Abstract
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A QTL for cold tolerance at the booting stage of rice cultivar ‘Kuchum’ was detected and delimited into a 1.36 Mb region, and a cold-tolerant line was developed by QTL pyramiding.
Abstract
Low temperature in summer causes pollen sterility in rice, resulting in a serious loss of yield. The second most widely grown rice cultivar in Japan, ‘Hitomebore’, has been developed as a cultivar highly tolerant to low temperature at the booting stage. However, even ‘Hitomebore’ exhibits sterility at a temperature lower than 18.5 °C. Further improvement of cold tolerance of rice is required. In the present study, QTLs for cold tolerance in a Bhutanese rice variety, ‘Kuchum’, were analyzed using backcrossed progenies and a major QTL, named qCT-4, was detected on chromosome 4. Evaluating cold tolerance of seven types of near isogenic lines having ‘Kuchum’ alleles around qCT-4 with a ‘Hitomebore’ genetic background, qCT-4 was delimited to a region of ca. 1.36 Mb between DNA markers 9_1 and 10_13. Homozygous ‘Kuchum’ alleles at qCT-4 showed an effect of increasing seed fertility by ca. 10 % under cold-water treatment. Near isogenic lines of ‘Hitomebore’ having ‘Silewah’ alleles of Ctb1 and Ctb2 and a ‘Hokkai PL9’ allele of qCTB8 did not exhibit higher cold tolerance than that of ‘Hitomebore’. On the other hand, a qLTB3 allele derived from a Chinese cultivar ‘Lijiangxintuanheigu’ increased cold tolerance of ‘Hitomebore’, and pyramiding of the qCT-4 allele and the qLTB3 allele further increased seed fertility under cold-water treatment. Since NILs of ‘Hitomebore’ with the ‘Kuchum’ allele of qCT-4 were highly similar to ‘Hitomebore’ in other agronomic traits, the qCT-4 allele is considered to be useful for developing a cold-tolerant cultivar.
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References
Abe N, Kotaka S, Toriyama K, Kobayashi M (1989) Development of the ‘Rice Norin-PL 8’with high tolerance to cool temperature at the booting stage (in Japanese with English summary). Res Bull Hokkaido Natl Agric Exp Stn 152:9–17
Andaya VC, Mackill DJ (2003) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica x indica cross. Theor Appl Genet 106:1084–1090
Asaga K (1981) A procedure for evaluating field resistance to blast in rice varieties (in Japanese with English summary). J Cent Agric Exp Stn 35:51–138
Dai L, Lin X, Ye C, Ise K, Saito K, Kato A, Xu F, Yu T, Zhang D (2004) Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of rice, Kunmingxiaobaigu. Breed Sci 54:253–258
Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y (2007) A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8. Theor Appl Genet 115:593–600
Kuroki M, Saito K, Matsuba S, Yokogami N, Ando T, Sato Y, Ando I, Shimizu H (2011) Detection of quantitative trait loci for cold tolerance at the booting stage in a rice breeding line, Hokkai-PL9 (in Japanese with English summary). Breed Res 13:11–18
Lincoln S, Daly M, Lander E (1992) Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report. 3rd edn. Massachusetts
Matsunaga K (2005) Establishment of an evaluation method for cold tolerance at the booting stage of rice using deep water irrigation system and development of highly cold—tolerant rice varieties by combining cold tolerance genes (in Japanese with English summary). Bull Miyagi Furukawa Agric Exp Stn 4:1–78
Mori M, Onishi K, Tokizono Y, Shinada H, Yoshimura T, Numao Y, Miura H, Sato T (2011) Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah. Breed Sci 61:61–68
Nishiyama I (1984) Climatic influence on pollen formation and fertilization. In: Tsunoda S, Takahashi N (eds) Biology of rice. Japan Sci Soc Press, Tokyo/Elsver, Amsterdam, pp 135–171
Saito K, Miura K, Nagano K, Hayano-Saito Y, Saito A, Araki H, Kato A (1995) Chromosomal location of quantitative trait loci for cool tolerance at the booting stage in rice variety ‘Norin-PL8’. Breed Sci 45:337–340
Saito K, Miura K, Nagano K, Hayano-Saito Y, Araki H, Kato A (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length. Theor Appl Genet 103:862–868
Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the rice cold tolerance gene Ctb1. Plant Sci 179:97–102
Sasaki T, Abe S, Matsunaga K, Okamoto E, Nagano K, Tanno K, Chiba Y, Kano A, Uematsu K (1994) A new rice cultivar ‘Hitomebore’ (in Japanese with English summary). Bull Miyagi Prefect Frukawa Agric Exp Stn 2:1–17
