Mapping and validation of a major quantitative trait locus qRN5a associated with increasing root number under low potassium in rice


Potassium (K) is an indispensable mineral constituent required for plant growth and many physiological processes. K deficiency and depletion in rice occurs frequently, resulting in limited growth, agronomical loss, and reduced yield. To investigate the genetics of low K (LK) tolerance, a set of high throughput genotyped chromosome segment substitution lines (CSSL) derived from the cross between Zhonghui9308 (ZH9308, susceptible to LK) and XieqingzaoB (tolerant to LK) was used to identify QTL for the shoot and root traits at the seedling stage. The experiment was conducted in hydroponic culture to explore the molecular basis of five seedling traits under two K conditions, LK and normal K (NK) and their ratio (LK/NK) for relative traits. A total of five QTL were identified on four chromosomes (3, 4, 5, and 6) with positive allelic effects from XieqingzaoB for root length (RL) and root number (RN) and negative allelic effects for shoot dry weight (SDW) and root dry weight (RDW). Two QTLs, qRN5a and qSDW4, were detected under LK and three QTLs, qRL6, qRN5b, and qRDW3, were identified under LK/NK ratio explaining 11.81% to 13.07% of total phenotypic variation. qRN5a, a novel QTL under LK, was validated in the F2 (BC5F2) population and delimited to a 1023 Kb interval between the markers InD78 to RM18472. These findings will serve as important breeding material for further genetic characterization like fine mapping and cloning, which may be useful in molecular marker-assisted breeding.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 199

This is the net price. Taxes to be calculated in checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Abbasi GH, Akhtar J, Ahmad R, Jamil M, Haq M, Ali S, Ijaz M (2015) Potassium application mitigates salt stress differentially at different growth stages in tolerant and sensitive maize hybrids. Plant Growth Regul 76:111.

  2. Adams E, Shin R (2014) Transport, signaling, and homeostasis of potassium and sodium in plants. J Integr Plant Biol 56:231–249.

  3. Alonso-Blanco C, Koornneef M (2000) Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci 5:22–29.

  4. Anis GB, Zhang Y, Wang H, Li Z, Wu WX, Sun LP, Riaz A, Cao LY, Cheng SH (2018) Genomic regions analysis of seedling root traits and their regulation in responses to phosphorus deficiency tolerance in CSSL population of elite super hybrid rice. Int J Mol Sci 19(5):1460.

  5. Buchanan BB, Gruissem W, Jones RJ (2002) Biochemistry & molecular biology of plants. Wiley, West Sussex, p 1366

  6. Chen YL (2012) Qtl for Traits Related with Potassium Deficiency Resistance in Rice. Msc thesis, Chinese Academy of Agricultural Sciences.

  7. Childs NW (2004) Production and utilization of rice. In: Champagne ET (ed) Rice chemistry and technology, 3rd edn. American Association of Cereal Chemists, St. Paul, MN, pp 1–23

  8. Doi K, Iwata N, Yosiiimura A (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of japonica rice (O. sativa L.). Rice Genet Newsl 14:39–41

  9. Fang Y, Wu W, Zhang X, Jiang H, Lu W, Pan J, Hu J, Guo L, Zeng D, Xue D (2015) Identification of quantitative trait loci associated with tolerance to low potassium and related ions concentrations at seedling stage in rice (Oryza sativa L.). Plant Growth Regulation 77(2):157–166.

  10. Hartley TN, Thomas AS, Maathuis FJM (2019) A role for the OsHKT 2;1 sodium transporter in potassium use efficiency in rice. J Exp Bot.

  11. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

  12. IRRI (International Rice Research Institute). (2018). Rough rice production by country and geographical region-USDA. Trend in the rice economy In: World Rice Statistics.

  13. Jiang S, Zhang X, Jiang H, Wang T, Ding G, Sun S, Bai L, Zhang F (2014) Identification of QTLs for new formed root architectural traits in rice (Oryza Sativa L.) after transplantation. Plant Omics 7(5):410–414

  14. Kurakazu T, Sobrizal IK, Sanchez PL, Doi K, Angeles ER, Khush GS, Yoshimura A (2001) Oryza meridionalis chromosomal segment introgression lines in cultivated rice O. sativa L. Rice Genet Newsl 18:81

  15. Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Lafitte HR, Jiang YZ, Rey JD, Vijayakumar CH, Maghirang R, Zheng TQ, Zhu LH (2005) Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol Biol 59:33–52.

  16. Lin HX, Zhu MZ, Yano MJ, Gao P, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260.

  17. Luan S, Lan W, Lee SC (2009) Potassium nutrition, sodium toxicity, and calcium signaling: connections through the CBL-CIPK network. Curr Opin Plant Biol 12:339–346.

  18. Lush JL (1937) Animal breeding plans. Iowa State Univ Press, Ames

  19. Marschner H (1995) Mineral nutrition of higher plants, 2nd edition. Academic Press Inc., London p 889.

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

  21. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207.

  22. Mengel K, Kirkby EA (eds) (2001) Principles of plant nutrition. Kluwer Academic Publishers, Dordrecht, pp 481–509

  23. Miyamoto T, Ochiaia K, Takeshitaa S, Matoha T (2012) Identification of quantitative trait loci associated with shoot sodium accumulation under low potassium conditions in rice plants. Soil Sci Plant Nutr 58:728–736.

  24. Moinuddin IP (2007) Evaluation of potassium compared to other osmolytes in relation to osmotic adjustment and drought tolerance of chickpea under water deficit environments. J Plant Nutr 30:517–535.

  25. Romheld V, Kirkby EA (2010) Research on potassium in agriculture: needs and prospects. Plant soil 335:155–180.

  26. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends in Plant Sci 10:297–304.

  27. Shen C, Wang J, Jin X, Liu N, Fan X, Dong C, Shen Q, Xu Y (2017) Potassium enhances the sugar assimilation in leaves and fruit by regulating the expression of key genes involved in sugar metabolism of Asian pears. Plant Growth Regul 83:287.

  28. Sobrizal IK, Sanchez PL, Doi K, Angeles ER, Khush GS, Yoshimura A (1999) Development of Oryza glumaepatula introgression lines in rice O. sativa L. Rice Genet Newsl 16:107–108

  29. Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker facilitated investigations of quantitative trait loci in maize: 2. Factors influencing yield and its component traitas. Crop Sci 27:639–648.

  30. Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580.

  31. Wang JK (2009) Inclusive composite interval mapping of quantitative trait genes. Acta Agron Sin 35:239–245 (in Chinese with English abstract)

  32. Wang S, Basten C, Zeng Z (2011) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC

  33. Wang Z, Chen Z, Cheng J, Lai Y, Wang J, Bao Y, Huang J, Zhang H (2012) QTL analysis of Na+ and K+ concentrations in roots and shoots under different levels of NaCl stress in rice (Oryza sativa L.). PLoS ONE 7(12):1–9.

  34. Wang HM, Xu XM, Zhan XD, Zhai RR, Wu WM, Shen XH, Dai GX, Cao LY, Cheng SH (2013) Identification of qRL7, a major quantitative trait locus associated with rice root length in hydroponic conditions. Breed Sci 63:267–274.

  35. Wang G, Lu W, Chen H, Zhang X, Xue D (2015) Seedling screening of rice germplasm resources with low potassium tolerance. J Hangzhou Normal Univ. 1:44–48

  36. Wu P, Ni J, Luo A, Jin G, Tao Q (1997) Investigation of QTLs underlying rice tolerance for potassium deficiency via molecular markers. Plant Nutr Fert Sci 3(3):209–217

  37. Wu P, Ni JJ, Luo AC (1998) QTLs underlying rice tolerance to low-potassium stress in rice seedlings. Crop Sci 38:1458–1462

  38. Yamamoto T, Yonemaru J, Yano M (2009) Towards the understanding of complex traits in rice: substantially or superficially? DNA Res 16:141–154.

  39. Yang XE, Liu JX, Wang WM, Ye ZQ, Luo AC (2004) Potassium internal use efficiency relative to growth vigor, potassium distribution, and carbohydrate allocation in rice genotypes. J Plant Nutr 27:837–852.

  40. Yano M (2001) Genetic and molecular dissection of naturally occurring variations. Curr Opin Plant Biol 4:130–135.

  41. Yoshida S, Fomo DA, Cock JH, Gomez KA (1976) Laboratory manual for physiological studies of rice. The third edition, Intl. Rice Res. Inst., Manila, Philippines, pp 60–66

  42. Zhu B, Xu Q, Zou Y, Ma S, Zhang X, Xie X, Wang L (2019) Effect of potassium deficiency on growth, antioxidants, ionome and metabolism in rapeseed under drought stress. Plant Growth Regul.

Download references


This work was supported by the Zhejiang Provincial Natural Science Foundation of China (Grant number LQ14C130003), the National Natural Science Foundation of China (Grant numbers 31871604 and 31521064), the National Key Transform Program (Grant number 2016ZX08001-002), and the Super Rice Breeding Innovation Team and Rice Heterosis Mechanism Research Innovation Team of the Chinese Academy of Agricultural Sciences Innovation Project (Grant number CAAS-ASTIP-2013-CNRRI).

Author information

Conceptualization: AI, WW, and YZ; Methodology: AI, WW, and GA; Formal analysis and investigation: AI, MHR and WA; Writing—original draft preparation: AI; Writing—review and editing: AI, WW, YZ, GA, MHR, WA, XS, LC and SC; Funding acquisition: WW, LC and SC; Resources: YZ and XS; Supervision: WW, SC, and LC.

Correspondence to Liyong Cao or Shihua Cheng or Weixun Wu.

Ethics declarations

Conflicts of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 364 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Islam, A., Zhang, Y., Anis, G. et al. Mapping and validation of a major quantitative trait locus qRN5a associated with increasing root number under low potassium in rice. Plant Growth Regul (2020) doi:10.1007/s10725-020-00574-8

Download citation


  • Rice
  • Chromosome segment substitution lines
  • Quantitative trait loci
  • Root number
  • Low potassium
  • Hydroponic culture