Genetic Diversity Within African Tomato Using Next Generation Sequencing
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Date
2018Author
Mungai, Grace W
Owino, Willis
Ambuko, Jane
Giovannoni, J.J
Nyende, A. B
Michuki, G
Type
ArticleLanguage
enMetadata
Show full item recordAbstract
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.
URI
https://profiles.uonbi.ac.ke/jane_ambuko/publications/genetic-diversity-within-african-tomato-using-next-generation-sequencinghttp://erepository.uonbi.ac.ke/handle/11295/153446
Citation
Mungai GW, Owino W, Ambuko J, Giovannoni JJ, Nyende AB, Michuki G. "Genetic diversity within African tomato using next generation sequencing." Plant Genetic Resources: Characterization and Utilization, . 2018;16(4): 296-305.Publisher
University of Nairobi
Rights
Attribution-NonCommercial-NoDerivs 3.0 United StatesUsage Rights
http://creativecommons.org/licenses/by-nc-nd/3.0/us/Collections
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