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A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites.

ABSTRACT: Solanum lycopersicum and Solanum habrochaites are closely related plant species; however, their cold tolerance capacities are different. The wild species S. habrochaites is more cold tolerant than the cultivated species S. lycopersicum.The transcriptomes of S. lycopersicum and S. habrochaites leaf tissues under cold stress were studied using Illumina high-throughput RNA sequencing. The results showed that more than 200 million reads could be mapped to identify genes, microRNAs (miRNAs), and alternative splicing (AS) events to confirm the transcript abundance under cold stress. The results indicated that 21% and 23% of genes were differentially expressed in the cultivated and wild tomato species, respectively, and a series of changes in S. lycopersicum and S. habrochaites transcriptomes occur when plants are moved from warm to cold conditions. Moreover, the gene expression patterns for S. lycopersicum and S. habrochaites were dissimilar; however, there were some overlapping genes that were regulated by low temperature in both tomato species. An AS analysis identified 75,885 novel splice junctions among 172,910 total splice junctions, which suggested that the relative abundance of alternative intron isoforms in S. lycopersicum and S. habrochaites shifted significantly under cold stress. In addition, we identified 89 miRNA sequences that may regulate relevant target genes. Our data indicated that some miRNAs (e.g., miR159, miR319, and miR6022) play roles in the response to cold stress.Differences in gene expression, AS events, and miRNAs under cold stress may contribute to the observed differences in cold tolerance of these two tomato species.

SUBMITTER: Chen H

PROVIDER: S-EPMC4458020 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites.

Chen Hongyu H Chen Xiuling X Chen Dong D Li Jingfu J Zhang Yi Y Wang Aoxue A

BMC plant biology 20150606

<h4>Background</h4>Solanum lycopersicum and Solanum habrochaites are closely related plant species; however, their cold tolerance capacities are different. The wild species S. habrochaites is more cold tolerant than the cultivated species S. lycopersicum.<h4>Results</h4>The transcriptomes of S. lycopersicum and S. habrochaites leaf tissues under cold stress were studied using Illumina high-throughput RNA sequencing. The results showed that more than 200 million reads could be mapped to identify ...[more]

PMID: 26048292

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Project description:BackgroundMicroRNA319 (miR319) acts as an essential regulator of gene expression during plant development and under stress conditions. Although the role of miR319a in regulating leaf development has been well studied in tomato (Solanum lycopersicum), the function of the recently discovered wild tomato Solanum habrochaites miRNA319d (sha-miR319d) remains poorly understood. In this study, we overexpressed sha-miR319d in cultivated tomato 'Micro-Tom' to further investigate its role in tomato temperature stress responses.ResultsUnder chilling or heat stress, sha-miR319d-overexpressing plants showed enhanced stress tolerance, including lower relative electrolyte leakage (REL), malondialdehyde (MDA) concentration, O2- generation and H2O2 concentration and higher chlorophyll contents and Fv/Fm values than wild-type (WT) plants. Overexpression of sha-miR319d enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), with possible correlation with elevated expression levels of the genes FeSOD, CuZnSOD and CAT. Moreover, different expression levels of key genes involved in chilling (MYB83 and CBF1), heat (HsfA1a, HsfA1b and Hsp90), and reactive oxygen species (ROS) (ZAT12 and ZAT10) signaling in transgenic plants and WT were determined, suggesting a role for sha-miR319d in regulating tomato temperature stress via chilling, heat and ROS signaling. Silencing GAMYB-like1 increased tomato chilling tolerance as well as the expression levels of CBF1, CuZnSOD, CAT, APX1, APX2, ZAT12 and ZAT10. Additionally, overexpression of sha-miR319d in tomato caused plant leaf crinkling and reduced height.ConclusionsOverexpression of sha-miR319d confers chilling and heat stress tolerance in tomato. Sha-miR319d regulates tomato chilling tolerance, possibly by inhibiting expression of GAMYB-like1 and further alters chilling, heat and ROS signal transduction. Our research provides insight for further study of the role of sha-miR319d in tomato growth and stress regulation and lays a foundation for the genetic improvement of tomato.

Project description:High temperature induced by climatic fluctuations are an important threat for plant growth, development and quality of agricultural produces. Adaptableness to environmental changes generally derives from a large set of genetic traits affecting physio-morphological, biochemical and agronomic parameters. Therefore, the identification of genotypes with higher yield and good quality parameters at high temperatures is becoming increasingly necessary for future breeding programs. Here, we analyzed the performance of different tomato genotypes grown under elevated temperatures in terms of yield and nutritional quality of the fruit. High temperature stress was induced from flower initiation to maturity stage by keeping the pots in a temperature controlled green house facility for 45 days. The quality and yield parameters were taken at the harvesting stage. Starch and soluble sugar concentration in the leaves of tomato genotypes showed significant reduction in its amount under heat stress. Titrable acidity (TA), total soluble solids (TSS) and ascorbic acid content of tomato fruits were highest under high temperature conditions compared to ambient condition but lycopene content decreased with rise in temperature. The yield attributes viz., number of fruits/plant, fruit set %, average fruit weight (g), yield per plant (g/plant) were significantly lower for Arka Saurabh, Arka Rakshak and Pusa Rohini when compared to other genotypes under study. Molecular characterization of selected 22 tomato genotypes were assessed using 25 simple sequence repeat (SSR) markers. Phylogenetic tree was constructed by the unweighted neighbour-joining method (UPGMA) using NTSYSpc cluster analysis software. The Jaccard's similarity matrix was constructed using the SIMQUAL method using UPGMA algorithm in NTSYSpc. Jaccard's similarity matrix among these tomato genotypes ranged from a minimum of 0.22 to a maximum of 1 with an average genetic similarity of 0.67. Hence this study has importance in identifying genotypes that could maintain good quality and higher yield under high temperature condition.

Dataset Information

A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites.

Publications

A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites.

Similar Datasets

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