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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

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dc.contributor.author Zhao, Pengshan
dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-
dc.contributor.author Shi, Yong
dc.contributor.author Zhao, Xin
dc.contributor.author Chen, Guoxiong
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Ma, Xiao-Fei
dc.date.accessioned 2015-12-18T09:15:57Z
dc.date.available 2015-12-18T09:15:57Z
dc.date.issued 2014
dc.identifier.citation Zhao P, Capella-Gutiérrez S, Shi Y, Zhao X, Chen G, Gabaldón T, Ma X. Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. BMC Genomics. 2014;15:872. DOI: 10.1186/1471-2164-15-872
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/25465
dc.description.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.
dc.description.sponsorship 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)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2014;15:872
dc.rights © 2014 Zhao et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0
dc.subject.other Plantes silvestres
dc.title Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-15-872
dc.subject.keyword Agriophyllum squarrosum
dc.subject.keyword Sand rice
dc.subject.keyword Salt tolerance
dc.subject.keyword Heat tolerance
dc.subject.keyword Comparative transcriptomics
dc.subject.keyword Wild plant domestication
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2012-37161
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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