Satake T, Hayase M (1970) Male sterility caused by cooling treatment at the young microspore stage in rice plants. V. Estimation of pollen developmental stage and the most sensitive stage to coolness. Proc Crop Sci Soc Jpn 39:468–473
Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y (2011) RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res 39:D1141–D1148
Shinada H, Iwata N, Sato T, Fujino K (2014) QTL pyramiding for improving of cold tolerance at fertilization stage in rice. Breed Sci 63:483–488
Shirasawa K, Maeda H, Monna L, Kishitani S, Nishio T (2007) The number of genes having different alleles between rice cultivars estimated by SNP analysis. Theor Appl Genet 115:1067–1074
Shirasawa S, Endo T, Nakagomi K, Yamaguchi M, Nishio T (2012) Delimitation of a QTL region controlling cold tolerance at booting stage of the rice cultivar ‘Lijiangxintuanheigu’. Theor Appl Genet 124:937–946
Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, Jena KK (2010) 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.). Theor Appl Genet 120:985–995
Takeuchi Y, Hayasaka H, Chiba B, Tanaka I, Shimano T, Yamagishi M, Nagano K, Sasaki T, Yano M (2001) Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate Japonica rice. Breed Sci 51:191–197
Thomson D, Henry R (1995) Single-step protocol for preparation of plant tissue for analysis by PCR. Biotechniques 19:394–400
Wang S, Basten CJ, Zeng ZB (2006) Department of Statistics, North Carolina State University, Raleigh, NC, USA. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012a) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954
Wang P, Xing Y, Li Z, Yu S (2012b) Improving rice yield and quality by QTL pyramiding. Mol Breed 29:903–913
Xu LM, Zhou L, Zeng YW, Wang FM, Zhang HL, Shen SQ, Li ZC (2008) Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near-isogenic line. Plant Sci 174:340–347
Ye C, Fukai S, Godwin I, Koh H, Reinke R, Zhou Y, Lambrides C, Snell P, Jiang W (2010) A QTL controlling low temperature induced spikelet sterility at booting stage in rice. Euphytica 176:291–301
Zhou L, Zeng Y, Hu G, Pan Y, Yang S, You A, Zhang H, Li J, Li Z (2012) Characterization and identification of cold tolerant near-isogenic lines in rice. Breed Sci 62:196–201
Acknowledgments
This work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of JAPAN (Development of a new rice varieties using genomic breeding technology).
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Supplementary Fig. 1. Plant materials for QTL analysis and NIL having qCT-4 with a ‘Hitomebore’ genetic background. a) Recurrent parent is ‘Chiyohonami’. b) Recurrent parent is ‘Hitomebore’ (PDF 118 kb)
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Supplementary Fig. 2. Substituted segments in NILs having Ctb1, Ctb2, and qCTB8 with a ‘Hitomebore’ genetic background. a) The donor of the cold tolerance QTL in groups from S1 to S6 is ‘Silewah’. b) that in groups H1 and H2 is ‘Hokkai PL9’. Boxes and lines represent chromosomal segments of the donor and those of ‘Hitomebore’, respectively. 4S, 4L, 8S, and 8L indicate the short arm (S) and the long arm (L) of chromosome 4 and 8, respectively (PDF 143 kb)
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Supplementary Fig. 3. Frequency distribution of seed fertility in the F2 and BIL populations. F2 population (CKC1) obtained by a cross between ‘Chiyohonami’ and ‘BI6-12’, which is a backcrossed inbred line between ‘Kuchum’ as a donor with ‘Chiyohonami’ as a recurrent parent. b) EBS6. c) EBS8. EBS6 and EBS8 are BC6F4 populations obtained by backcrossings of ‘Kuchum’ as a donor with ‘Hitomebore’ as a recurrent parent (PDF 163 kb)
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Supplementary Table 2. Cold tolerance evaluation of NILs shown in Supplementary Fig. 4. (PDF 55 kb)
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Supplementary Table 3. NILs having Ctb1, Ctb2 and qCTB8 with a ‘Hitomebore’ genetic background (PDF 68 kb)
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Supplementary Table 4. Agronomic traits of NILs having qCT-4 with a ‘Hitomebore’ genetic background (PDF 67 kb)
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Endo, T., Chiba, B., Wagatsuma, K. et al. Detection of QTLs for cold tolerance of rice cultivar ‘Kuchum’ and effect of QTL pyramiding. Theor Appl Genet 129, 631–640 (2016). https://doi.org/10.1007/s00122-015-2654-2
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DOI: https://doi.org/10.1007/s00122-015-2654-2