QTL mapping for heat stress tolerance in chickpea (Cicer arietinum L.)

DOI: 10.18805/LR-4121    | Article Id: LR-4121 | Page : 382-387
Citation :- QTL mapping for heat stress tolerance in chickpea (Cicer arietinum L.).Legume Research-An International Journal.2021.(44):382-387
Uday Chand Jha, Paresh Chandra Kole and Narendra Pratap Singh uday_gene@yahoo.co.in
Address : ICAR-Indian Institute of Pulses Research, Kanpur-208 024, Uttar Pradesh, India.
Submitted Date : 22-01-2019
Accepted Date : 20-03-2019


Rising evidence of heat stress (HS) is appearing as one of the major challenges to crop performance including chickpea affecting plant growth and yield significantly. Unprecedented advancements in chickpea genomic resources have resulted in remarkable progress for genetic dissection of various complex traits including biotic and abiotic stresses. However, these genomic resources have been limitedly utilized for developing HS tolerance in chickpea. Thus, the present study was aimed to capture genetic variability and to identify HS relevant quantitative trait loci (QTL) using 206 F2 individuals developed from DCP 92-3 × ICCV 92944 cross. Wide range of genetic variability for seventeen traits related to phenological, physiological and breeding importance was captured from the given population under HS condition by growing them in late sown condition.  A total of 78 SSR markers were used for genotyping of the given F2 individuals. Only 39 markers were fitted to Mendelian segregation and these were assigned to all linkage groups (LGs) except LG8, covering 859 cM of genome. QTL analysis revealed one QTL controlling primary branch number (PB) explaining 2% phenotypic variation (PV) on LG3 and another QTL related to chlorophyll content (CHL) on LG6 explaining 17.2% PV.  In future, fine mapping of these QTL controlling genomic regions may enable uncovering the underlying candidate gene(s) contributing in HS tolerance. Thus, these genomic regions could be promisingly utilized for marker assisted breeding for developing heat tolerant chickpea genotype. 


Chickpea Genomics Heat stress QTL SSR.


