits of combined abiotic and biotic stress resilience. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits compared with drought-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that suffer from salinization.

plant biology↗