Analyses of genomic regions linked with resistance to basal stem rot in sunflower (Helianthus annuus L.) under field conditions

Document Type : Research paper


1 Department of Plant Biotechnology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.

2 Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, P. O. Box: 165, Urmia, Iran.

3 Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran.


Sunflower (Helianthus annuus L.) is one of the four important sources of edible oil in the world. Fungal diseases are considered as major constraints for its seed yield and quality. Basal stem rot resulted by Sclerotinia sclerotiorum (Lib.) de Bary fungus, is known as a serious disease on oily sunflower, worldwide. In this project, genomic region linked with partial resistance to basal stem rot disease was identified using a population of recombinant inbred lines (RILs) created from the hybridization between PAC2 (♀) and RHA266 (♂) lines. Nine phenotypic characters related to disease resistance including PN4D, PN8D, PN12D, NCW100S, CW100S, NCPY, CPY, DP100S and DPY were measured under artificial infection in the field conditions. Newly developed genetic linkage map of sunflower was used for detecting and mapping QTLs. The linkage map includes 210 SSR and 11 SNP markers distributed in 17 groups. The analysis was carried out using composite interval mapping (CIM) procedure. High coefficient of variation (CV) was detected for those studied characters that reveal high genetic variability for susceptibility to disease in the studied sunflower RIL population. Totally, 56 putative QTLs were identified for the studied nine quantitative characters. The number of QTLs for each character ranged from 1 to 9, explaining 0.91 to 80.75% of phenotypic variation (R2). Additive effect sign was positive for 17 QTLs, suggesting that the promising allele has been transmitted from male parent (RHA266). In this project, major QTLs (LOD≥2.5 and R2≥10%) were identified for all of the studied characters, exceptifor NCW100S and CW100S characters. The major QTLs are important for running marker-aided selection (MAS) in resistant breeding programs.


