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Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm

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Abstract

Low-temperature germinability (LTG) is an important trait for breeding of varieties for use in direct-seeding rice production systems. Although rice (Oryza sativa L.) is generally sensitive to low temperatures, genetic variation for LTG exists and several quantitative trait loci (QTLs) have been reported. Most notably, the gene underlying the major effect QTL qLTG3-1 has been cloned and implicated in tissue weakening. The objective of this study was to develop molecular markers for use in selecting rice germplasm with enhanced LTG. A panel of japonica rice accessions (n = 180) from temperate regions in Asia was evaluated for LTG and genotyped with markers from qLTG3-1 and regions previously reported to harbor other LTG QTLs. In addition to the germplasm evaluation using these markers, an association analysis was conducted using SNP data generated by reduced representation sequencing of the panel. Eight SNP markers were found to be significantly associated with LTG using general and mixed linear models. Two of these markers were in close proximity (~35 kb) to each other on chromosome 4 in a region previously linked to LTG in rice. The identification of several markers strongly associated with LTG in locations not previously reported provides a foundation for further genetic dissection of this complex trait.

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Acknowledgments

This work was supported by the Rural Development Administration (RDA) of the Republic of Korea through the RDA/USDA-ARS Virtual Laboratory program (D.Y.H. and T.H.T.) and by the “Research Program for Agricultural Science & Technology Development (Project No. PJ008368 and PJ010871)” of the National Academy of Agricultural Science, RDA (D.Y.H). Additional support was provided by USDA-ARS CRIS Project 5306-21000-021-00D (T.H.T.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303.

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  1. Sang Ic Kim

    Present address: Dupont Crop Protection, Stine Haskell Research Center, Newark, DE, 19711, USA

Authors and Affiliations

  1. National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, Jeonju, Republic of Korea

    Do Yoon Hyun, Gi An Lee, Man Jung Kang, Myung Chul Lee, Jae Gyun Gwag & Yeon Gyu Kim

  2. USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA

    Diana Burkart-Waco & Thomas H. Tai

  3. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Diana Burkart-Waco, Sang Ic Kim & Thomas H. Tai

  4. Division of Biotechnology, Korea University, Seoul, Republic of Korea

    Jae Yoon Kim

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  1. Do Yoon Hyun
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Hyun, D.Y., Lee, G.A., Kang, M.J. et al. Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm. Mol Breeding 35, 104 (2015). https://doi.org/10.1007/s11032-015-0298-1

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