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.

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

“…In the present work, plants treated with the same concentration of salt did not display significant growth inhibition after 1 week of treatment, even though some visual symptoms of toxicity (wilting) were observed on the leaves. A similar lack of severe growth inhibition was reported in several other quinoa genotypes having a similar origin as R49, i.e., Real and Ollague [9]. In the case of this particular ecotype, its extremely slow growth rate could contribute to better tolerating stress as described by Raney et al [16] for Ollague exposed to drought conditions.…”

“…Sequencing of the quinoa genome [13] combined with three RNA-seq analyses [9,15,16] have increased the availability of genetic information for this halophytic seed-producing crop. The two former reports are on quinoa subjected to drought stress, while the latter considered the reference genome PI614886 [13], belonging to the "coastal" ecotype and originating from Maule (central Chile), under salt stress.…”

Soil drenching of paclobutrazol: An efficient way to improve quinoa performance under salinity

“…Quinoa can achieve optimal growth and biomass between 100 and 200 mM (10, 20 dS m −1 ) of salinity (Jacobsen et al , Hariadi et al , Iqbal et al ), and 400 mM salinity causes significant reduction in growth and yield (Hariadi et al , Yang et al , Waqas et al , Yang et al ). However, the salt tolerance potential of quinoa greatly differs among genotypes (Schmockel et al ). Several physiological, biochemical and molecular changes are responsible for the reduced performance of quinoa in response to salt stress.…”

Increasing Salinity Tolerance of Crops

“…On a scale of salt sensitivity, sugar beet has been reported as salt tolerant, cotton and tomatoes intermediate in tolerance, and chickpea, beans, and soybean as sensitive to salt [42,43]. Quinoa, which is considered as a potential new crop, exhibits high salinity tolerance [164]. It has been shown that some varieties of Chenopodium quinoa grow better in 300 mM of NaCl compared to 0 mM NaCl although there was no significant in the accumulation of Na + in their roots or shoots [164].…”

“…Quinoa, which is considered as a potential new crop, exhibits high salinity tolerance [164]. It has been shown that some varieties of Chenopodium quinoa grow better in 300 mM of NaCl compared to 0 mM NaCl although there was no significant in the accumulation of Na + in their roots or shoots [164]. Many fruit trees, such as citrus, are classified as very salt sensitive [43], due to their inability to exclude Cl À from their transpiration stream.…”