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Mapping and validation of QTLs for cold tolerance at seedling stage in rice from an indica cultivar Habiganj Boro VI (Hbj.BVI)

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Abstract

Yellowing, stunting, and seedling death associated with cold stress is a common problem in many Asian countries for winter rice cultivation. Improvement of cultivars through marker-assisted selection of QTLs for cold tolerance at seedling stage from locally adapted germplasm/cultivar is the most effective and sustainable strategy to resolve this problem. A study was undertaken to map QTLs from 151 F 2:3 progenies of a cross between a cold susceptible variety, BR1 and a locally adapted traditional indica cultivar, Hbj.BVI. A total of six significant QTLs were identified for two cold tolerance indices—cold-induced leaf discoloration and survival rate after a recovery period of seven days on chromosomes 6, 8, 11, and 12. Among these QTLs, qCTSL-8-1 and qCTSS-8-1 being co-localized into RM7027–RM339 on chromosome 8 and qCTSL-12-1 and qCTSS-12-1 into RM247–RM2529 on chromosome 12 showed 12.78 and 14.96% contribution, respectively, to the total phenotypic variation for cold tolerance. Validation of QTL effect in BC1F3 population derived a cross between a cold susceptible BRRI dhan28 and Hbj.BVI showed dominating effect of qCTSL-12-1 on cold tolerance at seedling stage and it became stronger when one or more other QTLs were co-segregated with it. These results suggest that the QTLs identified in this study are stable and effective on other genetic background also, which warrant the use of these QTLs for further study aiming to cultivar development for seedling stage cold tolerance.

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References

  • Andaya VC, Mackill DJ (2003) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 54:2579–2585

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Andaya VC, Tai TH (2007) Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breed 20:349–358. doi:10.1007/s11032-007-9096-8

    Article  CAS  Google Scholar 

  • Biswas PS, Khatun H, Anisuzzaman M, Hwang HG (2012) Study on the cold tolerant rice varieties for Bangladesh. Korea International Cooperation Agency (KOICA), The Republic of Korea

  • BRRI (2013) BRRI Annual Report 2012–13. Bangladesh Rice Research Institute Gazipur-1701, Bangladesh, p 334. http://brri.portal.gov.bd/sites/default/files/files/brri.portal.gov.bd/page/6d86d72e_953c_4f74_9157_3cfeaa80c2b1/BRRI_A_Report_2011-12.pdf

  • Chen DZ, Zhong PA, Xiao YQ, Huang YJ, Xie JK (2002) Identification of QTL for cold tolerance at seedling stage in Dongxiang wild rice (Oryza rufipogon Griff) by SSR markers. Acta Agriculturae Universitatis Jiangxiensis 24(6):753–756 (in Chinese with English abstract)

    CAS  Google Scholar 

  • Chen L, Lou Q, Sun Z, Xing Y, Yu X, Luo L (2006) QTL mapping of low temperature on germination rate of rice. Rice Sci 13:93–98

    Google Scholar 

  • Das N, Biswas PS (2017) Molecular characterization of parental lines of rice aiming to address high yield and nutritional quality under drought and cold stress condition. Curr Res Agril Sci 4:51–60. doi:10.18488/journal.68.2017.42.51.60

    Google Scholar 

  • Dashtmian FP, Hosseini MK, Esfahani M (2013) Methods for rice genotypes cold tolerance evaluation at germination stage. Intl J Agric Crop Sci 5:2111–2116

    Google Scholar 

  • Doherty CJ, Van Buskirk HA, Myers SJ, Thomashow MF (2009) Roles for arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 21(3):972–984

    Article  CAS  Google Scholar 

  • Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799

    Article  CAS  Google Scholar 

  • Han L, Qiao Y, Cao G, Zhang Y, An Y, Ye J, Koh H (2004) QTLs analysis of cold tolerance during early growth period for rice. Rice Sci 11:245–250

    Google Scholar 

  • Han LZ, Zhang SY, Qiao YL, Zhang JG, Ruan RC, Cao GL, Koh HJ (2005a) QTL analysis of root traits at the seedling stage in rice under cold irrigation. Acta Agron Sin 31:1415–1421

  • Han LZ, Qiao YL, Cao GL, Zhang YY, An YP, Ye JD, Koh HJ (2005b) QTL analysis on cold tolerance during early growth period in rice. Chin J Rice Sci 19:122–126. http://caod.oriprobe.com/orderhtm?id=626355&ftext=base (in Chinese with English abstract)

  • Han L, Qiao Y, Zhang S, Zhang Y, Cao G, Kim J, Lee K, Koh H (2007) Identification of quantitative trait loci for cold response of seedling vigor traits in rice. J Genet Genomics 34:239–246

    Article  CAS  Google Scholar 

  • IRRI (2013) Standard evaluation system of rice, 5th edn. International Rice Research Institute, Philippines, p 55p

    Google Scholar 

  • Ji ZJ, Zeng YX, Zeng DL, Ma LY, Li XM, Liu BX, Yang CD (2010) Identification and fine mapping of a major quantitative trait locus originating from wild rice controlling cold tolerance at the seedling stage. Mol Genet Genom 284:45–54

