Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality
RESEARCH ARTICLE

Mapping quantitative trait loci for cold tolerance at the booting stage in rice by using chromosome segment substitution lines

Jianguo Lei A C E , Shan Zhu A C E , Caihong Shao B E , Shusheng Tang C , Renliang Huang C , Changlan Zhu A D and Song Yan C D
+ Author Affiliations
- Author Affiliations

A Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, Jiangxi Province, China.

B Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi Province, China.

C Rice National Engineering Laboratory (Nanchang)/Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics/Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi Province, China.

D Corresponding authors. Emails: yans11@163.com, zhuchanglan@163.com

E These authors contributed equally to this work.

Crop and Pasture Science 69(3) 278-283 https://doi.org/10.1071/CP17329
Submitted: 13 June 2017  Accepted: 22 November 2017   Published: 22 February 2018

Abstract

Low temperature at the booting stage in rice (Oryza sativa L.) can cause male sterility, resulting in yield losses. A set of chromosome segment substitution lines derived from the varieties Sasanishiki (cold-tolerant, ssp. japonica) and Habataki (cold-susceptible, ssp. indica) was used for analysis across two natural, low-temperature environments to study the genetic basis for cold tolerance at the booting stage. Spikelet fertility was used as the evaluation index for cold tolerance identification. Eight quantitative trait loci (QTLs) for cold tolerance were detected, two of which were located on chromosomes 3 (qCTSF3.1 and qCTSF3.2), and the others on chromosomes 4 (qCTSF4), 5 (qCTSF5), 6 (qCTSF6), 7 (qCTSF7), 8 (qCTSF8) and 9 (qCTSF9). The phenotypic variation explained by each QTL ranged from 5.4% to 25.3%. Of the eight QTLs, six (qCTSF3.2, qCTSF5, qCTSF6, qCTSF7, qCTSF8, qCTSF9) were repeatedly detected in two environments. QTLs qCTSF3.1, qCTSF7 and qCTSF9 overlapped with previously reported QTLs. All tolerant alleles for all QTLs were contributed by Sasanishiki.

Additional keywords: CSSL, genetic map, phenotyping.


References

Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theoretical and Applied Genetics 116, 881–890.
Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice.CrossRef |

Dai L, Ye C, Yu T, Xu F (2002) Studies on cold tolerance of rice, Oryza sativa L. I. Description on types of cold injury and classifications of evaluation methods on cold tolerance in rice. Southwest China Journal of Agricultural Sciences 15, 41–45.

Dai LY, Lin XH, Ye CR, Ise K, Saito K, Kato A, Xu FR, Yu TQ, Zhang DP (2004) Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of Rice, Kunmingxiaobaigu. Breeding Science 54, 253–258.
Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of Rice, Kunmingxiaobaigu.CrossRef | 1:CAS:528:DC%2BD2MXhtFyisbjM&md5=27278300081986c8f3b7012864552308CAS |

Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141, 1147–1162.

Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proceedings of the National Academy of Sciences of the United States of America 105, 12623–12628.
Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice.CrossRef | 1:CAS:528:DC%2BD1cXhtVOju7zI&md5=f3a7b59f0fceba13e56eda54d187c578CAS |

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. Theoretical and Applied Genetics 115, 593–600.
A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8.CrossRef |

Lu G, Wu FQ, Wu W, Wang HJ, Zheng XM, Zhang Y, Chen X, Zhou K, Jin M, Cheng Z, Li X, Jiang L, Wang H, Wan J (2014) Rice LTG1 is involved in adaptive growth and fitness under low ambient temperature. The Plant Journal 78, 468–480.
Rice LTG1 is involved in adaptive growth and fitness under low ambient temperature.CrossRef | 1:CAS:528:DC%2BC2cXmslWrs74%3D&md5=7f91aa8a98dd260693b31b5a84e61e23CAS |

Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, Xiao J, Guo X, Xu S, Niu Y, Jin J, Zhang H, Xu X, Li L, Wang W, Qian Q, Ge S, Chong K (2015) COLD1 confers chilling tolerance in rice. Cell 160, 1209–1221.
COLD1 confers chilling tolerance in rice.CrossRef | 1:CAS:528:DC%2BC2MXjs1Omsbk%3D&md5=9377d54812f62b81840755e7c434d2b6CAS |

Mackill DJ, Lei X (1997) Genetic variation for traits related to temperate adaptation of rice cultivars. Crop Science 37, 1340–1346.
Genetic variation for traits related to temperate adaptation of rice cultivars.CrossRef |

McCouch SR (2008) Gene nomenclature system for rice. Rice 1, 72–84.
Gene nomenclature system for rice.CrossRef |

Mertz LM, Henning FA, Soares RC, Baldiga RF, Peske FB, Moraes DM (2009) Physiological changes in rice seeds exposed to cold in the germination phase. Revista Brasileira de Sementes 31, 254–262.

