Abstract
Low temperature is a serious abiotic stress affecting rice production in subtropical and temperate areas. In this study, cold tolerance of rice at the germination and seedling stages were evaluated using one recombinant inbred line (RIL) population derived from a cross between Daguandao (japonica), with highly cold-tolerant at the seedling stage, and IR28 (indica), with more cold-tolerant at the germination stage, and the quantitative trait loci (QTL) mapping was conducted using the multiple interval mapping (MIM) approach. Continuous segregation in low temperature germinability (LTG) and cold tolerance at the seedling stage (CTS) were observed among the RIL populations. Most RILs were moderately susceptible or tolerant at the germination stage, but were susceptible at the seedling stage. No significant relationship was found in cold tolerance between the germination and seedling stages. A total of seven QTLs were identified with limit of detection (LOD) >3.0 on chromosomes 3, 8, 11 and 12, and the amount of variation (R 2) explained by each QTL ranged from 5.5 to 22.4%. The rice LTG might be regulated by two minor QTLs, with the CTS controlled by one major QTL [qCTS8.1 (LOD = 16.1, R 2 = 22.4%)] and several minor loci. Among these loci, one simultaneously controls LTG (qLTG11.1) and CTS (qCTS11.1). Several cold-tolerance-related QTLs identified in previous studies were found to be near the QTLs detected here, and three QTLs are novel alleles. The alleles from Daguandao at six QTLs increased cold tolerance and could be good sources of genes for cold tolerance. In addition, only one digenic interaction was detected for CTS, with a R 2 value of 6.4%. Those major or minor QTLs could be used to significantly improve cold tolerance by marker-assisted selection (MAS) in rice.
Similar content being viewed by others
References
Alvarez R, Valbuena L, Calvo L (2007) Effect of high temperatures on seed germination and seedling survival in three pine species (Pinus pinaster, P. sylvestris and P. nigra). Intl J Wildl Fire 16:63–70
Andaya VC, Mackill DJ (2003) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 392:2579–2585
Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475
Andaya VC, Tai TH (2007) Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breeding 20:349–358
Baruah AR, Ishigo-Oka N, Adachi M, Oguma Y, Tokizono Y, Onishi K, Sano Y (2009) Cold tolerance at the early growth stage in wild and cultivated rice. Euphytica 165:459–470
Bedi S, Basra AS (1993) Chilling injury in germinating seeds: basic mechanisms and agricultural implications. Seed Sci Res 3:219–229
Bramlage WJ, Leopold AC, Specht JE (1979) Imbibitional chilling sensitivity among soybean cultivars. Crop Sci 19:811–814
Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567
Cheng C, Yun KY, Ressom HW, Mohanty B, Bajic VB, Jia Y, Yun SJ, de los Reyes BG (2007) An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics 8:175
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 3:963–971
Dellaporta SL, Wood T, Hicks TB (1983) A plant DNA mini preparation: version II. Plant Mol Bio Rep 1:19–21
Dias PM, Brunel-Muguet S, Dürr C, Huguet T, Demilly D, Wagner MH, eulat-Merah TB (2011) QTL analysis of seed germination and pre-emergence growth at extreme temperatures in Medicago truncatula. Theor Appl Genet 122:429–444
Edelstein M, Kigel J, Nerson H (1991) Relationships among germination, emergence and seedling development of muskmelon at low temperature. Sci Hortic 47:51–58
Foolad MR, Lin GY (2001) Genetic analysis of cold tolerance during vegetative growth in tomato, Lycopersicon esculentum Mill. Euphytica 122:105–111
Fracheboud Y, Jompuk C, Ribaut JM, Stamp P, Leipner J (2004) Genetic analysis of cold-tolerance of photosynthesis in maize. Plant Mol Biol 56:241–253
Fujino K (2004) A major gene for low temperature germinability in rice (Oryza sativa L.). Euphytica 136:63–68
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin S, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799
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. Proc Natl Acad Sci USA 105:12623–12628
Goode LK, Allen MF (2009) Seed germination conditions and implications for establishment of an epiphyte, Aechmea bracteata (Bromeliaceae). Plant Ecol 204:179–188
Ichie T, Ninomiya I, Ogino K (2001) Utilization of seed reserves during germination and early seedling. J Trop Ecol 17:371–378
Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H (2009) A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor Appl Genet 118:1477–1488
Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, Wan JM (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res 98:68–75
Knoll J, Gunaratna N, Ejeta G (2008) QTL analysis of early-season cold tolerance in sorghum. Theor Appl Genet 116:577–587
Koseki M, Kitazawa N, Yonebayashi S, Maehara Y, Wang ZX, Minobe Y (2010) Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage. Mol Genet Genomics 284:45–54
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
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Li ZK, Pinson SRM, Paterson AH, Park WD, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465
Lou QJ, Chen L, Sun ZX, Xing YZ, Li J, Xu XY, Mei HW, Luo LJ (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 158:87–94
McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature, Linkage, Rice Genetics Cooperative) (2008) Gene nomenclature system for rice. Rice 1:72–84
Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299
Nakagahra M, Okuno K, Vaughan D (1997) Rice genetic resources: history, conservation, investigative characterization and use in Japan. Plant Mol Biol 35:69–77
Nykiforuk CL, Johnson-Flanagan AM (1999) Storage reserve mobilization during low temperature germination and early seedling growth in Brassica napus. Plant Physiol Biochem 37:939–947
Rodiño AP, Lema M, Pérez-Barbeito M, Santalla M, De Ron AM (2007) Assessment of runner bean (Phaseolus coccineus L.) germplasm for tolerance to low temperature during early seedling growth. Euphytica 155:63–70
Sanguinetti CJ, Neto ED, Simpson AJ (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:914–921
Smallwood M, Bowles DJ (2002) Plants in a cold climate. Phil Trans R Soc Lond B 357:831–847
Stewart CR, Martin BA, Redding L, Cerwick S (1990) Seedling growth, mitochondrial characteristics and alternative respiratory capacity of corn genotypes differing in cold tolerance. Plant Physiol 92:761–766
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
Thompson K, Grime JP, Mason G (1977) Seed germination in response to diurnal fluctuations of temperature. Nature 267:147–149
Wang ZF, Wang JF, Bao YM, Wang FH, Zhang HS (2010) Quantitative trait loci analysis for rice seed vigor during the germination stage. J Zhejiang Univ Sci B 11:958–964
Wang ZF, Wang JF, Bao YM, Wu YY, Zhang HS (2011) Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178:297–307
Zhang ZH, Li S, Wei L, Wei C, Zhu YG (2005) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci 168:527–534
Acknowledgments
This work was supported by the National Natural Science Foundation of China (Grant No. 31000748), the Natural Science Foundation of Jiangsu Province (Grant No. BK2010452). We thank reviewers for the careful reading of the manuscript and constructive comments.
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Wang, Z., Wang, F., Zhou, R. et al. Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.). Euphytica 181, 405–413 (2011). https://doi.org/10.1007/s10681-011-0469-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10681-011-0469-z