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Delimitation of a QTL region controlling cold tolerance at booting stage of a cultivar, ‘Lijiangxintuanheigu’, in rice, Oryza sativa L.

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Abstract

Low temperature at the booting stage of rice causes male sterility resulting in severe yield loss. Cold tolerance has long been an important objective in rice breeding. We identified a quantitative trait locus (QTL) for cold tolerance on the long arm of chromosome 3 from the cold-tolerant breeding line ‘Ukei 840’ by using F2 and BC1F2 populations from crosses between ‘Ukei 840’ and ‘Hitomebore’. The cold tolerance of ‘Ukei 840’ is derived from the Chinese cultivar ‘Lijiangxintuanheigu’. The effect of this QTL on cold tolerance was confirmed by developing ‘Hitomebore’ chromosome segment substitution lines having ‘Lijiangxintuanheigu’ alleles on chromosome 3. By producing recombinants in chromosome 3, the QTL region for cold tolerance was delimited to the region of about 1.2-Mb region between RM3719 and RM7000. All lines heterozygous for the QTL showed seed fertilities as low as that of ‘Hitomebore’, suggesting that the ‘Lijiangxintuanheigu’ allele for cold tolerance in the QTL region is recessive. Determination of a 1.2-Mb nucleotide sequence of ‘Ukei 840’ and comparison with the published genomic sequence of ‘Nipponbare’ showed 254 SNPs, of which 11 were in coding regions of genes, seven in five genes being non-synonymous. SNPs were detected in the 5-kb upstream regions of 89 genes, but no differences of gene expression levels were detected between alleles of these genes. Although further delimitation is required to identify the gene responsible for cold tolerance of ‘Lijiangxintuanheigu’, SNP markers developed here will be useful for marker-assisted selection in a breeding program using ‘Lijiangxintuanheigu’ as a donor of cold tolerance.

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Acknowledgments

This study was partly supported by a Grant-in-Aid for Scientific Research (Research Activity Start-up: 22880005).

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Author notes

  1. T. Endo

    Present address: Miyagi Prefectural Furukawa Agricultural Experimental Station, 88 Osaki Fukoku, Osaki, Miyagi, 989-6227, Japan

  2. M. Yamaguchi

    Present address: National Agricultural Research Center for Tohoku Region, 4 Akahira, Shimo-Kuriyagawa, Morioka, Iwate, 020-0198, Japan

Authors and Affiliations

  1. Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan

    S. Shirasawa & T. Nishio

  2. Daisen Research Station, National Agricultural Research Center for Tohoku Region, 3 Shimo-furumichi, Yotsuya, Daisen, Akita, 014-0102, Japan

    T. Endo, K. Nakagomi & M. Yamaguchi

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  1. S. Shirasawa
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Correspondence to T. Nishio.

Additional information

Communicated by J. Dubcovsky.

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122_2011_1758_MOESM1_ESM.tif

Supplementary Fig. 1 QTL analysis using a backcrossed population. (a) Seed fertilities of backcross population after cultivation under low temperature conditions at the booting stage. (b) Position of a QTL detected using a backcrossed population. Black boxes indicate regions having segregated genotypes and white boxes show regions having a fixed genotype of homozygous ‘Hitomebore’ alleles. A circle represents a QTL region. A gray bar indicates candidate region of the QTL and a triangle shows the peak of the LOD score. (TIFF 86 kb)

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Shirasawa, S., Endo, T., Nakagomi, K. et al. Delimitation of a QTL region controlling cold tolerance at booting stage of a cultivar, ‘Lijiangxintuanheigu’, in rice, Oryza sativa L.. Theor Appl Genet 124, 937–946 (2012). https://doi.org/10.1007/s00122-011-1758-6

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  • DOI: https://doi.org/10.1007/s00122-011-1758-6

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