Nishiyama I (1976) Male sterility caused by cooling treatment at the young microspore stage in rice plants. XIII. Ultrastructure of tapetal hypertrophy without primary wall. Japanese Journal of Crop Science 45, 270–278.
Male sterility caused by cooling treatment at the young microspore stage in rice plants. XIII. Ultrastructure of tapetal hypertrophy without primary wall.CrossRef |

Pan Y, Zhang H, Zhang D, Li J, Xiong H, Yu J, Li J, Rashid MA, Li G, Ma X, Cao G, Han L, Li Z (2015) Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping. PLoS One 10, e0120590
Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping.CrossRef |

Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124, 735–742.

Saito K, Miura K, Nagano K, Hayanosaito 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’. Breeding Science 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. Theoretical and Applied Genetics 103, 862–868.
Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length.CrossRef | 1:CAS:528:DC%2BD38XivVOgsQ%3D%3D&md5=4e0d955621fa85cb81d061f869c8133aCAS |

Saito K, Hayano-Saito Y, Maruyama-Funatsuki W, Sato Y, Kato A (2004) Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice. Theoretical and Applied Genetics 109, 515–522.
Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice.CrossRef | 1:CAS:528:DC%2BD2cXmt1Krsro%3D&md5=43a60aa31762437eaa03442d326d1034CAS |

Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the rice cold tolerance gene Ctb1. Plant Science 179, 97–102.
Map-based cloning of the rice cold tolerance gene Ctb1.CrossRef | 1:CAS:528:DC%2BC3cXmslWhtbo%3D&md5=2e3b19d6238ca002a8dd2e1093987624CAS |

Sakata T, Oda S, Tsunaga Y, Shomura H, Kawagishi-Kobayashi M, Aya K, Saeki K, Endo T, Nagano K, Kojima M, Sakakibara H, Watanabe M, Matsuoka M, Higashitani A (2014) Reduction of gibberellin by low temperature disrupts pollen development in rice. Plant Physiology 164, 2011–2019.
Reduction of gibberellin by low temperature disrupts pollen development in rice.CrossRef | 1:CAS:528:DC%2BC2cXmsV2jsb8%3D&md5=83ad0cd9ecaf51f8b2304975eb35d882CAS |

Satake T (1976) Determination of the most sensitive stage to sterile-type cool injury in rice plants. Research Bulletin of the Hokkaido National Agricultural Experiment Station 113, 1–43.

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.). Theoretical and Applied Genetics 120, 985–995.
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.).CrossRef | 1:STN:280:DC%2BC3c7gtVGrsQ%3D%3D&md5=60c728e1b5713d6bab7e3a107969d427CAS |

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. Breeding Science 51, 191–197.
Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate japonica rice.CrossRef | 1:CAS:528:DC%2BD3MXotVemtb8%3D&md5=357545f6028a748ff04a1f614ff55ad7CAS |

Tang QY, Feng MG (2002) ‘DPS data processing system for practical statistics.’ (Science Press: Beijing)

Wen S, Yao H (2011) Global warming over the period 1961–2008 did not increase high-temperature stress but did reduce low-temperature stress in irrigated rice across China. Agricultural and Forest Meteorology 9, 1193–1201.

Ye C, Fukai S, Godwin I, Reinke R, Snell P, Schiller J, Basnayake J (2009) Cold tolerance in rice varieties at different growth stages. Crop & Pasture Science 60, 328–338.
Cold tolerance in rice varieties at different growth stages.CrossRef |

Yoshida S (1981) ‘Fundamentals of rice crop science.’ (International Rice Research Institute: Los Banõs, Philippines)

Zhang Z, Li J, Pan Y, Li J, Zhou L, Shi H, Zeng Y, Guo H, Yang S, Zheng W, Yu J, Sun X, Li G, Ding Y, Ma L, Shen S, Dai L, Zhang H, Yang S, Guo Y, Li Z (2017) Natural variation in CTB4a enhances rice adaptation to cold habitats. Nature Communications 8, 14788
Natural variation in CTB4a enhances rice adaptation to cold habitats.CrossRef | 1:CAS:528:DC%2BC2sXkvFWks7c%3D&md5=44cfc440a18effef25d2245bcedea974CAS |

Zhou L, Zeng Y, Zheng W, Tang B, Yang S, Zhang H, Li J, Li Z (2010) Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line. Theoretical and Applied Genetics 121, 895–905.
Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line.CrossRef | 1:CAS:528:DC%2BC3cXhtVahtrjF&md5=cbd30013a8a2ee83b7addff6acc61c97CAS |

Zhu Y, Chen K, Mi X, Chen T, Ali J, Ye G, Xu J, Li Z (2015) Identification and fine mapping of a stably expressed QTL for cold tolerance at the booting stage using an interconnected breeding population in rice. PLoS One 10, e0145704
Identification and fine mapping of a stably expressed QTL for cold tolerance at the booting stage using an interconnected breeding population in rice.CrossRef |



Rent Article (via Deepdyve) Export Citation