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Genetic diversity within African tomato using next generation sequencing

Published online by Cambridge University Press:  15 March 2018

Grace W. Mungai ,
Willis Owino ,
Jane Ambuko ,
J. J. Giovannoni ,
A. B. Nyende  and
G. Michuki
Grace W. Mungai
Affiliation:
Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000–00200, Nairobi, Kenya
Willis Owino*
Affiliation:
Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000–00200, Nairobi, Kenya
Jane Ambuko
Affiliation:
University of Nairobi, P.O. Box 29053-00625 Nairobi, Kenya
J. J. Giovannoni
Affiliation:
Boyce Thompson Institute of Plant Research, Cornell University, 533 Tower Road Ithaca, New York14853, USA
A. B. Nyende
Affiliation:
Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000–00200, Nairobi, Kenya
G. Michuki
Affiliation:
The Africa Genomics Centre and Consultancy Ltd P.O.BOX 381-00517 Nairobi, Kenya
*
*Corresponding author. E-mail: willis@agr.jkuat.ac.ke
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Abstract

Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). 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. The findings of this study reveal significant morphological variation among African tomato contributed by 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. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.

Keywords

biodiversityIlluminamorphologicalphylogenetic
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 4 , August 2018 , pp. 296 - 305
Copyright
Copyright © NIAB 2018 

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