  1. Bennett, D., Reynolds, M., Mullan, D., Izanloo, A., Langridge, P., Schnurbusch T. (2012). Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments. Theoretical and Applied Genetics, 125: 1473—1485.
  2. Bohra, A., Pandey, M.K., Jha, U.C., Singh, B., Singh, I.P., Datta, D., Chaturvedi, S.K., Nadarajan. N., Varshney, R.K. (2014). Genomics assisted breeding in four major pulse crops of developing countries: present status and prospects. Theoretical and Applied Genetics, 127:1263–1291.
  3. Choudhary, S., Sethy, N.K., Shokeen, B., Bhatia. S. (2009). Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics, 118:591–608.
  4. Choudhary, S., Gaur, R., Gupta, S., Bhatia, S. (2012). EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theoretical and Applied Genetics, 124(8):1449–1462.
  5. Devasirvatham, V., Gaur, P., Mallikarjuna, N., Raju, T.N., Trethowan, R.M., Tan, D.K.Y .(2012). Effect of high temperature on the reproductive development of chickpea genotypes under controlled environments. Functional and Plant Biology, 39(12): 1009-1018.
  6. Doyle, J.J., and Doyle J.L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19: 11–15.
  7. Elshafei, A.A., Saleh, M., Al-Doss, A.A., Moustafa, K.A., Al-Qurainy, F.H., Barakat, M.N.(2013). Identification of new SRAP markers linked to leaf chlorophyll content, flag leaf senescence and cell membrane stability traits in wheat under water-stressed condition. Australian Journal of Crop Science, 7:887–893.
  8. FAOSTAT. (2016). Food and Agriculture Organization of the United Nations, FAOSTAT . Rome, Italy. FAO; 2016. Available at: http:/    /fao.org/faostat/en/#data/QC(Accessed13Jan2018)
  9. Frova, C., and Sari-Gorla, M. (1993). Quantitative expression of maize HSPs: genetic dissection and association with thermo tolerance. Theoretical and Applied Genetics, 86: 213—220.
  10. Gaur, R., Sethy, N.K., Choudhary, S., Shokeen, B., Gupta, V., Bhatia, S .(2011). Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicerarietinum L.). BMC Genomics, 12:117.
  11. Gaur, P.M., Jukanti, A.K., Varshney, R.K .(2012). Impact of genomic technologies on chickpea breeding strategies. Agronomy, 2:199–222.
  12. Jha, U.C., Chaturvedi, S.K., Bohra, A., Basu, P.S., Khan, M.S., Debmalya, B .(2014). Abiotic stresses, constraints and improvement strategies in chickpea. Plant Breeding, 133:163–178.
  13. Jha, U.C., and Shil, S .(2015a). Association analysis of yield contributing traits of chickpea genotypes under high temperature condition. Trends in Bioscience, 8: 2335–2341.
  14. Jha, U.C., Basu, P.S., Singh, D.K. (2015). Genetic variation and diversity analysis of chickpea genotypes based on quantitative traits under high temperature stress. International Journal of Bio-resource and Stress Management, 6: 700-706.
  15. Jha, U.C., Bohra, A., Jha, R., Parida, S .(2017). Integrated ‘omics’ approaches to sustain major global grain legume productivity under heat stress. Plant Breeding, 136:437–459.
  16. Jha, U.C., Jha, R., Shil, S., Singh, N.P., Kole, P.C. (2018a).Heat tolerance indices and their role in selection of heat stress tolerant chickpea (Cicer arietinum) genotypes. Indian Journal of Agriculture Science, 88(2): 260–7.
  17. Jha, U.C., Jha, R., Bohra, A., Parida, S.K., Kole, P.C., Thakro, V., Singh, D., Singh, N.P. (2018b). Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.). 3 Biotech, 8:43.
  18. Jha, U.C., Kole, P.C., Singh, N.P. (2018c).Genetic variability and marker trait association analysis of various phenological and yield Related traits for heat tolerance in chickpea (Cicer arietinum L.). International Journal of Bio-resource and Stress Management, 9:345-352.
  19. Jha, U.C.(2018). Current advances in chickpea genomics: applications and future perspectives. Plant Cell Report, 37: 947–965.
  20. Kale, S.M., Jaganathan, D., Ruperao, P., Chen, C., Punna, R., Kudapa, H., Thudi, M., et al.,(2015). Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Report, 5:15296.
  21. Kalra, N., Chakraborty, D., Sharma, A., Rai, H.K., Jolly, M., Chander, S., Kumar, P.R., Bhadraray, et al., .(2008). Effect of temperature on yield on some winter crops in northwest India. Current Science, 94:82–88.
  22. Kosambi, D.D .(1944). The estimation of map distances from recombination values. Annals of Eugenics 12:172-175.
  23. Krishnamurthy, L., Gaur, P.M., Basu, P.S., Chaturvedi, S.K., Tripathi, S., Vadez, V., et al.,.(2011). Large genetic variation for heat tolerance in the reference collection of chickpea (Cicer arietinumL.) germplasm. Plant Genetic Resources, 9:59–69.
  24. Li, J., Zhang, F., Qian, X., Zhu, Y., Shen G .(2015). Quantification of rice canopy nitrogen balance index with digital imagery from unmanned aerial vehicle. Remote Sensing Letters, 6: 183-189.
  25. Lei, D., Tan, L., Liu, F., Chen, L., Sun, C. (2013). Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff). Plant Science, 201–202: 121—127.
  26. Mason, R.E., Mondal, S., Beecher, F., Hays, D .(2011). Genetic loci linking improved heat tolerance in wheat (Triticum aestivum L) to lower leaf and spike temperatures under controlled conditions. Euphytica, 180: 181—194.
  27. Paliwal, R., Rdoder, M.S., Kumar, U., Srivastava, J.P., Joshi, A.K. (2012). QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L). Theoretical and Applied Genetics, 125: 561—575.
  28. Paul, P.J., Samineni, S., Sajja, S.B., Rathore, A., Das, R.R., Khan, A.W., Chaturvedi, S.K., et al., .(2018a). Capturing genetic variability and selection of traits for heat tolerance in a chickpea recombinant inbred line (RIL) population under field conditions. Euphytica, 214:27.
  29. Paul, P.J., Samineni, S., Thudi, M., Sajja, S.B., Rathore, A., Das, R.R., Khan, A.W., et al.,(2018b). Molecular mapping of QTLs for heat tolerance in chickpea. International Journal of Molecular science, 19(8) pii: E2166.
  30. Saxena, M.S., Bajaj, D., Das, S., Kujur, A., Kumar, V., Singh, M., Bansal, K.C., Tyagi, A.K., Parida, S.K .(2014). An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea. DNA Research, 21:695-710. 
  31. Sethy, N.K., Shokeen, B., Bhatia, S. (2003). Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Molecular Ecology Notes, 3:428–430.
  32. Sethy, N.K., Shokeen, B., Edwards, K.J., Bhatia, S .(2006). Development of microsatellite markers and analysis of intra specific genetic variability in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics, 1:1416–1428.
  33. Talukder, S.K., Babar, M.A., Vijayalakshmi, K., Poland, J., Prasad, P.V., Bowden, R., Fritz, A. (2014). Mapping QTL for the traits associated with heat tolerance in wheat (Triticum aestivum L.). BMC Genetics, 15:97.
  34. Thudi, M., Upadhyaya, H.D., Rathore, A., Gaur, P.M., Krishnamurthy, L., Roorkiwal, M., Nayak, S.N., et al., .(2014). Genetic dissection of drought and heat tolerance in chickpea through genome wide and candidate gene-based association mapping approaches. PLoS One, 9:e96758.
  35. Udupa, S.M., Robertson, L.D., Weigand, F., Baum, M., Kahl, G .(1999). Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Molecular Genetics and Genomics, 261:354–363.
  36. Van Ooijen, J.W .(2006). Join Map 4: software for the calculations of genetic linkage maps in experimental populations. Kyazma B.V, Wageningen.
  37. Wang, S., Basten, C.J., Zeng, Z.B. (2010). Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
  38. Winter, P., Pfaff, T., Udupa, S.M., Huttel, B., Sharma, P.C., Sahi, S., Arreguin- Espinoza, R., Weigand, F., Muehlbauer, F.J., Kahl, G .(1999). Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Molecular Genetics and Genomics, 262:90–101.
  39. Ye, C., Argayoso, M.A., Redona, E.D., Sierra, S.N., Laza, M.A., Dilla, C.J., Mo, Y., Thomson, M.J.J, et al.,(2012). Mapping QTL for heat tolerance at flowering stage in rice using SNP markers. Plant Breeding, 131: 33—41. 

Global Footprints