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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 2 (2012 Deadline)

Harnessing genomics of edible African Solanaceae plants for improved nutritional and food security

PI: Willis Owino (Kenyatta University of Agriculture & Technology), with co-PI Jane Ambuko (University of Nairobi)
U.S. Partner: James Giovannoni (Cornell University)
Project Dates: August 2013 to January 2016

Plant genetic diversity is the principal resource for crop improvement efforts. Africa maintains thousands of wild crop relatives to be collected, studied, and documented to facilitate use in improved crop varieties to meet the challenges of food security in the face of rising food demand. Abundant genetic resources in the developed world for Solanaceae crops, including the tomato and the potato, has provided a springboard for plant genomics to assist in the exploitation of underutilized crops and enhance productivity, sustainability, and quality. In turn, developing world germplasm and scientific resources have significant potential for impact on developed world agriculture. There is great potential for both developed and developing countries to benefit from enhanced productivity and sustainable resource utilization to promote greater nutritional security.
The primary goal of this project is to use existing Solanaceae genome resources and state-of-the-art technologies in the Western world to characterize genetic diversity and nutrient/non-nutrient metabolite compounds in Solanaceae crops of importance to smallholder farmers and consumers. The project team aims to provide a foundation of plant genomics useful for improvement of indigenous African fruits and vegetables. The project team will engage local breeders to identify Solanaceae germplasm representing a spectrum of genetic diversity to be used in agronomic improvement programs targeting sustainability, nutrition, and food security. The resulting resources will aid in (1) variety identification, (2) assessment of genetic diversity, (3) development of genetic linkage maps, (4) marker-assisted selection of yield and nutritional traits, and (5) linkage to fruit nutrient and performance quality traits and postharvest loss relevant to local food security. Results obtained through this project will also be incorporated into the Solanaceae(SOL) Genomics Network Database, the NSF-funded project of the U.S. partner, which constitutes one of the main meeting, data storage, and data enabling resource for the Solanaceae community worldwide.

Summary of Recent Activities

 The project came to an end in April 2016. The PI and his team had the following work plan with the below specific objectives:

1. To create a stable and accurate African Solanaceae germplasm resource.
The team collected tomato and African eggplant accessions from various sources including the Kenya Gene Bank, farmers in Eastern and Western provinces and the World Vegetable Centre. To date they have established a germplasm collection at the Jomo Kenyatta University of Agriculture and Technology (JKUAT) comprising 67 tomato and 74 African eggplants accessions. They then characterized the tomato accessions to identify desirable morphological and agronomic traits that could be used in tomato crop improvement. Field and greenhouse experiments were laid out in a randomized complete block design with three replicates at the University of Nairobi’s Kabete field station, and in JKUAT in 2014 and 2015. Characters were evaluated based on International Plant Genetic Resources Institute tomato descriptor list on 14 Agronomic and 10 morphological traits at flowering and fruiting stages.
The analysis of variance indicated high significant differences in the accessions for all the agronomic traits evaluated. The results indicated that the characters contributing most to variability were growth type, foliage density, fruit size and fruit cross sectional shape. Cluster analysis using un-weighted pair group method with arithmetic mean classified the genotypes into two. Cluster I contained 63 accessions while cluster II had 6 accessions. Thus, this study revealed the presence of sufficient morphological and agronomic diversity among accessions evaluated that can be exploited further to establish existent genetic for tomato improvement.

As for the African eggplants, morphological data collected was subjected to Genstat’s univariate analysis, bivariate, multivariate and Darwin6 software for statistical analysis. The dendogram grouped the accessions into two main clusters with majority falling in cluster 2 revealing a narrow genetic base in the cluster. The findings of this study reveal significant variation among the selected African eggplant mainly contributed by plant height, leaf blade length, leaf blade width and fruit width. Substantial variation among the 67 accessions was also observed in fruit color, fruit shape, fruit texture, leaf base and leaf lade color. Variation in growth, fruit yield and nutritional quality exist among African eggplant accessions hence enabling the breeders to use the well adapted accessions like RV100200, RV100445 and GBK 050572 in breeding programs.

2. Development of whole genome and transcriptome DNA sequence resources using high throughput Next generation sequencing for better classification and characterization of orphan African Solanaceae species.

The mRNA extracted from leaf and fruit samples was sequenced using the Illumina next generation sequencer to evaluate the genetic makeup, Statistical data analysis was done using Genstat and Darwin 6 software. Seven (7) of 14 Principal components were significant accounting for 68.51 % of the total variation. Strong positive correlation between leaf length and leaf width (r= 0.7203**), fruit colour and fruit shoulder colour (r=0.7687**) was observed. Fruit length had strong positive correlation with fruit width, and fruit yield (r=0.6536** and 0.6571**) respectively. However, fruit length had a negative correlation to fruit surface texture (r=-0.2400**) while fruit width had strong correlation (r= 0.9301**) with fruit yield and negative correlation with fruit texture (r= -0.4040**)
The sequence data analyses is yet to be completed but we can generally conclude that African aggplant and Tomato has diverse fruit, vegetative traits and novel genes that can be utilized in plant breeding programs to improve the currently cultivated accessions for better yield and nutrition improvement.

 3. To evaluate the metabolite profiles of the collected accessions.
We established the effect of drought stress on carotenoid profiles of nineteen African eggplant accessions selected based on leaf and fruit morphological traits. Fresh leaves were sampled at different maturity stages; before stress, 2 weeks and 4 weeks after stress for carotenoid analysis. The fresh harvested leaf tissues were immediately frozen in liquid nitrogen and ground. Analysis was carried out using a Dionex HPLC machine coupled to Photo Array Detector and Chromeleon software package. Major carotenoids viz;. Xanthophylls (neoxanthin, violaxanthin, zeaxanthin and lutein) and carotenes (β–carotene and α–carotene), phytofluene, lycopene, phytoene as well as chlorophylls (chlorophyll-b and Chlorophyll-a) were targeted. The carotenoids increased with maturity stage of the crop. Although the stressed crops reported significantly decreased amount of carotenes, chlorophylls, neoxanthin and violaxanthin, the concentration of zeaxanthin increased with stress whereas lutein had no significant change. Chlorophyll-a was significantly high in all the control accessions. Two accessions reported significantly higher contents of carotenoids as compared to the other accessions. The results of this study indicate that water stress has significant impact on the concentration of some carotenoids and photosynthetic pigments. This knowledge if well exploited will have significant implications for farmers and could unlock the potential for stress management for improved food security and sustainable livelihoods in Africa.