Skip to main content Accessibility help

Genetic diversity within African tomato using next generation sequencing

  • Grace W. Mungai (a1), Willis Owino (a1), Jane Ambuko (a2), J. J. Giovannoni (a3), A. B. Nyende (a1) and G. Michuki (a4)...


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.


Corresponding author

*Corresponding author. E-mail:


Hide All
Chatfield, C and Collins, AJ (1980) Introduction to Multivariate Analysis. London: Chapman and Hall.
Dewey, CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with next-generation sequencing data. BMC Bioinformatics 12: 323. doi: 10. 1186/1471-2105-12-323.
Giovannoni, JJ (2007) Fruit ripening mutants yield insights into ripening control. Current Opinion in Plant Biology 10: 283289.
Hamilton, JP, Sim, SC, Stoffel, K, Van, DA, Buell, CR and Francis, DM (2012) Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome 5: 1729.
Hirakawa, H, Shirasawa, K, Ohyama, A, Fukuoka, H, Aoki, K, Rothan, C, Sato, S, Isobe, S and Tabata, S (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes. 20: 221233. doi: 10.1093/ dnares /dst005.
Kisua, J, Mwikamba, K, Makobe, M and Muigai, A (2015) Genetic diversity of sweet and grain sorghum populations using phenotypic markers. International Journal of Biosciences 6: 3446.
Kumar, R, Tyagi, AK and Sharma, AK (2011) Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Molecular Genetics and Genomics 285: 245260.
Lawal, IO, Grierson, DS and Afolayan, AJ (2015) Phytochemical and antioxidant investigations of a Clausena anisate hook, a South African medicinal plant. African Journal of Traditional, Complementary and Alternative medicines 12: 2837. doi: 10.4314/ajtcam.v12i1.5.
Lee, TH, Guo, H, Wang, X, Kim, C and Paterson, AH (2014) SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15: 162.
Ni, Y, Hall, AW, Battenhouse, A and Iyer, VR (2012) Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genetics 13: 46.
Nielsen, PR, Albrechtsen, A and Song, YS (2011) Genotype and SNP calling from or without a reference genome. BMC Bioinformatics 12: 323. doi: 10.1371/journal.pone.0037558
Pabinger, S, Dander, A, Fischer, M, Snajder, R, Sperk, M, Efremova, M, Krabichler, B, Speicher, MR, Zschocke, J and Trajanoski, Z (2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in Bioinformatics 15: 256278. 256–78. doi: 10.1093/bib/bbs086.
Patel, RK and Jain, M (2012) NGS QC toolkit: a toolkit for quality control of next generation PLoS ONE,
Reddy, BR, Reddy, MP, Reddy, DS and Begum, H (2013) Correlation and path analysis studies for yield and quality traits in tomato (Solanum lycopersicum L.) IOSR. Journal of Agriculture and Veterinary Science (IOSRJVS) 4: 5659.
Reddy, BV, Ramesh, SR, Reddy, PS and Kumar, AA (2009) Genetic enhancement for drought tolerance in sorghum. Plant Breeding Reviews 31: 189222.
Santos, PC, Alexandre, P, Marta, SM, Almy, JC and Daniele, LR (2017) Relationship between yield and fruit quality of passion fruit C0 progenies under different nutritional levels. ISSN . doi: 10.1590/0100-29452017691.
Sathya, B, Akila, PD and Gopal, RK (2015) NGS meta data analysis for identification of SNP and INDEL patterns in human airway transcriptome: 4–9 sequencing data. PLoS ONE 7: e30619.
Shafiei, SM 2015 Apolarity for determinants and permanents of generic matrices. Journal of Commutative Algebra 7 : 89123. doi: 10.1216/JCA-2015-7-1-89.
Shirasawa, K, Ishii, K, Kim, C, Ban, T, Suzuki, M, Ito, T, Muranaka, T, Kobayashi, M, Nagata, N, Isobe, S and Tabata, S (2013) Development of capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence. Molecular Breeding 31: 101110.
Wang, K, Li, M and Hakonarson, H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38, e164. doi: 10.1093/nar/gkq603.
Wencai, Y, Xiaodong, B, Eileen, K, Christina, E, Sophien, K, Esther van der, K and David, F (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Molecular Breeding 14: 2134.
Wu, Z, Yu, D, Wang, Z, Li, X and Xu, X (2015) Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient. Scientific Reports 5: 15618. doi: 10.1038/srep15618.
Yang, WC, Bai, XD, Kabelka, E, Eaton, C, Kamoun, S, vander Knaap, E and Francis, D. (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum. By computer aided analysis of expressed sequence tags. Molecular Breeding 14: 2134.
Zhang, X, Sebastiani, P, Liu, G, Schembri, F, Dumas, Y, Langer, E, Alekseyev, E, O'Connor, Y, Brooks, LD and Spira, M (2010) Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiological Genomics 41: 18.
Zhong, S, Joung, JG, Zheng, Y, Chen, Y, Liu, B, Shao, Y, Xiang, JZ, Fei, Z and Giovannoni, JJ (2011) High-throughput Illumina strand-specific RNAsequencing library preparation. Cold Spring Harbor Protocols 8: 940949.


Related content

Powered by UNSILO
Type Description Title
Supplementary materials

Mungai et al. supplementary material
Figures S1-S4 and Tables S1-S4

 Word (108 KB)
108 KB

Genetic diversity within African tomato using next generation sequencing

  • Grace W. Mungai (a1), Willis Owino (a1), Jane Ambuko (a2), J. J. Giovannoni (a3), A. B. Nyende (a1) and G. Michuki (a4)...


Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed.