Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice

Autoři: Saumya Ranjan Barik aff001;  Elssa Pandit aff001;  Sharat Kumar Pradhan aff001;  Shakti Prakash Mohanty aff001;  Trilochan Mohapatra aff002
Působiště autorů: ICAR-National Rice Research Institute, Cuttack, Odisha, India aff001;  Indian Council of Agricultural Research, New Delhi, India aff002
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article


Reproductive stage drought stress is an important yield reducing factor in rainfed rice. Genetic mapping of morpho-physiological traits under the stress will help to develop cultivars suitable for drought prone environments through marker-assisted breeding (MAB). Though various yield QTLs under reproductive stage drought tolerance are available for MAB, but no robust markers controlling different morho-physiological traits are available for this stress tolerance. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL) using bulk segregant analysis (BSA) strategy. Wide variations were observed in the RILs for eleven morpho-physiological traits involved during the stress. A total of 401 SSR primers were surveyed for parental polymorphism of which 77 were detected to be polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were also detected to be linked and found to control the two traits. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and may be useful in MAB programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for improvement of reproductive stage drought tolerance in rice.

Klíčová slova:

Drought adaptation – Chromosome mapping – Leaves – Panicles – Plant resistance to abiotic stress – Quantitative trait loci – Rice – Water resources


1. USDA. World Agricultural Production, United States Department of Agriculture, Foreign Agricultural Service. 2019; Circular Series WAP 3–19.

2. Pennisi E. The Blue Revolution, drop by drop, gene by gene. Science. 2008; 320: 171–173. doi: 10.1126/science.320.5873.171 18403686

3. Bernier JR, Serraj R, Kumar A, Venuprasad R, Impa S, Gowda RPV, et al. The large-effect drought-resistance QTL qtl12.1 increases water uptake in upland rice. Field Crops Research. 2009; 110:139–146.

4. Barik SR, Pandit E, Pradhan SK, Singh S, Mohapatra T. QTL mapping for relative water content trait at reproductive stage drought tolerance in rice. Indian Journal of genetics and plant breeding. 2018; 78(4): 401–408.

5. Santhanalakshmi S, Saikumar S, Roa S, Saiharini A, Khera P, Shashidar HE, et al. Mapping genetic locus linked to brown plant hopper resistance in rice Oryza sativa L. Int Jour of Plant Breed & Genet. 2010; 4: 13–22.

6. Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Cruz MTS, et al. Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theoretical and Applied Genetics. 2009; 120:177–190. doi: 10.1007/s00122-009-1168-1 19841886

7. Bate BC, Kundzewicz ZW, Wu S, Palutikof JP. Climate change and water. Technical paper of the Intergovernmental Panel on Climate Change IPCC Secretariat, Geneva. 2008: 210.

8. Wassmann R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, Ismail A, et al. Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. Advance Agronomy. 2009; 102: 91–133.

9. Fleury D, Jeferies S, Kuchel H, Langridge P. Genetic and genomic tools to improve drought tolerance in wheat. Journal of Experimental Botany.2010; 61(12): 3211–3222. doi: 10.1093/jxb/erq152 20525798

10. Liu Q, Wu X, Ma J, Li T, Zhou X, Guo T. Effects of high air temperature on rice grain quality and yield under field condition. Agronomy Journal. 2013; 105: 446–454.

11. Anjum SA, Xie XY, Wang LC, Saleem MF, Man C, Lei W. Morphological, physiological and biochemical responses of plants to drought stress. African Journal of Agricultural Research. 2011; 6(9): 2026–2032.

12. Chang TT, Loresto GC, Tagumpay O. Screening of rice germplasm for drought resistant. Sabrao Journal. 1974; 6(1): 9–16.

13. Farooq M, Kobayashi N, Ito O, Wahid A, Serraj R. Broader leaves result in better performance of indica rice under drought stress. Journal of Plant Physiology. 2010; 167(13): 1066–1075. doi: 10.1016/j.jplph.2010.03.003 20392520

14. Singh CS, Kumar B, Mehandi, Chandra K. Effect of Drought Stress in Rice: A Review on Morphological and Physiological Characteristics. Trends in Bioscience. 2012; 5(4): 261–265

15. Price A. Courtois B. Mapping QTLs associated with drought resistance in rice: progress, problems and prospects. Plant Growth Regulation.1999; 29:123–133.

16. Nguyen TL, Bui CB. Fine mapping for drought tolerance in rice (Oryza sativa L.). Omonrice.2008; 16:9–15.

17. Sarvestani ZT, Pirdashti H, Sanavy SAM, Balouchi H. Study of water stress effects in different growth stages on yield and yield components of differentrice (Oryza sativa L.) cultivar. Pakistan Journal of Biological Science. 2008; 11(10):1303–1309.

18. Serraj R, Kumar A, McNally KL, Slamet-Loedin I, Bruskiewich R, Mauleon R, et al. Improvement of drought resistance in rice. Advance Agronomy. 2009; 103:41–99.

19. Xu Q, Yuan XP, Yu HY, Wang YP, Tang SX, Wei X. Mapping QTLs for drought tolerance at seedling stage in rice using doubled haploid population. Rice Science. 2011; 18(1):23–28.

20. Al-Shugeairy Z, Price AH, Robinson D. Genome wide association mapping for drought recover y trait in rice (Oryza sativa L.). International Journal Applied Agricultural Science. 2015; 1(1): 11–18.

21. Fang Y, Xiong L. General mechanisms of drought response and their application in drought resistance improvement in plants. Cell Molecular Life Science. 2015; 72(4):673–689.

22. Muthukumar C, Subathra T, Aiswarya J, Gayathri V, Chandra Babu R. Comparative genome-wide association studies for plant production traits under drought in diverse rice (Oryza sativa L.) lines using SNP and SSR markers. Current Science.2015; 109:139–147.

23. Todaka D, Shinozaki K, Yamaguchi-Shinozaki K. Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought—tolerant transgenic rice plants. Frontier in Plant Science. 2015; I6: 84–104.

24. Sudeshna P, Sekhar Garg H, Mandi V, Sarkar KK, Bhattacharya C. Effect of water stress at tillering stage on different morphological traits of rice (Oryza sativa L.) genotypes. International Journal of Agriculture Science Research. 2017; 7(3):471–480.

25. Hoang TH, Dinh LV, Nguyen TT, Ta NK, Gathignol F, Mai CD, et al. Genome-wide association study of a panel of Vietnamese rice landraces reveals new QTLs for tolerance to water deficit during the vegetative phase. 2019; 12: 4.

26. Lanceras JC, Pantuwan G, Jongdee B, Toojinda T. Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiology. 2004; 35:384–399.

27. Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K, et al. Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics. 2006; 172(2):1213–28. doi: 10.1534/genetics.105.045062 16272419

28. Kamoshita A, Babu RC, Boopathi NM, Fukai S. Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rain-fed environments. Field Crops Resources. 2008; 109: 1–23.

29. Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Cruz MTS, et al. Association mapping of yield and yield-related traits under reproductive stage drought stress in rice (Oryza sativa L.). Rice. 2017; 10:21. doi: 10.1186/s12284-017-0161-6 28523639

30. Singh CS, Kumar B, Mehandi, Chandra K. Effect of Drought Stress in Rice: A Review on Morphological and Physiological Characteristics. Trends in Biosciences. 2012; 5 (4): 261–265.

31. Kumar R, Sarawgi AK, Ramos C, Amarante ST, Ismail AM, Wade WJ. Partioning of dry matter during drought stress in rainfed lowland rice. Field Crops Research. 2006; 96: 455–465.

32. Davatgar N, Neishabouri MR, Sepaskhah AR., Soltani A. Physiological and morphological responses of rice (Oryza sativa L.) to varying water stress management strategies. International Journal of Plant Production. 2009; 3(4): 19–32.

33. Kumar R, Sreenu K, Singh N, Jain N, Singh NK, Rai V. Effect of drought stress on contrasting cultivars of rice. International Journal of Tropic Agriculture. 2015; 33(2): 1559–1564.

34. Torres R O, Henry A. Yield stability of selected rice breeding lines and donors across conditions of mild to moderately severe drought stress. Field Crop research. 2018; 220: 37–45.

