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

Oyiga, Benedict Chijioke; Ogbonnaya, Francis C.; Sharma, R. C.; Baum, Michaël; Léon, Jens; Ballvora, Agim

doi:10.1007/s00122-018-3220-5

Cited by 22 publications

(24 citation statements)

References 113 publications

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“…The Turkish cultivar Altay2000 (salt-tolerant) and the Uzbek cultivar Bobur (salt-susceptible) were the winter wheat genotypes identified in an earlier study as contrasting for shoot accumulation of K + and Na + at 24 days ASE among other stress-related traits [59]. These genotypes included in a panel used in association mapping studies [28,29], were selected to analyze the leave transcriptome during the ionic stress response. The seeds for the study were delivered by the International Winter Wheat Improvement Program, as described in Oyiga et al [28,29,59].…”

Section: Contrasting Genotypes From the Mapping Populations And Tissumentioning

confidence: 99%

“…These genotypes included in a panel used in association mapping studies [28,29], were selected to analyze the leave transcriptome during the ionic stress response. The seeds for the study were delivered by the International Winter Wheat Improvement Program, as described in Oyiga et al [28,29,59].…”

Section: Contrasting Genotypes From the Mapping Populations And Tissumentioning

confidence: 99%

“…Subgenome-specific primers for the salt-responsive genes TraesCS2D02G173600 and TraesCS5D02G238700 were designed using the web-based tool GSP [101] and are available in the Additional file 10. The amplification efficiencies of the internal control primers TaEf-1.1 and TaEf-1.2 [28,29] and each target gene were compared. The RT-qPCR reaction of 20 μl consisted on 0.25 μM of each primer, 10.12 μl of DyNamo Color Flash SYBR Green 2X-master mix with ROX (Thermo Scientific, Waltham, MA, USA) and 2.5 μl of 1:20 diluted cDNA template.…”

Section: Real-time Quantitative Pcr Analysismentioning

confidence: 99%

“…The genetic mapping studies have allowed the detection of statistical associations of molecular markers with phenotypic values of a quantitative trait to find locations of quantitative trait loci (QTL) in the genome of a given species [ 23 , 24 ]. Several mapping analyses in bread wheat have identified QTL with effect on salt stress-related traits [ 25 – 29 ]. Because of the limited mapping resolution of most of these studies, each QTL interval contains many potential quantitative trait genes (QTGs) influencing the trait variation.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. Conclusion The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

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Section: Contrasting Genotypes From the Mapping Populations And Tissumentioning

confidence: 99%

Section: Contrasting Genotypes From the Mapping Populations And Tissumentioning

confidence: 99%

Section: Real-time Quantitative Pcr Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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“…Genome-wide association study (GWAS) based on linkage disequilibrium (LD) has been applied in crops to dissect the genetic and molecular basis of several highly complex quantitative traits (Jighly et al, 2015; Contreras-Soto et al, 2017; Fang et al, 2017;Oyiga et al, 2018Oyiga et al, , 2019Ogbonnaya et al, 2017;Thoen et al, 2017). Decades of research have led to the uncovering of genes involved in root growth and development, such as Deeper Rooting 1 (Uga et al, 2013;Arai-Sanoh et al, 2014), Retarded Root Growth (Zhou et al, 2011), Roothairless5 (Nestler et al, 2014), Root Systems Architecture 1 (Rosas et al, 2013), and Crown Root-less1 (Coudert et al, 2015).…”

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Genetic components of root architecture and anatomy adjustments to water‐deficit stress in spring barley

Oyiga

Palczak

Wojciechowski

et al. 2019

Plant Cell & Environment

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Roots perform vital roles for adaptation and productivity under water‐deficit stress, even though their specific functions are poorly understood. In this study, the genetic control of the nodal‐root architectural and anatomical response to water deficit were investigated among diverse spring barley accessions. Water deficit induced substantial variations in the nodal root traits. The cortical, stele, and total root cross‐sectional areas of the main‐shoot nodal roots decreased under water deficit, but increased in the tiller nodal roots. Root xylem density and arrested nodal roots increased under water deficit, with the formation of root suberization/lignification and large cortical aerenchyma. Genome‐wide association study implicated 11 QTL intervals in the architectural and anatomical nodal root response to water deficit. Among them, three and four QTL intervals had strong effects across seasons and on both root architectural and anatomical traits, respectively. Genome‐wide epistasis analysis revealed 44 epistatically interacting SNP loci. Further analyses showed that these QTL intervals contain important candidate genes, including ZIFL2, MATE, and PPIB, whose functions are shown to be related to the root adaptive response to water deprivation in plants. These results give novel insight into the genetic architectures of barley nodal root response to soil water deficit stress in the fields, and thus offer useful resources for root‐targeted marker‐assisted selection.

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Harnessing Genetic Diversity for Addressing Wheat‐based Time Bound Food Security Projections

Mujeeb‐Kazi¹,

Ali²,

Dundas³

et al. 2022

Bioresource Technology

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

Cited by 22 publications

References 113 publications

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Genetic components of root architecture and anatomy adjustments to water‐deficit stress in spring barley

Harnessing Genetic Diversity for Addressing Wheat‐based Time Bound Food Security Projections

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