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Candidate gene markers associated with cold tolerance in vegetative stage of rice (Oryza sativa L.)

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Abstract

Low temperature inhibits seedling emergence and early vegetative growth of rice (Oryza sativa L.), especially in cultivars of the subspecies indica, which are the most productive in the temperate region of South America. To improve breeding efficiency, we identified molecular markers associated with cold response related phenotypes, such as membrane integrity, photoinhibition and visual assessment of damage. A candidate gene approach was used to select genomic simple sequence repeat (gSSR) markers. For marker-trait association two strategies were used, candidate gene association mapping (CGAM) and single marker analysis (SMA) in a segregating F2:3 population. Thirty-six gSSR were identified but only 14 were polymorphic in the CGAM population. Using this approach, we found marker RM22034 associated with membrane integrity, RM6547 and RM14978 with photoinhibition, and RM144 with visual assessment of damage. The SMA strategy identified markers RM6651, RM14978, RM22034 and RM4 associated with membrane integrity and RM22034 with photoinhibition. All markers are currently available for marker assisted selection in rice breeding programs located in temperate regions.

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Acknowledgments

The authors wish to thank Dr. Ariel Castro for useful comments and suggestions for improving the manuscript; and Maribel Ceppa, Sara Murchio, Belén Bonilla, Marlene Bentancor and Daniela Deppa for their assistance with electrolyte leakage determinations. This work was supported by INIA (Instituto Nacional de Investigación Agropecuaria). The research was conducted at the Uruguayan National Agriculture Research Institute (INIA) and Latin American Fund for Irrigated Rice (FLAR).

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Correspondence to Victoria Bonnecarrère.

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Victoria Bonnecarrère, Gastón Quero have contributed equally to this work

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Bonnecarrère, V., Quero, G., Monteverde, E. et al. Candidate gene markers associated with cold tolerance in vegetative stage of rice (Oryza sativa L.). Euphytica 203, 385–398 (2015). https://doi.org/10.1007/s10681-014-1290-2

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