35. Maisura, Chozin MA, Lubis I, Junaedi A, Ehara H. Some physiological character responses of rice under drought conditions in a paddy system. Journal of the International Society for Southeast Asian Agricultural Sciences. 2014; 20(1):104–114.

36. Mostajeran A, Rahimi-Eichi V. Effects of drought stress on growth and yield of rice (Oryza sativa L.) cultivars and accumulation of proline and soluble sugars in sheath and blades of their different ages leaves. American-Eurasian Journal of Agricultural & Environmental Science. 2009; 5: 264–272.

37. Kumar S, Dwivedi SK, Singh SS, Bhatt BP, Mehta P, Elanchezhian R, et al. Morpho-physiological traits associated with reproductive stage drought tolerance of rice (Oryza sativa L.) genotypes under rain-fed condition of eastern Indo-Gangetic Plain. Indian Journal of Plant Physiology. 2014; 19(2): 87–93.

38. Hsiao TC. Plant responses to water stress. Annual Review of Plant Physiology. 1973; 24: 519–570.

39. Boonjung H, Fukai S. Effects of soil water deficit at different growth stages on rice growth and yield under upland conditions. Field Crops Research. 1996; 48: 47–55.

40. Kamoshita A, Rodriguez R, Yamauchi A, Wade L. Genotypic variation in response of rainfed lowland to prolonged drought and rewatering. Plant Production Science. 2004; 7(4): 406–420.

41. Tripathy JN, Zhang J, Robin S, Nguyen TT, Nguyen HT. QTLs for cell- membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theoretical and Applied Genetics. 2000; 100: 1197–1200.

42. Babu RC, Shashidhar HE, Lilley JM, Thanh ND, Ray JD, Sadasivam S, et al. Variation in root penetration ability, osmotic adjustment and dehydration tolerance among accessions of rice to rain-fed lowland and upland ecosystems. Plant Breeding. 2001; 120: 233–238.

43. Price AH, Townend J, Jones MP, Audebert A, Courtois B. Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa. Plant Molecular Biology. 2002; 48: 683–695. doi: 10.1023/a:1014805625790 11999843

44. Robin S, Pathan MS, Courtois B, Lafitte R, Carandang C, Lanceras S, et al. Mapping osmotic adjustment in an advanced back cross inbred population of rice. Theoretical and Applied Genetics. 2003; 107: 1288–1296. doi: 10.1007/s00122-003-1360-7 12920518

45. Gomez SM, Satheesh Kumar P, Jeyaprakash P, Suresh R, Biji KR, Boopathi MN, et al. Mapping QTLs linked to physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.) in the target environment. American Journal of Biochemistry and Biotechnology. 2006; 2(4):161–169.

46. Lin MH, Lin CW, Chen JC, Lin YC, Cheng SY, Liu TH, et al. Tagging rice drought related QTL with SSR DNA markers. Crop, Environment & Bioinformatics. 2007; 4(1): 65–76.

47. Srinivasan S, Gomez SM, Kumar SS, Ganesh SK, Biji KR, Senthil A, et al. QTLs linked to leaf epicuticular wax, physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.). Plant Growth Regulation. 2008; 56(3): 245–256.

48. Kanagaraj P, Prince KSJ, Sheeba JA, Biji KR, Paul SB, Senthil A, et al. Microsatellite markers linked to drought resistance in rice (Oryza sativa L.). Current Science. 2010; 98: 836–839.

49. Salunkhe AKS, Poornima R, Prince KSJ, Kanagaraj P, Sheeba JA, Amudha K, et al. Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis. Molecular Biotechnology. 2011; 49(1):90–95. doi: 10.1007/s12033-011-9382-x 21298364

50. Prince SJ, Beena R, Gomez SM, Senthivel S, Babu RC. Mapping consistent rice (Oryza sativa L.) yield QTLs under drought stress in target rain-fed environments. Rice. 2015; 8(1):25.

51. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G. A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Science. 2007; 47(2): 507–518.

52. Li ZK, Xu JL. Breeding for drought and salt tolerant rice (Oryza sativas L.): progress and perspectives. In: (Eds. Jenks MA, Hasegawa PM, Jain SM.). Advances in molecular breeding toward drought and salt tolerant crops. Springer: 531–564.

