Identification of putative transmembrane proteins involved in salinity tolerance in chenopodium quinoa by integrating physiological data, RNAseq, and SNP analyses

Sandra M. Schmöckel, Damien J. Lightfoot, Rozaimi Mohamad Razali, Mark Tester, David E. Jarvis

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Article number1023
JournalFrontiers in Plant Science
Volume8
DOIs
Publication statusPublished - 21 Jun 2017
Externally publishedYes

Fingerprint

Chenopodium quinoa
transmembrane proteins
salinity
Chenopodium
genes
Chenopodium berlandieri
genome
Amaranthaceae
salt tolerance
food security
topology
single nucleotide polymorphism
salt stress
genomics
prediction
crops

Keywords

  • Chenopodiumquinoa
  • Comparative genomics
  • Hydroponics
  • Plant physiology
  • Quinoa
  • RNAseq
  • Salinity tolerance
  • Transporters

ASJC Scopus subject areas

  • Plant Science

Cite this

Identification of putative transmembrane proteins involved in salinity tolerance in chenopodium quinoa by integrating physiological data, RNAseq, and SNP analyses. / Schmöckel, Sandra M.; Lightfoot, Damien J.; Mohamad Razali, Rozaimi; Tester, Mark; Jarvis, David E.

In: Frontiers in Plant Science, Vol. 8, 1023, 21.06.2017.

Research output: Contribution to journalArticle

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