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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #310293

Research Project: Generation and Characterization of Novel Genetic Variation in Rice for the Enhancement of Grain Quality and Agronomic Performance

Location: Crops Pathology and Genetics Research

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

Author
item Hyun, Do-yoon - Korean Rural Development Administration
item Lee, Gi An - Korean Rural Development Administration
item Kang, Man Jung - Korean Rural Development Administration
item Burkart-waco, Diana
item Kim, Sang-ic - University Of California
item Lee, Myung Chul - Korean Rural Development Administration
item Gwag, Jae Gyun - Korean Rural Development Administration
item Kim, Yeon Gyu - Korean Rural Development Administration
item Tai, Thomas

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2015
Publication Date: 3/1/2015
Publication URL: http://link.springer.com/article/10.1007/s11032-015-0298-1
Citation: Hyun, D., Lee, G., Kang, M., Burkart-Waco, D., Kim, S., Lee, M., Gwag, J., Kim, Y., Tai, T. 2015. Development of low temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm. Molecular Breeding. 35:104.

Interpretive Summary: Transplanting rice is the predominant cultivation practice in Asia, but due to the increasing scarcity of labor and natural resources, direct-seeding is becoming more widespread. Direct-seeded rice (DSR) varieties must have good vigor during the germination and seedling growth stages to ensure a uniform, high yielding crop. Low temperature germinability (LTG) is an important trait for DSR varieties, but is a difficult target to integrate into breeding programs. In this study, markers for previously reported genetic loci that affect LTG were developed and tested on a set of rice lines which were also evaluated for their LTG. In addition, new loci were identified by analyzing DNA sequence data from these lines in conjunction with their LTG trait data. Together, these markers will enable selection of germplasm for breeding programs and may be used to assist in development of new varieties with improved LTG in a more rapid and consistent manner than field evaluation methods.

Technical 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 major effect QTL qLTG3-1, which has been cloned, has been implicated in tissue weakening and likely contributes to germination vigor in general. 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 harboring other LTG QTLs. In addition to the evaluation of markers from previously reported LTG QTLs, an association analysis was conducted using SNP data generated by reduced representation sequencing of the panel. Eight SNP markers were found to be 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 reported. The remaining six markers represent novel candidates for LTG loci.