Morphological and Transcriptome Analysis of Selected African Tomato and Eggplant Accesions for Improved Adaptability, Quality and Quantity

Abstract

RNA sequence (RNASeq), a high – throughput sequencing technology that can generate information for characterizing RNA content and the composition of a given sample. African Solanaceae crops survive in very harsh conditions and have been used in Africa for decades as a source of food and for income. Despite the economic and nutrition importance of the African tomato and African eggplants have been underutilized because of lack of adequate information on their morphological and transcriptomic analysis. The main objectives of this study were to analyze the African tomato and eggplant transcriptome using morphological and RNASeq techniques to unveil genes associated with resistance to biotic and abiotic stress as well as genes associated with able to improve productivity and quality of the currently cultivated exotic varieties. Complete randomized block design and balanced block chain design were used to set up morphological and transcriptomic experiments respectively. A total of 67 African tomato and 72 African eggplant accessions morphological traits were analyzed using the standard phenotype descriptors. Out of the initial accessions, ten African eggplants and seventeen African tomato accessions were selected and planted, each with three biological replicates for transcriptomic analysis. Genstat and Darwins softwares were used to analyze data generated from vegetative and reproduction morphology characterization experiments. Vegetative and reproduction morphological traits were sampled for mophological characterization. For transcriptome analyses, leaf samples were collected 3 weeks after planting while fruit samples at mature green, mature breaker and mature red stage. Raw Sequences were cleaned and filtered using the Next Generation Sequencing Tool kit while TopHat software was used to identify differential gene expression, Single nucleotide polymorphism mining, gene ontology and gene of interest comparison. The filtered sequences of African tomato were aligned to the reference genome using TopHat while in African eggplants, de novo assembly was done using Trinity software. An in house reference genome was constructed using all the 80 African eggplant sample sequence from all the four stages. The generated reference genome was used to align the African eggplant accessions using TopHat. The findings of the morphological study reveal significant variation within African tomato and eggplant contributed by their plant growth habit and fruit morphology. A total of 329,018,858 and 303,754,051 sequences for African eggplant and tomato respectively, were obtained after filtering. A total of 18,129 and 173,194 genes were differentially expressed from African tomato and eggplant respectively. Significant differential gene expression was observed between the various fruiting stages in both African tomato and African eggplant at α 0.001. African tomato, African eggplant accessions expressed unknown genes which could be characterized more to unveil novel genes among them for breeding. The generated African eggplant reference genome is of great use in improving the current eggplant database. The SNPs in African tomato and African eggplant accessions revealed that variation among the accessions was more dependant on epigenetic factors since they grouped according to geographical locations. Variation in the African tomato and African eggplant accession transcriptomes was mainly dependent on the fruit development stage rather than the accession. This study revealed that environmental variables have an impact on gene flow patterns, which may influence spatial and progressive dispersal of genetic variation. For the gene comparative analysis, gene expression profiles indicated that African tomato and African eggplant are closely related. There were many similar genes in the African tomato and African eggplant that confer resistance to abiotic, biotic stresses, that can be used to improve shelf life and yield to cultivated commercial cultivars. Transcriptome analysis is able to reveal genes that are being actively expressed in specific tissue and species of interest.