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

Authors :
Guoxiong Chen
Toni Gabaldón
Yong Shi
Salvador Capella-Gutierrez
Xin Zhao
Xiao-Fei Ma
Pengshan Zhao
Source :
BMC Genomics, Recercat. Dipósit de la Recerca de Catalunya, instname
Publication Year :
2014
Publisher :
Springer Science and Business Media LLC, 2014.

Abstract

Background. Sand 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./nResults. We 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./nConclusions. The 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. TG group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union's Seventh Framework/nProgramme (FP/2007-2013)/ERC (Grant Agreement n. ERC-2012-StG-310325)

Details

ISSN :
14712164
Volume :
15
Database :
OpenAIRE
Journal :
BMC Genomics
Accession number :
edsair.doi.dedup.....b94fa370d1fff5b00aa96190b5b30e9f
Full Text :
https://doi.org/10.1186/1471-2164-15-872