Amouzadeh M., Darvishzadeh R., Haddadi P., Abdollahi-Mandoulakani B., and Rezaee-Danesh Y. (2013). Genetic analysis of partial resistance to basal stem rot (Sclerotinia sclerotiorum) in sunflower. Genetika, 45: 737–748.
Amoozadeh M., Darvishzadeh R., Davar R., Abdollahi Mandoulakani B., Haddadi P., and Basirnia A. (2015). Quantitative trait loci associated with isolate specific and isolate non-specific partial resistance to Sclerotinia sclerotiorum in sunflower. Journal of Agricultural Science and Technology, 17(1): 213–226.
Bert P., Jouan F., Tourvieille de Labrouhe D., Seere F., Nicolas P., and Vear F. (2002). Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.) 1. QTL involved in resistance to Sclerotinia sclerotiorum and Diaporthe helianthi. Theoretical and Applied Genetics, 105: 985–993.
Bert P. F., Dechamp-Guillaume G., Serre F., Jouan I., Tourvieille de Labrouhe D., Nicolas P., and Vear F. (2004). Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.) 3. Characterisation of QTL involved in resistance to Sclerotinia sclerotiorum and Phoma macdonaldi. Theoretical and Applied Genetics, 109: 865–874.
Bolton M. D., Thomma B. P. H. J., and Nelson B. D. (2006). Sclerotinia sclerotiorum (Lib.) de Bary: Biology and molecular traits of a cosmopolitan pathogen. Molecular Plant Pathology, 7: 1–16.
Davar R., Darvishzadeh R., Majd A., Ghosta Y., and Sarrafi A. (2010). QTL mapping of partial resistance to basal stem rot in sunflower using recombinant inbred lines. Phytopathologia Mediterranea, 49: 330–341.
Delgado S. G., Castaño F., Cendoya M. G., Salaberry M. T., and Quiróz F. (2020). Analysis of genetic determination of partial resistance to white rot in sunflower. Helia, 43(72): 1–14. DOI:
Doerge R. W., and Churchill G. A. (1996). Permutation test for multiple loci affecting a quantitative character. Genetics, 142: 285–294.
Filippi C. V., Zubrzycki J. E., Di Rienzo J. A., Quiroz F. J., Puebla A. F., Alvarez D., Maringolo C. A., Escande A. R., Hopp H. E., Heinz R. A., Paniego N. B., and Lia V. V. (2020). Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower. BMC Plant Biology, 20: 322. DOI:
Fusari C. M., Di Rienzo J. A., Troglia C., Nishinakamasu V., Moreno M. V., and Maringolo C.(2012). Association mapping in sunflower for Sclerotinia head rot resistance. BMC Plant Biology, 12: 93.
Gentzbittel L., Vear F., Zhang Y. X., Berville A., and Nicolas P. (1995). Development of a consensus linkage RFLP map of cultivated sunflower (Helianthus annuus L.). Theoretical and Applied Genetics, 90: 1079–1086.
Gulya T. J., Rashid K. Y., and Masirevic S. M. (1997). Sunflower diseases. In: Schneiter A. A. (Ed.) Sunflower Technology and Production. Soil Science Society of America Inc. Madison, 263–379.
Haddadi P., Ebrahimi A., Langlade N. B., Yazdi-Samadi B., Berger M., and Calmon A. (2012). Genetic dissection of tocopherol and phytosterol in recombinant inbred lines of sunflower through QTL analysis and the candidate gene approach. Molecular Breeding, 29: 717–729.
Hittalmani S., Huang N., Courtois B., Venuprasad R., Shashidhar H. E., and Zhuang J. Y. (2003). Identification of QTL for growth and grain yield-related traits in rice across nine locations of Asia. Theoretical and Applied Genetics, 107: 679–690.
Ibrahim A. K., Zhang L., Niyitanga S., Afzal M. Z., Xu Y., Zhang L., Zhang L., and Qi J. (2020). Principles and approaches of association mapping in plant breeding. Tropical Plant Biology, 13: 212–224. DOI:
Jaganathan D., Bohra A., Thudi M., and Varshney R. K. (2020). Fine mapping and gene cloning in the postNGS era: advances and prospects. Theoretical and Applied Genetics, 133: 1791–1810.
Kane N. C., Gill N., King M. G., Bowers J. E., Berges H., Gouzy J., Bachlava E., Langlade N. B., Lai Z., Stewart M., Burke J. M., Vincourt P., Knapp S. J., and Rieseberg L. H. (2011). Progress towards a reference genome for sunflower. Botany, 89: 429–437.
Laroche A., Frick M., Graf R. J., Larsen J., and Laurie J. D. (2019). Pyramiding disease resistance genes in Canadian elite winter wheat germplasm. The Crop Journal, 7(6): 739–749.
Mbedzi P. P., van der Hoven L., Vorster B. J., and van der Waals J. E. (2019). Screening for Sclerotinia sclerotiorum resistance using detached leaf assays and simple sequence repeat markers in soybean cultivars. Crop Protection, 125: 104909.
Mestries E., Gentzbittel L., Tourvieille de Labrouhe D., Nicolas P., and Vear F. (1998). Analysis of quantitative trait loci associated with resistance to Sclerotinia sclerotiorum in sunflowers (Helianthus annuus L.) using molecular markers. Molecular Breeding,4: 215–226.
Micic Z., Hahn V., Bauer E., Schön C., Knapp S. J., and Tang S. (2004). QTL mapping of Sclerotinia midstalk rot resistance in sunflower. Theoretical and Applied Genetics, 109: 1474–1484.
