Show simple item record

dc.contributor.authorAl Tamimi, Nadia
dc.contributor.authorBrien, Chris
dc.contributor.authorOakey, Helena
dc.contributor.authorBerger, Bettina
dc.contributor.authorSaade, Stephanie
dc.contributor.authorShwen, Ho
dc.contributor.authorSchmöckel, Sandra M.
dc.contributor.authorTester, Mark A.
dc.contributor.authorNegrão, Sónia
dc.date.accessioned2016-11-21T06:53:12Z
dc.date.available2016-11-21T06:53:12Z
dc.date.issued2016-11-17
dc.identifier.citationAl-Tamimi N, Brien C, Oakey H, Berger B, Saade S, et al. (2016) Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communications 7: 13342. Available: http://dx.doi.org/10.1038/ncomms13342.
dc.identifier.issn2041-1723
dc.identifier.doi10.1038/ncomms13342
dc.identifier.urihttp://hdl.handle.net/10754/621845
dc.description.abstractHigh-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.
dc.description.sponsorshipThe research reported in this publication was supported by funding from King Abdullah University of Science and Technology. We thank Michael Dingkuhn, Brigitte Courtois, Kenneth McNally and Julie Mae Pasuquin from the Global Rice Phenotyping Network. All seed material was kindly provided by the International Rice Genebank (International Rice Research Institute, Philippines). We thank Professor Susan McCouch (Cornell University) for providing the ‘HDRA 700kK SNPs’ data for the GWAS and analytical comments. We thank all members at The Plant Accelerator: Dr Rachel Burton, Helli Meinecke, Dr Trevor Garnett, Dr Alex Garcia, Richard Norrish, Dr Guntur Tanjung, George Sainsbury, Evi Guidolin, Robin Hosking, Lidia Mischis, Nicky Bond, Sepideh Azizi Taramsary, Kate Dowling and Fiona Groskreutz for providing technical support in the collection of phenotypic data. The Plant Accelerator, Australian Plant Phenomics Facility, is supported under the National Collaborative Research Infrastructure Strategy of the Australian Government. We thank Heno Hwang for scientific illustrations of the Smarthouses illustration of pot design. We also thank Bo Li and Inês Silva Pires for critical comments.
dc.publisherSpringer Nature
dc.relation.urlhttp://dx.doi.org/10.1038/ncomms13342
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectGenome-wide association studies
dc.subjectPlant genetics
dc.subjectSalt
dc.titleSalinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentPlant Science
dc.identifier.journalNature Communications
dc.relation.referencesAl-Tamimi, N., Brien, C., Oakey, H., Berger, B., Saade, S., Ho, Y. S., … Negrão, S. (2016). Data from: Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping (Version 1) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.3118j
dc.relation.referencesDOI:10.5061/DRYAD.3118J
dc.relation.referencesHANDLE:http://hdl.handle.net/10754/618220
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionUniversity of South Australia, Phenomics and Bioinformatics Research Centre, Adelaide, South Australia 5001, Australia
dc.contributor.institutionUniversity of Adelaide, Australian Plant Phenomics Facility, The Plant Accelerator, Urrbrae, South Australia 5064, Australia
kaust.personAl-Tamimi, Nadia
kaust.personOakey, Helena
kaust.personSaade, Stephanie
kaust.personShwen, Ho
kaust.personSchmöckel, Sandra M.
kaust.personTester, Mark A.
kaust.personNegrão, Sónia
refterms.dateFOA2018-06-14T03:11:49Z
dc.date.published-online2016-11-17
dc.date.published-print2016-12


Files in this item

Thumbnail
Name:
ncomms13342.pdf
Size:
999.6Kb
Format:
PDF
Description:
Main article
Thumbnail
Name:
ncomms13342-s1.pdf
Size:
8.678Mb
Format:
PDF
Description:
Supplemental files
Thumbnail
Name:
ncomms13342-s2.gif
Size:
6.705Mb
Format:
GIF image
Description:
Supplemental files
Thumbnail
Name:
ncomms13342-s3.xlsx
Size:
25.72Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Thumbnail
Name:
ncomms13342-s4.pdf
Size:
307.9Kb
Format:
PDF
Description:
Supplemental files

This item appears in the following Collection(s)

Show simple item record

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Except where otherwise noted, this item's license is described as This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/