Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation.

Salvador Capella-Gutíerrez,Guoxiong Chen,Xiao-Fei Ma,Yong Shi,Pengshan Zhao,Toni Gabaldón,Xin Zhao

doi:10.1186/1471-2164-15-872

Abstract

BackgroundSand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been historically consumed by local populations in the desert regions of northwest China. Sand rice is a potential food crop resilient to ongoing climate change; however, partly due to the scarcity of genetic information, this species has undergone only little agronomic modifications through classical breeding during recent years.ResultsWe generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741 unigenes. Phylogenetic analysis based on 221 single-copy genes showed close relationship between sand rice and the recently domesticated crop sugar beet. Transcriptomic comparisons also showed a high level of global sequence conservation between these two species. Conservation of sand rice and sugar beet orthologs assigned to response to salt stress gene ontology term suggests that sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far more tolerant to high temperature. A set of genes likely relevant for resistance to heat stress, was functionally annotated according to expression levels, sequence annotation, and comparisons corresponding transcriptome profiling results in Arabidopsis.ConclusionsThe present work provides abundant genomic information for functional dissection of the important traits in sand rice. Future screening the genetic variation among different ecotypes and constructing a draft genome sequence will further facilitate agronomic trait improvement and final domestication of sand rice.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-872) contains supplementary material, which is available to authorized users.

Highlights

Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia
The clean reads were assembled by Trinity program (Table 1; [19]) and 104,118 transcripts were generated with average length of 1107 bp and an N50 length of 1950 bp (Additional file 4)
Comparative transcriptomics showed a high level of conservation in terms of gene content and sequence similarity between sand rice and sugar beet

Summary

Introduction

Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. Sand rice is a potential food crop resilient to ongoing climate change; partly due to the scarcity of genetic information, this species has undergone only little agronomic modifications through classical breeding during recent years. The plant species diversity is low and new evidence has shown that speciation in such environments is extensively driven by recent climate and habitat changes [7,8]. The intrinsic adaptation and survival strategies throughout the different stages of the life cycle of these desert species do not lend themselves easy to transfer to our major crop plants. Domestication of a potential crop species from desert environments, which is able to buffer the ongoing climate change, promises to be an effective strategy to keep food security

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