Micic Z., Hahn V., Bauer E., Schön C. C., and Melchinger A. E. (2005a). QTL mapping of resistance to Sclerotinia midstalk rot in RIL of sunflower population NDBLOS x CM625. Theoretical and Applied Genetics,110: 1490–1498.
Micic Z., Hahn V., Bauer E., Melchinger A. E., Knapp S. J., and Tang S. (2005b). Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by selective genotyping. Theoretical and Applied Genetics, 111: 233–242.
Najafzadeh R., Darvishzadeh R., Musa-Khalifani Kh., Abrinbana M., and Alipour H. (2018). Retrotransposonable regions of sunflower genome having relevance with resistance to Sclerotiniaspecies: S. sclerotiorum and S. minor. Australasian Plant Pathology, 47: 511–519.
Pereyra V. R., and Escande A. (1994). Manual de reconocimiento de enfermedades del Girasol en la Argentina. Ed del INTA CERBAS, Balcarce, Buenos Aires, Argentina, 122–130.
Poormohammad-Kiani S., Grieu P., Maury P., Hewezi T., Gentzbittel L., and Sarrafi A. (2007). Genetic variability for physiological traits under drought conditions and differential expression of water stress associated genes in sunflower (Helianthus annuus L.). Theoretical and Applied Genetics, 114: 193–207.
Qasim M. U., Zhao Q., Shahid M., Samad R. A., Ahmar S., Wu J., Fan C., and Zhou Y. (2020). Identification of QTLs containing resistance genes for Sclerotinia stem rot in Brassica napus using comparative transcriptomic studies. Frontiers in Plant Science, 11: 776. DOI: 10.3389/fpls.2020.00776.
Rönicke, S., Hahn V., Horn R., Gröne I., Brahm L., Schnabl H., and Freidt W. (2004). Interspecific hybrids of sunflower as a source of Sclerotinia resistance. Plant Breeding, 123: 152–157.
Schneiter A.A. and Miller J.F. (1981). Description of sunflower growth stages. Crop Science, 21: 901–903.
Seiler G. J., Misar C. G., Gulya T. J., Underwood W. R., Flet B. C., Gille M. A., and Marke S. G. (2017). Identification of novel sources of resistance to Sclerotinia basal stalk rot in South African sunflower germplasm. Plant Health Progress, 18: 87–90.
Seiler G. J., and Jan C. C. (2014). Wild sunflower species as a genetic resource for resistance to sunflower broomrape (Orobanche cumana Wallr.). Helia, 37: 129–139.
Soleri D. (1993). Hopi crop diversity and change. Journal of Ethnobiology, 13: 203–231.
Talukder Z. I., Underwood W., Ma G., Seiler G. J., Misar C. G., Cai X., and Qi L. (2020). Genetic dissection of Phomopsis stem canker resistance in cultivated sunflower using high density SNP linkage map. International Journal of Molecular Sciences, 21: 1497. DOI: 10.3390/ijms21041497.
Talukder Z. I., Seiler G. J., Song Q., Ma G., and Qi L. (2016). SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing. The Plant Journal, 9(3): 1–16.
Talukder Z. I., Hulke B. S., Marek L. F., and Gulya T. J. (2014a). Sources of resistance to sunflower diseases in a global collection of domesticated USDA plant introductions. Crop Science, 54: 694–705.
Talukder Z. I., Hulke B. S., Qi L., Scheffler B. E., Pegadaraju V., McPhee K., and Gulya T. J. (2014b). Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs. Theoretical and Applied Genetics, 127: 193–209.
Tang S., Yu J. K., Slabaugh M. B., Shintani D. K., and Knapp S. J. (2002). Simple sequence repeat map of the sunflower genome. Theoretical and Applied Genetics, 105: 1124–1136.
Tuberosa R., Sanguineti M. C., Landi P., Giuliani M. M., Salvi S., and Conti S. (2002). Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes. Plant Molecular Biology, 48: 697–712.
Van-Becelaere G., and Miller J. F. (2004). Combining ability for resistance to Sclerotinia head rot in sunflower. Crop Science, 44: 1542–1545.
Vear F., and Grezes-Besset B. (2010). Progress in breeding sunflowers for resistance to Sclerotinia. Proceeding of I.S.A. Symposium “Sunflower breeding for resistance to diseases”, Krasnodar, Russia, 19-21(6): 30-35.
Voorrips R. (2002). Map Chart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93: 77–78.
Wang S., Basten C. J., and Zeng Z. B. (2005). Windows QTL Cartographer V2.5. Department of Statistics, North Carolina State University, Raleigh NC, Available from /qtlcart/WQTLCart.htm.
Xu Y., Li P., Yang Z., and Xu C. (2017). Genetic mapping of quantitative trait loci in crops. The Crop Journal, 5(2): 175–184.
Zubrzycki J., Fusari C., Maringolo C., Di Rienzo J., Cervigni G., and Nishinakamasu V. (2012). Biparental QTL and association mapping for Sclerotinia head rot resistance in cultivated sunflower. In: Proceeding of 18th International Sunflower Conference, Mar del Plata, Argentina, 99-102.
  • Receive Date: 16 July 2020
  • Revise Date: 27 September 2020
  • Accept Date: 01 October 2020
  • First Publish Date: 01 October 2020