Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

Nadia Al Tamimi; Chris Brien; Helena Oakey; Bettina Berger; Stephanie Saade; Ho Shwen; Sandra M. Schmöckel; Mark A. Tester; Sónia Negrão

doi:10.1038/ncomms13342

Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

Nadia Al Tamimi, Chris Brien, Helena Oakey, Bettina Berger, Stephanie Saade, Ho Shwen, Sandra M. Schmöckel, Mark A. Tester, Sónia Negrão

Research output: Contribution to journal › Article › peer-review

183 Scopus citations

Abstract

High-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.

Original language	English (US)
Journal	Nature Communications
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/ncomms13342
State	Published - Nov 17 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: The 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.

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10.1038/ncomms13342

https://repository.kaust.edu.sa/bitstream/10754/621845/1/ncomms13342.pdf

Cite this

@article{19521dc4bef14e2a8d236748ef37204b,

title = "Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping",

abstract = "High-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.",

author = "{Al Tamimi}, Nadia and Chris Brien and Helena Oakey and Bettina Berger and Stephanie Saade and Ho Shwen and Schm{\"o}ckel, {Sandra M.} and Tester, {Mark A.} and S{\'o}nia Negr{\~a}o",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: The 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 {\textquoteleft}HDRA 700kK SNPs{\textquoteright} 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 In{\^e}s Silva Pires for critical comments.",

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AU - Schmöckel, Sandra M.

AU - Tester, Mark A.

AU - Negrão, Sónia

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: The 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.

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N2 - High-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.

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Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

Abstract

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Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

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