Evaluation of Retrotransposon-based Markers for Identification of Genetic Loci Associated with Agro-morphological Characteristics and Resistance to Sclerotinia Basal Stem rotin Oily Sunflower (Helianthus annuusL.) under Filed Conditions

پژوهشهای زراعی ایران

Article 4, Volume 16, Issue 1 - Serial Number 49, April 2018, Pages 83-96   

Document Type: Research Article

DOI: 10.22067/gsc.v16i1.58597

Authors

R Paknia¹; F Shahriari^{* 1}; R Darvishzadeh²; S Malekzadeh Shafaroudi¹

¹Ferdowsi University of Mashhad

²Urmia University

Abstract

Introduction
Sunflower (Helianthus annuus L.) is one of the most important crops grown mainly for edible oil. Sclerotinia sclerotiorum (Lib.) de Bary is a common and widespread pathogen of sunflower. Sclerotinia stem rot is one of the most damaging diseases of sunflower in world, causing average yield reductions of 10 to 20%. It causes total production loss under favorable environmental conditions. Hence, plant improvement projects must focus on creating of new genotypes with higher resistance against diseases. Resistance to S. sclerotiorum (Lib.) de Bary has been described as quantitatively inherited with additive and dominant gene effects. Identification of chromosome regions controlling partial resistance to sclerotinia stem rot can increase understanding about the genetic control of the diseases and developing cultivars with improved partial resistance. In this study, retrotranposon-based molecular markers associated with resistance to disease as well as some important agromorphological traits identified using general and mixed linear models in Tassel software.
Material and Method
A collection of 100 sunflower lines, kindly provided by several research centers in Europe, Iran and the United States, were evaluated using a 10´10 simple lattice design with two replications. Each plot comprised 2 lines 5 m long, with a spacing of 65 × 25 cm between lines and plants, respectively. The experiment was conducted in 2015 at a farm in ‘Vaghaslo-e-Sofla’ village on Urmia. Five plants per genotype in each replication were inoculated with a fungal isolate collected from naturally infected sunflower plants of this farm in previous year.Some resistant and agronomical traits including  percentage of necrotic area after 4, 8, 12 days inoculation, 100 seeds weight of non contaminated plants, 100 seeds weight of contaminated plants, yield per plant in non contaminated plants, yield per plant in contaminated plants, 100 seeds weight loss, and per plant yield loss were  measured. The genetic profile of population was prepared with 28 rerotransposon markers.
Result and Discussion
Based on molecular marker data, the studied association panel was subdivided into two subpopulations (K=2). Association analysis using mixed linear model (MLM) identified 27 loci significantly (P<0.01) associated with studied traits. Maximum number of markers (5) was identified for percentage of necrotic area after 4 days and yield per plant in contaminated plants. Some common markers were identified for studied traits. Common markers for traits can be due to pleiotropic effects or linkage between genomic regions involved in controlling traits. Results of the current study present useful information about the genetic basis of the studied traits and can be used in different sunflower breeding programs including marker aided selection. In future studies, coding regions of important agronomical and resistance traits could be identified by sequencing loci with highest R².
Conclusions
In sum, 27 loci associated with genomic regions controlling studied agro-morphological and resistant traits were identified. By converting identified retrotranspos-based molecular markers to SCAR, it is possible to use them directly in breeding activities such as identification of appropriate parents for developing mapping population, developing hybrid cultivars as well as marker assisted selection programs.

Keywords

Association mapping; Linkage disequilibrium; Molecular Marker; Population structure; Sunflower

References

1. Abdi, N., Darvishzadeh, R., Jafari, M., Pirzad, A., and Haddadi, P. 2012. Genetic analysis and QTL mapping of agro-morphological traits in sunflower (Helianthus annuus L.) under two contrasting water treatment conditions. Plant Omics 5 (2): 149-158.

2. Allinne, C., Maury, P., Sarrafi, A., and Grieu, P. 2009. Genetic control of physiological traits associated to low temperature growth in sunflower under early sowing conditions. Plant Science 177: 349-359.

3. Anandhan, T., Manivannan, N., Vindhiyaman, P., and Jeykaumar, P. 2010. Single marker analysis in sunflower (Helianthus annuus L.). Electronic Journal of Plant Breeding 1 (4): 1227-1234.

4. Andaya, V. C., Tabanao, D., Maramara, G., and Sebastian, L. S. 1996. Correlation of molecular diversity with heterosis in nine lowland rice. Philippine Journal of Crop Science 21: 4.

5. Aranzana, M. J., Kim, S., Zhao, K., Bakker, E., Horton, M., Jakob, K., Lister, C., Molitor, J., Shindo, C., Tang, C., Toomajian, C., Traw, B., Zheng, H., Bergelson, J., Dean, C., Marjoram, P., and Nordborg, M. 2005. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1(5): e60.

6. 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: 1-166.

7. Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Randoss, Y., and Buckler, E. S. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.

8. Breseghello, F., and Sorrells, M. E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.

9. Campbell, M. A., Fitzgerald, H. A., and Ronald, P. C. 2002. Engineering pathogen resistance in crop plants. Transgenic Research 11: 599-613.

10. Carson, M. L. 1991. Relationship between phoma black stem severity and yield losses in hybrid sunflower. Plant Disease 75: 1150-1153.

11. Darvishzadeh, R. 2012. Association of SSR markers with patial resistance to Sclerotinia sclerotiorum isolates to sunflower. Australian Journal of Crop Science 6 (2): 276-282.

12. Ebrahimi, A., and Sarrafi, A. 2012. Genetic Variability and identification of markers in gamma-irradiation induced mutants of sunflower under water stress condition. Iranian Journal of Genetics and Plant Breeding 1 (2): 1-8.

