Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

Chowdhury, Avidyuti; Guttikonda, Haritha; Sunitha, Thota; Krishnamurthy, S. L.; Balakrishnan, Divya; Padmavathi, G.; Ram, T.; Neelamraju, Sarla

doi:10.1016/j.rsci.2016.05.003

Cited by 32 publications

(15 citation statements)

References 26 publications

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“…The tolerant FL478 had the largest number of genes whose expression profiles were similar from either parent, of which a much greater number were from the sensitive parent IR29. This trend was not surprising given that FL478 is a specific selection in IRRI's breeding program for the growth and developmental attributes of IR29, and limited introgression from Pokkali including SalTol (Walia et al, 2005;Cotsaftis et al, 2011;Chowdhury et al, 2016). Consistent with these trends, FL478 also had the smallest number of genes with Pokkali-type expression profiles (Figure 4).…”

Section: General Trends In the Mrna Transcriptomes Of Recombinant Inbmentioning

confidence: 68%

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks

et al. 2020

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Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesisdriven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na + exclusion mechanism (SalTol-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokininregulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory (OsRR23, OsHK5) and biosynthetic (OsIPT9) genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors (OsIBH1, TAC3) that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs (miR169, miR397, miR827) were also identified as

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Section: General Trends In the Mrna Transcriptomes Of Recombinant Inbmentioning

confidence: 68%

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks

et al. 2020

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“…We evaluated a panel of 162 diverse rice ( Oryza sativa L.) accessions from URMC that represented four rice subpopulations: Tropical japonica (TRJ), Temperate japonica (TEJ), Indica (IND), and Aus (AUS) [35]. Six cultivars were included as salt-sensitive (IR29, Nerica 6, A69-1) and salt-tolerant (Pokkali, IR45427-2B-2-2B-1-1, IR65196-3B-5-2-2) checks [17,46,47]. A detailed view of all the traits measured in this study is provided in Table 1a,b.…”

Section: Resultsmentioning

confidence: 99%

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

Rohila

Edwards

Tran³

et al. 2019

Plants

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Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m−1 salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.

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“…The salt tolerant indica recombinant inbred line (RIL) FL478 is a novel source of salt tolerance at the seedling stage in rice (Chowdhury et al 2016). FL478, developed from crossing between Pokkali (tolerant) and IR29 (sensitive), has shown to outperform the original Pokkali in seedling stage salinity tolerance, be photoperiod insensitive, and flower earlier than Pokkali (Cotsaftis et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes

Mansuri

Shobbar

Jelodar

et al. 2019

Rice

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Background Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique. Results A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL , OsNAAT , OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29. Conclusions The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k + , ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent. Electronic supplementary material The online version of this article (10.1186/s12284-019-0273-2) contains supplementary material, which is available to authorized users.

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Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

Cited by 32 publications

References 26 publications

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes

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