Zhao et al. BMC Genomics 2014, 15:872
http://www.biomedcentral.com/1471-2164/15/872
Transcriptomic analysis of a psammophyte food
crop, sand rice (Agriophyllum squarrosum) and
identification of candidate genes essential for
sand dune adaptation
Pengshan Zhao1,2*, Salvador Capella-Gutíerrez3,4,5, Yong Shi1,2, Xin Zhao1,2, Guoxiong Chen1,2,
Toni Gabaldón3,4,6* and Xiao-Fei Ma1,2
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.
Results: We generate 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.
Conclusions: 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.
Keywords: Agriophyllum squarrosum, Sand rice, Salt tolerance, Heat tolerance, Comparative transcriptomics, Wild plant domestication