Salt tolerance in Solanum pennellii: antioxidant response and related QTL

Frary, Anne; Göl, Deniz; Keleş, Davut; Ökmen, Bilal; Pınar, Hasan; Şığva, Hasan Özgür; Yemenicioğlu, Ahmet; Doğanlar, Sami

doi:10.1186/1471-2229-10-58

Cited by 125 publications

(75 citation statements)

References 37 publications

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“…Evidence suggests that similar conditions for salt stress, as used in the present study, also cause simultaneous osmotic stress; therefore, altered expression of tomato DMTases under low and high salt conditions could be due to the combined effect of these two stress conditions (Zhao et al 2010). S. pennellii is a stress-tolerant tomato species that accumulated lower levels of all antioxidants than cultivated tomato under control conditions; however, it showed greater induction of all antioxidants except peroxidase under stress conditions (Frary et al 2010). Moreover, a multiple stress-responsive gene ERD15, responsible for stress tolerance, has been identified from S. pennellii (Ziaf et al 2011).…”

Section: Discussionmentioning

confidence: 57%

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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DNA methyltransferase (DMTase) enzymes contribute to plant development and stress responses by de novo establishment and subsequent maintenance of DNA methylation during replication. However, the molecular mechanism underlying this activity remains obscure, especially in crop species. Using DMTase homolog complement in six Solanaceae species, we demonstrated here that their number remained conserved in Solanum lineage, whereas it was expanded in both pepper and Nicotiana benthamiana. Non-synonymous vs synonymous (Ka/Ks) substitution ratio revealed that most of the Solanaceous DMTase homologs undergo purifying selection. The genomic sequences of tomato DMT homologs in its wild relative, Solanum pennellii, remained highly conserved in their exons and methyltransferase domains. Structure analysis further revealed highly similar folding of DMTase homologs and conservation in the residues participating in protein-protein interaction in Solanum lineage, whereas a considerable diversification was observed of pepper homologs. Transcript profiling of DMTases highlighted both similar and distinct expression patterns of tomato homologs in other species during fruit development and stress responses. Overall, our analysis provides a strong basis for in-depth exploration of both conserved as well as distinct functions of tomato DMTase homologs in other economically important Solanaceae species.

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Section: Discussionmentioning

confidence: 57%

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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“…Homologs of the aluminum transporter ALUMINUM SENSITIVE 1 and the calcium uptake transporter MID1-COMPLEMENTING ACTIVITY 1 also showed significantly elevated dN/dS pointing to positive selection in response to abiotic factors, such as soil chemistry (26,27). This second set of genes is particularly interesting considering the high salt tolerance observed in wild tomato relatives (28).…”

Section: Characterization Of Sequence Diversity In Wild and Cultivatedmentioning

confidence: 93%

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Koenig

Jiménez‐Gómez²,

Kimura

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

338

268

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Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.domestication | biotic stress | abiotic stress D omestication has long served as an important example of severe phenotypic divergence in response to selection. Darwin recognized the parallel between the processes of domestication and adaptation in the wild and used this analogy to emphasize the power of selection in generating phenotypic diversity (1). The genetic basis of domestication-associated phenotypes has been examined in several instances, most notably in maize, rice, tomato, and dogs (reviewed in refs. 2-5). The clear conclusion from these studies is that the rapid phenotypic divergence associated with domestication is often attributable to very few genetic loci (6). Improvements to DNA sequence technologies have allowed studies of the effect of domestication at the whole-genome level. Early population genetic analyses in maize found that very few genes (∼5%) show evidence of positive selection during domestication of maize (7), and recent work using whole-genome resequencing has found a similar proportion of the genome was under positive selection (8). Evidence for strong selective sweeps at a limited number of loci has also been found in rice and dog genomes (9). Together with the previous genetic mapping work, these studies support the model that relatively few mutations experienced extremely strong selection by humans during domestication.Although not the target of direct positive selection, the rest of the genome still experiences a dramatic shift in evolutionary pressures during domestication. Most characterized domestication events are associated with an extreme genetic bottleneck and alleviation of selective constraints in the original niche (10). These factors are predicted to increase the relative rate of nonsynonymous to synonymous (dN/dS) substitution, potentially resulting in the fixation of deleterious alleles (11). Previous studies comparing the distribution ...

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“…Recently, QTLs related to antioxidant content and the response of tomato antioxidants to salt-stress have also been identified. Although these QTLs may be useful for the development of higher antioxidant tomato cultivars, whether or not a direct correlation between antioxidant levels and salinity tolerance exists is more difficult to prove (Frary, Gol, Keles, Okmen, Pinar, Sigva, et al, 2010). Contrary to the notion that multiple traits introduced by breeding into crop plants are needed to implement salt-tolerant plants, one of the main strategies for improving plant salt tolerance has been through the overexpression of single genes that are either induced by stress and/or have been shown to be required for normal levels of tolerance.…”

Section: Engineering Salt Tolerance In Plantsmentioning

confidence: 99%