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

Handle URI:
http://hdl.handle.net/10754/625182
Title:
Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses
Authors:
Schmöckel, Sandra M.; Lightfoot, Damien ( 0000-0003-3824-8856 ) ; Razali, Rozaimi; Tester, Mark A. ( 0000-0002-5085-8801 ) ; Jarvis, David Erwin ( 0000-0002-0072-9112 )
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Schmöckel SM, Lightfoot DJ, Razali R, Tester M, Jarvis DE (2017) Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses. Frontiers in Plant Science 8. Available: http://dx.doi.org/10.3389/fpls.2017.01023.
Publisher:
Frontiers Media SA
Journal:
Frontiers in Plant Science
Issue Date:
21-Jun-2017
DOI:
10.3389/fpls.2017.01023
Type:
Article
ISSN:
1664-462X
Sponsors:
The research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST).
Additional Links:
http://journal.frontiersin.org/article/10.3389/fpls.2017.01023/full
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorSchmöckel, Sandra M.en
dc.contributor.authorLightfoot, Damienen
dc.contributor.authorRazali, Rozaimien
dc.contributor.authorTester, Mark A.en
dc.contributor.authorJarvis, David Erwinen
dc.date.accessioned2017-07-12T07:20:55Z-
dc.date.available2017-07-12T07:20:55Z-
dc.date.issued2017-06-21en
dc.identifier.citationSchmöckel SM, Lightfoot DJ, Razali R, Tester M, Jarvis DE (2017) Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses. Frontiers in Plant Science 8. Available: http://dx.doi.org/10.3389/fpls.2017.01023.en
dc.identifier.issn1664-462Xen
dc.identifier.doi10.3389/fpls.2017.01023en
dc.identifier.urihttp://hdl.handle.net/10754/625182-
dc.description.abstractChenopodium 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.en
dc.description.sponsorshipThe research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST).en
dc.publisherFrontiers Media SAen
dc.relation.urlhttp://journal.frontiersin.org/article/10.3389/fpls.2017.01023/fullen
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectquinoaen
dc.subjectChenopodium quinoaen
dc.subjecthydroponicsen
dc.subjectsalinity toleranceen
dc.subjectRNAseqen
dc.subjectplant physiologyen
dc.subjecttransportersen
dc.subjectcomparative genomicsen
dc.titleIdentification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analysesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalFrontiers in Plant Scienceen
dc.eprint.versionPublisher's Version/PDFen
kaust.authorSchmöckel, Sandra M.en
kaust.authorLightfoot, Damienen
kaust.authorRazali, Rozaimien
kaust.authorTester, Mark A.en
kaust.authorJarvis, David Erwinen
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