Dataset Information

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.

ABSTRACT: Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

SUBMITTER: Schmockel SM

PROVIDER: S-EPMC5478719 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in <i>Chenopodium quinoa</i> by Integrating Physiological Data, RNAseq, and SNP Analyses.

Schmöckel Sandra M SM Lightfoot Damien J DJ Razali Rozaimi R Tester Mark M Jarvis David E DE

Frontiers in plant science 20170621

<i>Chenopodium quinoa</i> (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially e ...[more]

PMID: 28680429

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Project description:Background and aimsThe activity of H(+)-ATPase is essential for energizing the plasma membrane. It provides the driving force for potassium retention and uptake through voltage-gated channels and for Na(+) exclusion via Na(+)/H(+) exchangers. Both of these traits are central to plant salinity tolerance; however, whether the increased activity of H(+)-ATPase is a constitutive trait in halophyte species and whether this activity is upregulated at either the transcriptional or post-translation level remain disputed.MethodsThe kinetics of salt-induced net H(+), Na(+) and K(+) fluxes, membrane potential and AHA1/2/3 expression changes in the roots of two halophyte species, Atriplex lentiformis (saltbush) and Chenopodium quinoa (quinoa), were compared with data obtained from Arabidopsis thaliana roots.Key resultsIntrinsic (steady-state) membrane potential values were more negative in A. lentiformis and C. quinoa compared with arabidopsis (-144?±?3·3, -138?±?5·4 and -128?±?3·3?mV, respectively). Treatment with 100?mm NaCl depolarized the root plasma membrane, an effect that was much stronger in arabidopsis. The extent of plasma membrane depolarization positively correlated with NaCl-induced stimulation of vanadate-sensitive H(+) efflux, Na(+) efflux and K(+) retention in roots (quinoa?>?saltbush?>?arabidopsis). NaCl-induced stimulation of H(+) efflux was most pronounced in the root elongation zone. In contrast, H(+)-ATPase AHA transcript levels were much higher in arabidopsis compared with quinoa plants, and 100?mm NaCl treatment led to a further 3-fold increase in AHA1 and AHA2 transcripts in arabidopsis but not in quinoa.ConclusionsEnhanced salinity tolerance in the halophyte species studied here is not related to the constitutively higher AHA transcript levels in the root epidermis, but to the plant's ability to rapidly upregulate plasma membrane H(+)-ATPase upon salinity treatment. This is necessary for assisting plants to maintain highly negative membrane potential values and to exclude Na(+), or enable better K(+) retention in the cytosol under saline conditions.

Project description:BackgroundQuinoa is an increasingly popular seed crop frequently studied for its tolerance to various abiotic stresses as well as its susceptibility to heat. Estimations of quinoa pollen viability through staining methods have resulted in conflicting results. A more effective alternative to stains is to estimate pollen viability through in vitro germination. Here we report a method for in vitro quinoa pollen germination that could be used to understand the impact of various stresses on quinoa fertility and therefore seed yield or to identify male-sterile lines for breeding.ResultsA semi-automated method to count germinating pollen was developed in PlantCV, which can be widely used by the community. Pollen collected on day 4 after first anthesis at zeitgeber time 5 was optimum for pollen germination with an average germination of 68% for accession QQ74 (PI 614886). The optimal length of pollen incubation was found to be 48 h, because it maximizes germination rates while minimizing contamination. The pollen germination medium's pH, boric acid, and sucrose concentrations were optimized. The highest germination rates were obtained with 16% sucrose, 0.03% boric acid, 0.007% calcium nitrate, and pH 5.5. This medium was tested on quinoa accessions QQ74, and cherry vanilla with 68%, and 64% germination efficiencies, respectively.ConclusionsWe provide an in vitro pollen germination method for quinoa with average germination rates of 64 and 68% on the two accessions tested. This method is a valuable tool to estimate pollen viability in quinoa, and to test how stress affects quinoa fertility. We also developed an image analysis tool to semi-automate the process of counting germinating pollen. Quinoa produces many new flowers during most of its panicle development period, leading to significant variation in pollen maturity and viability between different flowers of the same panicle. Therefore, collecting pollen at 4 days after first anthesis is very important to collect more uniformly developed pollen and to obtain high germination rates.

Dataset Information

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.

Publications

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in <i>Chenopodium quinoa</i> by Integrating Physiological Data, RNAseq, and SNP Analyses.

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