53. Kumar R, Venuprasad R, Atlin GN. Genetic analysis of rainfed lowland rice drought tolerance under naturally occurring stress in eastern India: heritability and QTL effects. Field Crop Resources.2007; 103: 42–52.

54. Vikram P, Swamy BPM, Dixit S, Ahmed HU, Cruz MTS, Singh AK, et al. QDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic back-grounds. BMC Genetics. 2011; 12(89).

55. Yadaw RB, Dixit S, Raman A, Mishra KK, Vikram P, Swamy BPM, et al. A QTL for high grain yield under lowland drought in the background of popular rice variety Sabitri from Nepal. Field Crops Research. 2013; 144: 281–287.

56. Kam H, Fofana M, Zongo A, Taiwo S. Grain yield and related traits under drought and irrigated conditions. International Journal of Current Advanced Research. 2018; 07 (1):9059–9066.

57. Swamy BPM, Vikram P, Dixit S, Ahmed HU, Kumar A. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics. 2011; 2:319.

58. Ghimire KH. Identification and mapping of QTL (qDTY1.1) with a consistent effect on GY under RS. Field Crops Research. 2012; 131, 88–96.

59. Swamy BPM, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P. Physiological and gene expression analyses reveal multiple QTLs enhance the yield of rice mega-variety IR64 under drought. PLoS One. 2013. 8:e62795. doi: 10.1371/journal.pone.0062795 23667521

60. Dixit S, Singh A, Cruz MTS, Maturan PT, Amante M, Kumar A. Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities. BMC Genetics. 2014; 15:16. doi: 10.1186/1471-2156-15-16 24491154

61. Kumar A, Dixit S, Ram T, Yadaw RB, Mishra KK, Mandal NP. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches. Journal of Experimental Botany. 2014. doi: 10.1093/jxb/eru363 25205576

62. Noraziyah AAS, Swamy BPM, Wickneswari R, Teressa SC, Anitha R, Kumar A. Marker-assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219. BMC Genetics. 2016: 17:30. doi: 10.1186/s12863-015-0323-8

63. IRRI (International Rice Research Institute). SES (Standard Evaluation System for Rice). International Network for Genetic Evaluation of Rice. 2013; IRRI, Los Baños, Philippines.

64. Barr HD, Weatherley PE. A re-examination of the relative turgidity technique for estimating water deficit in leaves. Australian Journal of Biological Science. 1962; 15:413–428.

65. Blum A, Ebercon A. Cell membrane stability as a measure of drought and heat tolerance in wheat. Crop Science. 1981; 21:43–47.

66. Murray MG, Thomson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research. 1980; 8(19): 4321–326. doi: 10.1093/nar/8.19.4321 7433111

67. Wang J, Li H, Zhang L, Meng L. Users’ Manual of QTL Ici-Mapping. 2014. The Quantitative Genetics Group, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China, and Genetic Resources Program, International Maize and Wheat Improvement Centre (CIMMYT), Apdo. Postal 6–641, 06600 Mexico, D.F., Mexico.

68. Payne RW, Murray DA, Harding SA, Baird DB, Soutar DM. An Introduction to GenStat for Windows (14th Edition). 2011. VSN International, Hemel Hempstead, UK.

69. McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M, Morishima H, et al. Report on QTL nomenclature. Rice Genetics Newsletter. 1997; 14:11–13.

70. Babu RC, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, et al. Genetic analysis of drought resistance in rice by molecular markers: Association between secondary traits and field performance. Crop Science. 2003; 43:1457–1469.

71. Fukai S, Pantuwan G, Jongdee B, Cooper M. Screening for drought resistance in rainfed lowland rice. Field Crops Research. 1999; 64:61–74.

72. Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, et al. Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theoretical and Applied Genetics. 2001; 103(1): 19–29.

73. Courtois B, McLaren G, Sinha PK, Prasad K, Yadav R, Shen L. Mapping QTL associated with drought avoidance in upland rice. Molecular Breeding. 2000; 6:55–66.

74. Biswal AK, Kohli A. Cereal flag leaf adaptations for grain yield under drought: knowledge status and gaps. Molecular Breeding. 2013; 31: 749–766. doi: 10.1007/s11032-013-9847-7

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