QTL Mapping of Salt Tolerance Traits with Different Effects at the Seedling Stage of Bread Wheat

Masoudi, Bahram; Mardi, Mohsen; Hervan, Eslam Majidi; Bihamta, Mohammad Reza; Naghavi, Mohammad Reza; Nakhoda, Babak; Amini, Ata

doi:10.1007/s11105-015-0874-x

Cited by 48 publications

(37 citation statements)

References 64 publications

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“…The variable expressions of these genes are essential components of plant salt stress response and adaptation mechanisms and may be genotype specific and/or transcriptionally regulated by cis-regulatory elements (CREs). Several studies have revealed the association of DNA polymorphisms with ST in wheat (Genc et al 2010; Xu et al 2013; Masoudi et al 2015; Turki et al 2015), but are yet to be elucidated due to lack of functional and molecular validation. The understanding of how potential molecular cues relate to salt stress response remains a major challenge in molecular biology, as transcriptional mechanisms contribute to the regulation of nearly all cellular processes (Li et al 2006; von Korff et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Oyiga

Ogbonnaya

Sharma³

et al. 2018

Theor Appl Genet

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Key messageSNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties.AbstractThe dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R2 = 0.12–63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na+ and K+ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R2 ≥ 14.7%) and 68.45 cM (R2 ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na+-uptake, shoot K+/Na+ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3220-5) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Oyiga

Ogbonnaya

Sharma³

et al. 2018

Theor Appl Genet

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“…Which was supported by Mwadzingeni et al [22] who reported similar correlations between YPP and both BM and GN under drought-stress conditions. QTL clusters and colocalized QTL for grain yield and component traits related to salinity stress have been reported [26,39,[59][60][61]. In addition, an unusually high correlation between agronomic traits controlled by pleiotropic QTL exists [22,26,[60][61][62][63][64].…”

Section: Qtl Clusters For Grain Yield and Related Traits Under Salinimentioning

confidence: 98%

“…QTL clusters and colocalized QTL for grain yield and component traits related to salinity stress have been reported [26,39,[59][60][61]. In addition, an unusually high correlation between agronomic traits controlled by pleiotropic QTL exists [22,26,[60][61][62][63][64]. Two occurrences might be responsible for the co-localization of QTL associated with different traits: rst, genes affecting various traits or the same traits were strongly linked; and second, single gene might have a series of effects on related traits or affect two or more independent traits [62].…”

Section: Qtl Clusters For Grain Yield and Related Traits Under Salinimentioning

confidence: 99%

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Zheng

Luo

et al. 2020

Preprint

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Background Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. Result In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTL were significantly associated with traits under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14–50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. Conclusion Utilizing a Wheat660K SNPs chip, QTL for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

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“…For agronomically important traits, linkage maps are necessary for mapping the QTLs as they are constructed from genotypic data from multiplexed marker assays [32][33][34][35]. High-density linkage maps also offers a genomic resource for positional cloning of significant genes.…”

Section: Qtl Mapping For Abiotic Stressmentioning

confidence: 99%

“…They can also be applied in comparative genomics to assess chromosomal organization and evolution as they are constructed from sequence tagged markers. In the linkage map, markers are helpful in identifying regions having QTLs of selected traits and several QTLs have mapped previously for salt tolerance [36,17,35] and drought tolerance [37][38][39]…”

Section: Qtl Mapping For Abiotic Stressmentioning

confidence: 99%

Omics Approaches for Engineering Wheat Production under Abiotic Stresses

Shah¹,

Xu²,

Zou³

et al. 2018

Preprint

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Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence, and heavy metals. The effective management at molecular level is mandatory for thorough understanding of plant response to abiotic stress. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in wheat. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in wheat. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in wheat. This review also provides a comprehensive catalog of available online omic resources for wheat and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in wheat.

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QTL Mapping of Salt Tolerance Traits with Different Effects at the Seedling Stage of Bread Wheat

Cited by 48 publications

References 64 publications

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Omics Approaches for Engineering Wheat Production under Abiotic Stresses

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