13. Evanno, G., Reganut, E., and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620.

14. Eyvaznejad, N., and Darvishzadeh, R. 2014. Identification of QTLs for grain yield and some agro-morphological traits in sunflower (Helianthus annuus L.) using SSR and SNP markers. Journal of Plant Molecular Breeding 2 (2): 68-87

15. Flint-Garcia, S. A., Thornsberry, J. M., and Buckler, E. S. 2003. Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54: 357-374.

16. Fusari C. M., Rienzo J. A. D., Troglia C., Nishinakamasu V., Moreno M. V., Maringolo C., Quiroz F., Álvarez D., Escande A., Hopp E., Heinz R., Lia V. V., and Paniego N. B. 2012. Association mapping in sunflower for sclerotinia head rot resistance. BMC Plant Biology 12 (93): 1-13.

17. Gulya, T. J., Rashid, K. Y., and Masirevic, S. N. 1997. Sunflower diseases. In Sunflower technology and production, Madison, Wisconsin, USA, p. 263-379.

18. Hahn, V. 2002. Genetic variation for resistance to Sclerotinia head rot in sunflower inbred lines. Field Crops Research 77: 153-159

19. Inostroza, L., Pozo, A. D., Matus, I., Castillo, D., Hayes, P., Machado, S., and Corey, A. 2009. Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. Vulgare background. Molecular Breeding 23: 365-376.

20. Jun, T. H., Van, K., Kim, M. Y., Lee, S. H., and Walker, D .R. 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 62: 179-191.

21. Liue, L., Wang, L., Yao, J., Zheng, Y., and Zhao, C. 2010. Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.). Molecular Plant Breeding 1 (5): 1-10.

22. Mandel, J. R., Nambeesan, S., Bowers, J. E., Marek, L. F., Ebert, D., Rieseberg, L. H., Knapp, J. M., and Burk, J. M. 2013. Association mapping and the genomic consequence of selection in sunflower. Genetics 9 (3): 1-13.

23. Masirevic, S., and Gulya, T. J. 1992. Sclerotinia and phomopsis-two devastating sunflower pathogens. Field Crops Research 30: 271-300.

24. Micic, Z., Hahn, V., Bauer, E., Schon, C. C., Knapp, S. J., Tang, S., and Melchinger, A. E. 2004. QTL mapping of Sclerotinia midstalk rot resistance in sunflower. Theoretical and Applied Genetics 109: 1474-1484.

25. Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., and Buckler, E. S. 2009. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.

26. Onemli, F., and Gucer, T. 2010. Response to drought of some wild species of Helianthus at seedling growth stage. Helia 33 (53): 45-54.

27. Pritchard, J. K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.

28. Purdy, L. H. 1979. Sclerotinia sclerotiorum: History, diseases and symptomatology, host range, geographic distribution and impact. Phytopathology 69: 875-880.

29. Rafalski, J. A. 2002a. Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5: 94-100.

30. Rafalski, J. A. 2002b. Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science 162: 329-333.

31. Rönicke, S., Hahn, V., and Friedt, W. 2005. Resistance to Sclerotinia sclerotiorum of ‘high oleic’ sunflower inbred lines. Plant Breeding 124: 376-381

32. Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivotovsky, L. A., and Feldman, M. W. 2002. Genetic structure of human populations. Science 298: 2381-2385.

33. Roy, J. K., Bandopadhyay, R., Rustgi, S., Balyan, H. S., and Gupta, P. K. 2006. Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Current Science 90: 5-10.

34. Spataro, G., Tiranti, B., Arcaleni, P., Bellucci, E., Attene, G., Papa, R., Spagnoletti Zeuli, P., and Negri, V. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122: 1281-1291.

35. Speed, D., Hemani, G., Johnson, M. R., and Balding, D. J. 2012. Improved heritability estimation from genome-wide SNPs. American Journal of Human Genetics 91: 1011-1021.

36. Sukumaran, S., Xiang, W., Bean, S. R., Pedersen, J. F., Kresovich, S., Tuinstra, M. R., Tesso, T. T., Hamblin, M. T., and Yu, J. 2012. Association mapping for grain quality in a diverse sorghum collection. The Plant Genome 5: 126-135.

37. Talukder, I. Z., Hulke, S. B., Qi, L., Scheffler, E. B., Pegadaraju, V., McPhee, K., and Gulya, J. T. 2014. 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.

38. Thornsberry, J. M., Goodman, M. M., Doebley, J., Kresovich, S., and Nielsen, D. 2001. Dwarf8 polmorphisms associate with variation in flowering time. Nature Genetics 28: 286-89.

39. Tuberosa, R., Salvi, S., Sanguineti, M. C., Landi, P., Maccaferri, M., and Conti, S. 2002. Mapping QTLs regulating morpho-physiological traits and yield in drought-stressed maize: case studies, shortcomings and perspectives. Annals of Botany 89: 941-963.

40. Wang, W. Y. S., Barratt, B. J., Clayton, D. G., and Todd, J. A. 2005. Genome-wide association studies: theoretical and practical concerns. Nature Reviews Genetics 6: 109-118.

41. Würschum, T., Anyanga, W. O., and Hahn, V. 2014. Inheritance of Sclerotinia Midstalk Rot Resistance in Elite Sunflower Breeding Germplasm. Helia 37 (61): 193-203.

42. Yue, B., Radi, S. A., Vick, B. A., Cai, X., Tang, S., Knapp, S. J., Gulya T. J., Miller J. F., and Hu, J. 2008. Identifying quantitative trait loci for resistance to Sclerotinia head rot in two USDA sunflower germplasms. Phytopathology 98: 926-931.

43. Zhu, C., Gore, M., Buckler, E. S., and Yu, J. 2008. Status and prospects of association mapping in plants. Plant Genome 1: 5-20.