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:: Volume 5, Issue 1 (2018) ::
pgr 2018, 5(1): 39-54 Back to browse issues page
Identification of Informative Alleles Controlling Rice Traits under Flooding and Drought Stress Conditions‌‌
Halbibi Badirdast , Seyed Yahya Salehi-Lisar , Hossain Sabouri * , Ali Movafeghi , Ebrahim Gholamalalipour Alamdari
Department of Plant Production, Faculty of Agriculture and Natural Resources, University of Gonbad Kavus, Gonbad Kavus, Iran , sabouri@gonbad.ac.ir
Abstract:   (16512 Views)
One of the main objectives of plant breeding is defining the relationship between genotype and phenotype. Nowadays, molecular markers provide powerful tools to evaluate this relationship for plant breeders. In this study, genetic diversity of 112 rice lines was evaluated by 20 pairs of SSR markers which linked to drought tolerant alleles. Totally, 77 polymorphic alleles with mean of 3.85 alleles per primer pairs were amplified. The minimum number of alleles was belonged to RM28199 and RM212 markers with 2 alleles, and the maximum number of alleles was belonged to RM72 marker with 6 alleles. The range of PIC for the examined markers was 0.30 to 0.72 and the mean of PIC was 0.58. The maximum amount of PIC was belonged to RM85 and RM20A markers and the minimum of PIC was belonged to RM28099 marker. Considering the gene diversity coeficient, RM28099 and RM 85 markers had minimum (0.33) and maximum (0.76) diversity, respectively. The stepwise regression analysis of the microsatellite data and morphologic traits identified 62 and 54 informative alleles for the evaluated traits in flooding and drought conditions, respectivly. Cluster analysis based on molecular data divided the genotypes into 7 groups. Considering the appropriate distribution of amplified DNA by the studied markers in this study, markers that have high separation power and high association with important agronomic traits in drought stress condition (if further experiments confirmed them), could be employed in plant breeding programs of drought stress.
Keywords: Rice, Cluster analysis, Drought stress, Genetic variety, SSR marker
Full-Text [PDF 1173 kb]   (1615 Downloads)    
Type of Study: Research | Subject: Plant genetics
Accepted: 2019/03/31
References
1. Aalami, A. and Karami, K. (2016). The study of genetic diversity in iranian rice cultivars using ISSR, IRAP and REMAP markers. Journal of Crop Breeding, 20: 41-51 (In Persian).
2. Amini Nasab, R., Ebrahimi M.A., Ebadi, A.A. and Ghodsi, M. (2012). Study of genetic variation in Iranian rice (Oryza sativa L.) varieties by using molecular markers linked with drought resistance genes. Crop Biotechnology, 2: 15-2 (In Persian).
3. Amiri, P., Ismaili, A. and Hadian, J. (2017). Evaluation of Genetic Diversity of Styrian Pumpkin (Cucurbita pepo var. styriaca) Populations, Using ISSR Molecular Markers. Plant Genetic Researches, 4: 17-28 (In Persian). [DOI:10.29252/pgr.4.2.17]
4. Anandan, A., Anumalla, M., Pradhan, Sh.K. and Ali, J. (2016). Population structure, diversity and trait association analysis in rice (Oryza sativa L.) germplasm for early seedling vigor (ESV) using trait linked SSR markers. PLOS ONE, DOI:10.1371/journal.pone.0152406. [DOI:10.1371/journal.pone.0152406]
5. Awasthi, S. and Lal, J.P. (2014). Marker assisted selection for the improvement of Sarjoo-52 for drought tolerance by introgression of MQTL1.1 from the source Nagina-22. Journal of Plant Molecular Breeding, 2: 43-55.
6. Azizi, H., Aalami, A., Esfahani, M. and Ebadi, A.K. (2017). Association and structure analysis of some of rice (Oryza sativa L.) genetic resources based on microsatellite markers. Cereal Research, 7: 1-16 (In Persian).
7. Fazeli, F. and Cheghamirza, K. (2011). Investigation of genetic diversity in iranian landrace chickpea bulks using ISSR marker. Seed and Plant Improvement Journal, 6: 97-104 (In Persian).