    Article  Google Scholar 

  • Jiang L, Xun MM, Wang JK, Wan JM (2008) QTL analysis of cold tolerance at seedling stage in rice (Oryza sativa L.) using recombination inbred lines. J Cereal Sci 48:173–179

    Article  CAS  Google Scholar 

  • Kaneda C, Beachell HM (1973) Response of indica-japonica rice hybrids to low temperatures. SABRAO J 6:17–32

    Google Scholar 

  • Khatun H, Biswas PS (2015) BR18 and HbjBVI: Potential donors for QTLs/genes conferring seedling stage cold tolerance in rice. In: Saleque MA, Kashem MA, Ali MA, Kabir MS (eds) Bangladesh Rice Research Abstracts 2014. Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh. http://brriportalgovbd/sites/default/files/files/brriportalgovbd/page/b3bb0382_9b99_43f3_8490_20455d2ec5e4/Bangladesh%20Rice%20Research%20Abstract%202014pdf

  • Khatun H, Biswas PS, Hwang HG, Kim KM (2016) A quick and simple in-house screening protocol for cold tolerance at seedling stage in rice. Plant Breed Biotech 4:373–378. doi:10.9787/PBB.2016.4.3.373

    Article  Google Scholar 

  • Kim SM, Suh JP, Lee CK, Le JH, Kim YG, Jena KK (2014) QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Genet Genomics 289:333–343

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Krishnasamy V, Seshu DV (1989) Seed germination rate and associated characters in rice. Crop Sci 29:904–908

    Article  Google Scholar 

  • Kundu A (2015) Haplotype diversity analysis in cold tolerant rice. MS thesis, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1703, Bangladesh

  • Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y (2009) Quantitative trait locus analysis for cold tolerance at the booting stage in a rice cultivar, Hatsushizuku. JARQ 43 (2):115–121. http://www.jircas.affrc.go.jp

  • Lee MH, Fukai S, Basnayake J (2001) Increased lowland rice production in the Mekong Region. In: Proceedings of an international workshop, Vientiane, Laos, 30th October to 2nd November, 2000 at Australian Center for International Agricultural Research, Canberra, Australia on Low temperature tolerance in rice: The Korean Experience, pp 109–117

  • Liu FX, Xu WY, Song Q, Tan LB, Liu JY, Zhu ZF, Fu YC, Su Z, Sun CQ (2013) Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice. Mol Plant 6:757–767. doi:10.1093/mp/sss161

  • Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu X, Mei H, Luo L (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 158:87–97

    Article  CAS  Google Scholar 

  • Maclean JL, Dawe DC, Hardy B, Hettel GP (2002) Rice almanac: source book for the most important economic activity on earth, 3rd edn. CABI Publishing, UK

    Google Scholar 

  • McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) (2008) Gene nomenclature system for rice. Rice 1:72–84

  • McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:88–99

    Article  Google Scholar 

  • Mohiuddin SJ (2016) Molecular mapping of quantitative trait loci conferring grain zinc content in rice (Oryza sativa L). MS Thesis, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur, Bangladesh

  • Nakagahra M, Okuno K, Vaughan D (1997) Rice genetic resources: history, conservation, investigative characterization and use in Japan. Plant Mol Biol 35:69–77

    Article  CAS  Google Scholar 

  • Park IK, Oh CS, Kim DM, Yeo SM, Ahn SN (2013) QTL Mapping for cold tolerance at the seedling stage using introgression lines derived from an inter-subspecific cross in Rice. Plant Breed Biotech 1:1–8. doi:10.9787/PBB.2013.1.1.001

    Article  Google Scholar 

  • Qian Q, Zeng DL, He P, Zheng X, Chen Y, Lihuang Z (2000) QTL analysis of the rice seedling cold tolerance in a double haploid population derived from anther culture of a hybrid between indica and japonica rice. Chin Sci Bull 145(5):448–453

    Article  Google Scholar 

  • Qu TT, Chen LY, Zhang ZH, Hu ZH, Liping ZH, Lihuang ZY (2003) Molecular mapping of genes conferring cold tolerance at seedling stage using doubled haploid lines from an indica × japonica cross in rice. J Wuhan Bot Res 21:385–389

    Google Scholar 

  • Ranawake AL, Manangkilb OE, Yoshidac S, Ishiid T, Morie N, Nakamura C (2014) Mapping QTLs for cold tolerance at germination and the early seedling stage in rice (Oryza sativa L.). Biotechnol Biotechnol Equip 28:989–998. doi:10.1080/13102818.2014.978539

    Article  Google Scholar 

  • Sheng T, Dali Z, Qian Q, Yasufumi K, Danian H, Lihuang Z (2001) QTL analysis of rice low temperature germinability. Chin Sci Bull 46:1800–1803

    Article  Google Scholar 

  • Singh BK, Singh AK, Ngasepam TM, Mukharjee A, Mandal N (2016) QTL mapping for cold tolerance at the seedling stage in rice. Int J Biores Stress Mgt 7:1214–1224

