Genetic diversity within African tomato using next generation sequencing

Authors: MUNGAI, GRACE - Boyce Thompson Institute; OWINO, WILLIS - Jomo Kenyatta University; AMBUKO, JANE - Jomo Kenyatta University; Giovannoni, James; NYENDE, BERNARD - Jomo Kenyatta University; MICHUKI, GEORGE - African Agricultural Technology Foundatin

Submitted to: Plant Genetic Resources: Characterization and Utilization
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2017
Publication Date: 3/15/2018
Citation: Mungai, G., Owino, W., Ambuko, J., Giovannoni, J.J., Nyende, B., Michuki, G. 2018. Genetic diversity within African tomato using next generation sequencing. Plant Genetic Resources: Characterization and Utilization. 16:296-305. https://doi.org/10.1017/S1479262117000314.
DOI: https://doi.org/10.1017/S1479262117000314

Interpretive Summary: The African tomato is an important fruit and vegetable crop. It is widely used in salads as well as for culinary purposes. The fruit contains significant amounts of vitamin A and C, lycopene, beta-carotene, magnesium, iron, phosphorus, potassium, riboflavin, niacin, sodium and thiamine with antioxidant properties and potential beneficial health effects. The African tomato exhibits broad diversity and can be produced in peripheral areas. The identification of variability among landraces is essential to the maintenance and utilization of germplasm resources. Here we performed comprehensive phenotyping and used RNA-sequencing of African tomato germplasm to identify DNA sequence variation that can be useful in varietal distinction, phylogeny and breeding. The resulting DNA sequence and trait analysis indicates broad genetic diversity, instances of common heritage and points to opportunities for genetic improvement of African tomato within existing African tomato genotypes.

Technical Abstract: Full potential of African tomato has not been tapped due to lack of information regarding its characterization. We explored the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological and transcriptome data indicated the landraces clustered into three clusters. A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. This study revealed significant morphological variation among African tomato reflected in plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations indicating common ancestry and origins and point to cultivars that may be useful in contributing relevant allelic diversity to specific African breeding programs.