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Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin ? Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses.

ABSTRACT: In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin ?/Importin (KPN? or Imp?) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPN?s have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPN? gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPN? (Solanum tuberosum KPN?) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-? N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPN?s. Phylogenetic analysis indicated that members of StKPN? could be classified into 16 subgroups in accordance with their homology to human KPN?s, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPN?3d and StKPN?4, almost all StKPN?s were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPN?s were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPN?3a, a SA- and H2O2-inducible KPN? genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPN? gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs.

SUBMITTER: Xu Y

PROVIDER: S-EPMC7037939 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses.

Xu Ya Y Liu Lu L Zhao Pan P Tong Jing J Zhong Naiqin N Zhang Hongji H Liu Ning N

International journal of molecular sciences 20200131 3

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana</i ...[more]

PMID: 32023817

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Project description:BackgroundPotato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, which is mainly diploid and represents an important genetic resource for potato breeding. The objective of this research was to identify novel genetic variants related with frying quality in loci with key functions in carbohydrate metabolism, with the purpose of discovering genetic variability useful in breeding programs. Therefore, an association analysis was implemented with 109 SNP markers identified in ten candidate genes.ResultsThe analyses revealed four associations in the locus InvGE coding for an apoplastic invertase and one association in the locus SssI coding for a soluble starch synthase. The SNPs SssI-C 45711901 T and InvGE-C 2475454 T were associated with sucrose content and frying color, respectively, and were not found previously in tetraploid genotypes. The rare haplotype InvGE-A 2475187 C 2475295 A 2475344 was associated with higher fructose contents. Our study allowed a more detailed analysis of the sequence variation of exon 3 from InvGE, which was not possible in previous studies because of the high frequency of insertion-deletion polymorphisms in tetraploid potatoes.ConclusionThe association mapping strategy using a candidate gene approach in Group Phureja allowed the identification of novel SNP markers in InvGE and SssI associated with frying color and the tuber sugar content measured by High Performance Liquid Chromatography (HPLC). These novel associations might be useful in potato breeding programs for improving quality traits and to increase crop genetic variability. The results suggest that some genes involved in the natural variation of tuber sugar content and frying color are conserved in both Phureja and tetraploid germplasm. Nevertheless, the associated variants in both types of germplasm were present in different regions of these genes. This study contributes to the understanding of the genetic architecture of tuber sugar contents and frying color at harvest in Group Phureja.

Dataset Information

Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin ? Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses.

Publications

Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in <i>Solanum tuberosum</i> Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses.

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