Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.) |
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Authors: | J P Suh J U Jeung J I Lee Y H Choi J D Yea P S Virk D J Mackill K K Jena |
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Institution: | (1) IRRI-Korea Office, National Institute of Crop Science, RDA, 209 Seodun-Dong, Suwon, 441-857, Republic of Korea;(2) Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines;(3) Rice Research Division, National Institute of Crop Science, RDA, 209 Seodun-Dong, Suwon, 441-857, Republic of Korea; |
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Abstract: | Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing
countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth,
the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this
study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo,
to produce 153 F8 recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence
repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance
with respect to percent seed set using cold-water (18–19°C) irrigation in the field and controlled air temperature (17°C)
in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high
percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution
of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366.
Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under
cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers
associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production. |
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