Dataset Information

Genomic Analysis of the SUMO-Conjugating Enzyme and Genes under Abiotic Stress in Potato (Solanum tuberosum L.).

ABSTRACT: SUMO-conjugating enzymes (SCE) and SUMO (Small Ubiquitin-Like Modifiers) genes are important components of SUMOylation. SCE has a crucial role during the SUMOylation process which acts as a catalyst to transfer SUMO to the target protein. Comprehensive studies on SCE and SUMO have been performed in some plants, but studies on these genes remain limited in potato. This study is aimed at exploring the role of StSCE and StSUMO genes in abiotic stress conditions. Nine and seven putative StSCEs and StSUMO genes, respectively, were identified using different methods and databases available for potato. Chromosomal localization showed that SCE and StSUMO genes are unevenly distributed on 7 different chromosomes. Potato genome database was accessed for the expression profile of StSCE and StSUMO genes, and these genes were differentially expressed in different tissues and organs during different phases of plant growth. The expression patterns on different treatments were further evaluated using qRT-PCR for all the StSCE and StSUMO genes. The expression was upregulated in StSCE1/5/6 and 7 under salt and PEG treatment. StSUMO 1/2 and 4 were upregulated under salt stress whereas StSCE9 and StSUMO2 and 4 were observed downregulated under PEG treatment. The results of this study could be useful to explore the role of StSCE genes in potato improvement.

SUBMITTER: Ghimire S

PROVIDER: S-EPMC7335410 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genomic Analysis of the SUMO-Conjugating Enzyme and Genes under Abiotic Stress in Potato (Solanum tuberosum L.).

Ghimire Shantwana S Tang Xun X Zhang Ning N Liu Weigang W Qi Xuehong X Fu Xue X Si Huaijun H

International journal of genomics 20200624

SUMO-conjugating enzymes (SCE) and SUMO (Small Ubiquitin-Like Modifiers) genes are important components of SUMOylation. SCE has a crucial role during the SUMOylation process which acts as a catalyst to transfer SUMO to the target protein. Comprehensive studies on SCE and SUMO have been performed in some plants, but studies on these genes remain limited in potato. This study is aimed at exploring the role of StSCE and StSUMO genes in abiotic stress conditions. Nine and seven putativ ...[more]

PMID: 32802829

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Project description:Drought stress can seriously affect tuberization, yield and quality of potato plant. However, the precise molecular mechanisms governing potato stolon's response to drought stress and water supply are not very well understood. In this work, a potato (Solanum tuberosum L.) variant, Ningshu 4, was subjected to severe drought stress treatment (DT) and re-watering treatment (RWT) at tuber bulking stage. Strand-specific cDNA libraries of stolon materials were constructed for paired-end transcriptome sequencing analyses and differentially expressed gene (DEG) examination. In comparison to untreated-control (CT) plants, 3189 and 1797 DEGs were identified in DT and RWT plants and 4154 solely expressed DEGs were screened out from these two comparison groups. Interestingly, 263 genes showed opposite expression patterns in DT and RWT plants. Among them, genes homologous to Protein Phosphatase 2C (PP2C), Aspartic protease in guard cell 1 (ASPG1), auxin-responsive protein, Arabidopsis pseudo response regualtor 2 (APRR2), GA stimulated transcripts in Arabidopsis 6 (GASA6), Calmodulin-like protein 19 (CML19), abscisic acid 8'-hydroxylases and calcium-transporting ATPase, et al. were related with drought-stress and water stimulus response. Sixteen DEGs involved in starch synthesis, accumulation and tuber formation exhibited significantly different expression upon re-watering. In addition, 1630, 1527 and 1596 transcription factor encoding genes were detected in CT, DT and RWT. DEGs of ERF, bHLH, MYB, NAC, WRKY, C2H2, bZIP and HD-ZIP families accounted for 50% in three comparison groups, respectively. Furthermore, characteristics of 565 gene ontology (GO) and 108 Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were analyzed with the 4154 DEGs. All these results suggest that the drought- and water-stimulus response could be implemented by the regulated expression of metabolic pathway DEGs, and these genes were involved in the endogenous hormone biosynthesis and signal transduction pathways. Our data provide more direct information for future study on the interaction between key genes involved in various metabolic pathways under drought stress in potato.

Project description:BackgroundInvertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (Solanum tuberosum), invertases are involved in 'cold-induced sweetening' of tubers, an adaptive response to cold stress, which negatively affects the quality of potato chips and French fries. Linkage and association studies have identified quantitative trait loci (QTL) for tuber sugar content and chip quality that colocalize with three independent potato invertase loci, which together encode five invertase genes. The role of natural allelic variation of these genes in controlling the variation of tuber sugar content in different genotypes is unknown.ResultsFor functional studies on natural variants of five potato invertase genes we cloned and sequenced 193 full-length cDNAs from six heterozygous individuals (three tetraploid and three diploid). Eleven, thirteen, ten, twelve and nine different cDNA alleles were obtained for the genes Pain-1, InvGE, InvGF, InvCD141 and InvCD111, respectively. Allelic cDNA sequences differed from each other by 4 to 9%, and most were genotype specific. Additional variation was identified by single nucleotide polymorphism (SNP) analysis in an association-mapping population of 219 tetraploid individuals. Haplotype modeling revealed two to three major haplotypes besides a larger number of minor frequency haplotypes. cDNA alleles associated with chip quality, tuber starch content and starch yield were identified.ConclusionsVery high natural allelic variation was uncovered in a set of five potato invertase genes. This variability is a consequence of the cultivated potato's reproductive biology. Some of the structural variation found might underlie functional variation that influences important agronomic traits such as tuber sugar content. The associations found between specific invertase alleles and chip quality, tuber starch content and starch yield will facilitate the selection of superior potato genotypes in breeding programs.

Dataset Information

Genomic Analysis of the SUMO-Conjugating Enzyme and Genes under Abiotic Stress in Potato (Solanum tuberosum L.).

Publications

Genomic Analysis of the SUMO-Conjugating Enzyme and Genes under Abiotic Stress in Potato (<i>Solanum tuberosum</i> L.).

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