Resistance to Salinity and Water Scarcity in Higher Plants. Insights from Extremophiles and Stress-Adapted Plants: Tools, Discoveries and Future Prospects

Editorial

02 April 2019

Editorial: Resistance to Salinity and Water Scarcity in Higher Plants. Insights From Extremophiles and Stress-Adapted Plants: Tools, Discoveries and Future Prospects

Ruth Grene

Nicholas J. Provart

and

José M. Pardo

2,860 views

6 citations

Editors

Ruth Grene

Virginia Tech

Nicholas Provart

University of Toronto

Jose M Pardo

Institute of Plant Biochemistry and Photosynthesis, Spanish National Research Council (CSIC)

Impact

Comparison of growth conditions in transcriptome, proteome, metabolome, and physiological studies of extremophiles.

Mini Review

15 May 2018

Plant Life in Extreme Environments: How Do You Improve Drought Tolerance?

Ulrike Bechtold

Systems studies of drought stress in resurrection plants and other xerophytes are rapidly identifying a large number of genes, proteins and metabolites that respond to severe drought stress or desiccation. This has provided insight into drought resistance mechanisms, which allow xerophytes to persist under such extreme environmental conditions. Some of the mechanisms that ensure cellular protection during severe dehydration appear to be unique to desert species, while many other stress signaling pathways are in common with well-studied model and crop species. However, despite the identification of many desiccation inducible genes, there are few “gene-to-field” examples that have led to improved drought tolerance and yield stability derived from resurrection plants, and only few examples have emerged from model species. This has led to many critical reviews on the merit of the experimental approaches and the type of plants used to study drought resistance mechanisms. This article discusses the long-standing arguments between the ecophysiology and molecular biology communities, on how to “drought-proof” future crop varieties. It concludes that a more positive and inclusive dialogue between the different disciplines is needed, to allow us to move forward in a much more constructive way.

21,328 views

73 citations

Original Research

23 April 2018

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

Manas R. Prusty

, 5 more and

Kshirod K. Jena

9,010 views

67 citations

Original Research

20 November 2018

Jie-Jun Xi

, 6 more and

Suo-Min Wang

7,503 views

38 citations

Original Research

07 September 2018

Genome-Wide Analysis of Glycine soja Response Regulator GsRR Genes Under Alkali and Salt Stresses

Chao Chen

, 7 more and

Yanming Zhu

3,636 views

9 citations

Original Research

21 February 2018

Genotyping by Sequencing and Genome–Environment Associations in Wild Common Bean Predict Widespread Divergent Adaptation to Drought

Andrés J. Cortés

and

Matthew W. Blair

Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations (GEA) in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using genotyping by sequencing (GBS) to discover single nucleotide polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1 Mb containing associated SNPs had more positive Tajima’s D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.

8,723 views

90 citations

Conserved motifs (A) and gene structures (B) of cassava CBL proteins and genes, respectively. (A) The conserved motifs were identified using the MEME program and are arranged according to the phylogenetic tree. Different motifs are highlighted with different color boxes. The length of boxes corresponds to motif length. (B) The gene structures were drawn using the GSDS program and arranged according to the phylogenetic tree. The yellow boxes represent exons, the blue boxes represent upstream and downstream UTRs and the lines represent introns.

Original Research

02 March 2018

Expression Patterns and Identified Protein-Protein Interactions Suggest That Cassava CBL-CIPK Signal Networks Function in Responses to Abiotic Stresses

Chunyan Mo

, 4 more and

Xingyu Jiang

6,230 views

57 citations

Original Research

12 February 2018

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

Sergei A. Filichkin

, 6 more and

Pankaj Jaiswal

Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns – a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.

Dynamics of stress-driven IR in mRNA encoding poplar ovarian cancer related transcription factor (ptOCR2-L, POTRI.002G102500). This example illustrates that stress-induced increase in copy number of the fully spliced ptocr-lptocr-lptocr2-l mRNA occurs concomitantly with a decrease in the relative ratios of both retained introns. (A) RNA-Seq coverage of ptocr-lptocr-lptocr2-l locus and design of splice junction (SJ)-specific primers. Primers designated as “Spliced” detect only the isoform with fully spliced introns 4 and 5 (gene model POTRI.002G102500.1); “I4R” – intron 4 is retained whereas intron 5 is spliced (reverse primer spans I4 SJ); “IR5” – I5 is retained whereas I4 is spliced (corresponds to gene model.3; forward primer spans I4 SJ). Stars indicate Cufflinks transcript assemblies supporting retention of both fourth and fifth introns (I4R + I5R) under the heat stress in roots and the fifth intron (I5R) in xylem. Y-axis indicates the number of Illumina reads aligned to the genome. (B) Gene model and differentially retained introns of ptOCR2-L transcripts. (C–E) Quantification of mRNA absolute copy number and relative ratios of the differentially retained introns vs. fully spliced transcripts in tissues under various stress treatments. Absolute copy number of mRNA was quantified using reverse transcription – droplet digital PCR (RT-ddPCR) and event-specific primers as described in Section “Materials and Methods.”

12,641 views

110 citations

Salt tolerance evaluation of introgression line DJ15. (A) Germination rate of rice seeds after treatment at 0, 100, and 150 mM NaCl for 3 days at 35°C. (B) Survival rate of 10-day-old seedlings after treatment at 0, 100, and 150 mM for 10 days and subsequent recovery for 7 days. (C–H) Field performance of rice under non-stress field conditions (ECe = 1.3 dS m−1, pH 7.01) and under salt-stress field conditions (ECe = 5.7 dS m−1, pH 8.45). *Indicates significant difference at P < 0.05 in Tukey's multiple comparisons test after ANOVA; **Indicates significant difference at P < 0.01 in Tukey's multiple comparisons test after ANOVA.

Original Research

17 January 2018

Improvement of Salt Tolerance Using Wild Rice Genes

Ruidang Quan

, 8 more and

Rongfeng Huang

Salt stress causes significant reductions in rice production worldwide; thus, improving salt tolerance is a promising approach to meet the increasing food demand. Wild rice germplasm is considered a valuable genetic resource for improving rice cultivars. However, information regarding the improvement of salt tolerance in cultivated rice using wild rice genes is limited. In this study, we identified a salt-tolerant line Dongxiang/Ningjing 15 (DJ15) under salt-stress field conditions from the population of a salt tolerant Dongxiang wild rice × a cultivated rice variety Ningjing16 (NJ16). Genomic resequencing analysis of NJ16, DJ15 and Dongxiang wild rice revealed that the introgressed genomic fragments were unevenly distributed over the 12 chromosomes (Chr.) and mainly identified on Chr. 6, 7, 10, and 11. Using quantitative trait locus (QTL) mapping, we found 9 QTL for salt tolerance (qST) at the seedling stage located on Chr. 1, 3, 4, 5, 6, 8, and 10. In addition, sequence variant analysis within the QTL regions demonstrated that SKC1/HKT8/HKT1;5 and HAK6 transporters along with numerous transcriptional factors were the candidate genes for the salt tolerant QTL. The DJ15/Koshihikari recombinant inbred lines that contained both qST1.2 and qST6, two QTL with the highest effect for salt tolerance, were more tolerant than the parental lines under salt-stress field conditions. Furthermore, the qST6 near-isogenic lines with IR29 background were more tolerant than IR29, indicating that qST1.2 and qST6 could improve salt tolerance in rice. Overall, our study indicates that wild rice genes could markedly improve the salt tolerance of cultivated rice.

13,744 views

100 citations