Salt stress responses and SNP-based phylogenetic analysis of Thai rice cultivars

Profiling of Key Hub Genes Using a Two-State Weighted Gene Co-Expression Network of 'Jao Khao' Rice under Soil Salinity Stress Based on Time-Series Transcriptome Data

RNA-sequencing enables the comprehensive detection of gene expression levels at specific time points and facilitates the identification of stress-related genes through co-expression network analysis. Understanding the molecular mechanisms and identifying key genes associated with salt tolerance is crucial for developing rice varieties that can thrive in saline environments, particularly in regions affected by soil salinization. In this study, we conducted an RNA-sequencing-based time-course transcriptome analysis of 'Jao Khao', a salt-tolerant Thai rice variety, grown under normal or saline (160 mM NaCl) soil conditions. Leaf samples were collected at 0, 3, 6, 12, 24, and 48 h. In total, 36 RNA libraries were sequenced. 'Jao Khao' was found to be highly salt-tolerant, as indicated by the non-significant differences in relative water content, cell membrane stability, leaf greenness, and chlorophyll fluorescence over a 9-day period under saline conditions. Plant growth was slightly retarded during days 3-6 but recovered by day 9. Based on time-series transcriptome data, we conducted differential gene expression and weighted gene co-expression network analyses. Through centrality change from normal to salinity network, 111 key hub genes were identified among 1,950 highly variable genes. Enriched genes were involved in ATP-driven transport, light reactions and response to light, ATP synthesis and carbon fixation, disease resistance and proteinase inhibitor activity. These genes were upregulated early during salt stress and RT-qPCR showed that 'Jao Khao' exhibited an early upregulation trend of two important genes in energy metabolism: RuBisCo (LOC_Os10g21268) and ATP synthase (LOC_Os10g21264). Our findings highlight the importance of managing energy requirements in the initial phase of the plant salt-stress response. Therefore, manipulation of the energy metabolism should be the focus in plant resistance breeding and the genes identified in this work can serve as potentially effective candidates.

QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F2 progeny of Thai salt-tolerant rice donor line "Jao Khao"

Introduction

Owing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety.

Methods

A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or Δ(SNP index).

Results

Both methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the Δ(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a Δ(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait.

Conclusion

The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice

We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL groups; next, we focused on OsCUL3c, the third CUL3 of the CUL3 family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the OsCUL3c region, representing 79 haplotypes (haps), were found. Haplotyping revealed that group I (hap A and hap C) and group II (hap B1 and hap D) were different mutated variants, which showed their association with phenotypes under salt stress. These results were supported by cis-regulatory elements (CREs) and transcription factor binding sites (TFBSs) analyses. We found that LTR, MYC, [AP2; ERF], and NF-YB, which are related to salt stress, drought stress, and the response to abscisic acid (ABA), have distinct positions and numbers in the haplotypes of group I and group II. An RNA Seq analysis of the two predominant haplotypes from each group showed that the OsCUL3c expression of the group I representative was upregulated and that of group II was downregulated, which was confirmed by RT-qPCR. Promoter changes might affect the transcriptional responses to salt stress, leading to different regulatory mechanisms for the expression of different haplotypes. We speculate that OsCUL3c influences the regulation of salt-related responses, and haplotype variations play a role in this regulation.

Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.