    Google Scholar 

  • Su CF, Wang YC, Hsieh TH, Lu CA, Tseng TH, Yu SM (2010) A novel MYBS3-dependent pathways confers cold tolerance in rice. Plant Physol 153:145–158

    Article  CAS  Google Scholar 

  • 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-tolerance genotypes of rice (Oryza sativa L.). Theor Appl Genet 120:985–995

    Article  CAS  Google Scholar 

  • Suh JP, Lee CK, Lee JH, Kim JJ, Kim SM, Cho YC, Park SH, Shin JC, Kim YG, Jena KK (2012) Identification of quantitative trait loci for seedling cold tolerance using RILs derived from a cross between japonica and tropical japonica rice cultivars. Euphytica 184:101–108

    Article  Google Scholar 

  • Swamy BPM, Kaladhar K, Ramesha MS, Viraktamath BC, Sarla N (2011) Molecular mapping of QTLs for yield and related traits in Oryza sativa cv Swarna × O. nivara (IRGC81848) backcross population. Rice Sci 18:178–186

    Article  Google Scholar 

  • Swamy BPM, Kaladhar K, Rani SN, Prasad GSV, Viraktamath BC, Reddy GA, Sarla N (2012) QTL analysis for grain quality traits in 2 BC2F2 Populations Derived from Crosses between Oryza sativa cv Swarna and 2 Accessions of O. nivara. J Heredity 103:442–452

    Article  CAS  Google Scholar 

  • Swamy M, Kaladhar K, Reddy GA, Viraktamath BC, Sarla N (2014) Mapping and introgression QTLs for yield and related traits in two backcross populations derived from O. sativa cv Swarna and two accessions of O. nivara. J Genet 93:643–654

    Article  Google Scholar 

  • Syed MA, Iftekharuddaula MK, Mian MAK, Rasul MG, Rahmam GKMM, Panaullah GM, Lauren JG, Duxbury JM, Biswas PS (2016) Main effect QTLs associated with arsenic phyto-toxicity tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 209:805–814. doi:10.1007/s10681-016-1683-5

  • Wang Z, Cheneg J, Chen Z, Huang J, Boo Y, Wang J, Zhang H (2012) Identification of QTLs with main, epistatic and QTL × Environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125:807–815. doi:10.1007/s00122-012-1873-z

  • Wang D, Liu J, Li C, Kang H, Wang Y, Tan X, Liu M, Deng Y, Wang Z, Liu Y, Zhang D, Xiao Y, Wang GL (2016) Genome-wide association mapping of cold tolerance genes at seedling stage in rice Rice 9:10–61. doi:10.1186/s12284-016-0133-2

  • Yang Z, Huang D, Tan W, Zheng Y, Liang K, Cutler AJ, Wu W (2013) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. PLoS One 8(7):e68433. doi:10.1371/journal.pone.0068433

  • Yoshida S (1981) Fundamentals of rice crop science. International Rice Research Institute, Los Banos, p 269

    Google Scholar 

  • Yoshida R, Kanno A, Sato T, Kameya T (1996) Cool temperature induced chlorosis in rice plant. Plant Physiol 110:997–1005

    Article  CAS  Google Scholar 

  • Zhan QC, Zhu KY, Chen ZW, Zeng SZ (2005) Studies on the QTL for cold tolerance related characters of rice seedling by molecular markers. Hybrid rice 20(1):50–55 (in Chinese with English abstract)

    Google Scholar 

  • Zhang ZH, Su L, Li W, Chen W, 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

    Article  CAS  Google Scholar 

  • Zhang S, Zheng J, Liu B, Peng S, Leung H, Zhao J, Wang X, Yang T, Huang Z (2014) Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment. Euphytica 195:95–104. doi:10.1007/s10681-013-0977-0

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Acknowledgements

The authors deeply acknowledge the Integrated Agricultural Productivity Project (IAPP)—BRRI part, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh for financial support for this work. We also acknowledge Dr. Tamal Lata Aditya, Head of Plant Breeding Division, Bangladesh Rice Research Institute for sharing germplasm and allowing us to use laboratory and experiment field. We also acknowledge laboratory and field technicians for their continuous assistance in conducting phenotyping and genotyping works.

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Authors and Affiliations

  1. International Rice Research Institute, Philippines, Los Baños, Philippines

    Partha S. Biswas & Hasina Khatun

  2. Jahangirnagar University, Savar, Dhaka, Bangladesh

    Nomita Das

  3. Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur, 1706, Bangladesh

    Md. Mahathir Sarker

  4. Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh

    Partha S. Biswas, Hasina Khatun & M. Anisuzzaman

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  1. Partha S. Biswas
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  2. Hasina Khatun
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Correspondence to Partha S. Biswas.

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This study was funded by the Integrated Agricultural Productivity Project (IAPP)-BRRI part, Bangladesh Rice Research Institute, Gazipur-1701.

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Biswas, P.S., Khatun, H., Das, N. et al. Mapping and validation of QTLs for cold tolerance at seedling stage in rice from an indica cultivar Habiganj Boro VI (Hbj.BVI). 3 Biotech 7, 359 (2017). https://doi.org/10.1007/s13205-017-0993-1

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