8. Jahani, M., Nematzadeh, G.H. and Mohammadi-Nejad, G.H. (2016). Genetic diversity analysis in a global panel of rice genotypes by microsatellites. Journal of Agricultural Biotechnology, 8: 20-32 (In Persian).
9. Jedari Kouhi, B., Garoosi, G.H. and Hosseini, R. (2011). Investigation on genetic variation in seedless grapevine cultivars, using RAPD molecular marker. Cell & Tissue Journal, 2: 99-106 (In Persian).
10. Haussmann, B.I., Parzies, H.K., Presterl, T., Susic, Z. and Miedaner, T. (2004). Plant genetic resources in crop improvement. Plant Genetic Resources, 2: 3-21. [DOI:10.1079/PGR200430]
11. Honarvar, F., Saoburi, H. and Dadras, A.M. (2016). Study of genetic diversity of rice genotypes by SSR markers and association analysis for related traits to cold tolerance. Journal of Agricultural Biotechnology, 8: 166-173 (In Persian). [DOI:10.18869/acadpub.jcb.8.17.173]
12. Gharekhani, M., Navabpour, S., Sabouri, H. and Ramezanpour, S.S. (2016). Study of genetic variation in Iranin rice (Oryza sativa L.) using SSR Markers. Journal of Agricultural Biotechnology, 8: 107-115 (In Persian).
13. Ghiasy, M., Farahbakhsh, H., Sabouri, H. and Mohamadi Nejad, G.H. (2013). Evaluation of rice cultivars in drought and normal conditions based on sensitive and tolerance indices. Electronic Journal of Crop Production, 6: 55-75 (In Persian).
14. Masoudi, M., Sabouri, H., Taliey, F. and Jafarby, J.A. (2017). Genetic diversity and association analysis for morphophenolgic traits and resistance to Powdery mildew using ISSR, IRAP and iPBS markers. Crop Biotechnology, 18: 41-56 (In Persian).
15. Matus, I.A. and Hayes, P.M. (2002). Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome, 45: 1095-1106. [DOI:10.1139/g02-071]
16. Miah, G., Rafii, M.Y., Ismailm M.R., Puteh, A.B., Rahim, H.A., Nurul Islam, Kh. and Abdul Latif, M. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International Journal of Molecular Sciences, 14: 22499-22528. [DOI:10.3390/ijms141122499]
17. Mishra, K.K., Vikram, P., Yadaw, R.B., Swamy, B.M., Dixit, SH., Cruz, M.T.S., Maturan, P., Marker, S.H. and Kumar, A. (2013). qDTY12.1: a locus with a consistent effect on grain yield under drought in rice. BMC Genetics, 14: 1-10. [DOI:10.1186/1471-2156-14-12]
18. Mohammadi, S.A. and Prasanna, B.M. (2003). Analysis of genetic diversity in crop plant- salient statistical tools and consideration. Crop Science, 43: 1235-1248. [DOI:10.2135/cropsci2003.1235]
19. Nikzade Talebi, S., Aalami, A., Esfahani, M. and Ebadi, A.A. (2016). Evaluation of allic frequency and association analysis of microsatellite markers with some traits related to pre-harvest sprouting in rice (Oryza sativa L.) cultivars. Iranian Journal of Crop Sciences, 18: 49-62 (In Persian).
20. Park, G.H, Kim, J.H. and Kim, K.M. (2014). QTL analysis of yield components in rice using acheongcheong/nagdong doubled haploid genetic map. American Journal of Plant Sciences, 5: 1174-1180. [DOI:10.4236/ajps.2014.59130]
21. Raiesi, T. and Sabouri, A. (2015). Validation and association analysis of microsatellite markers related to drought and salinity tolerance in aerobic and Iranian rice under osmotic stress. Crop Biotechnology 10: 57-72 (In Persian).
22. Ranjbar, M., Naghavi, M.R., Zali, A., Aghaei, M.J. and Mardi, M. (2009). Identification of informative markers of SSR in Aegilops crassa accessions of Iran. Journal of Agriculture, 11: 48-57 (In Persian).
23. Ribeiro-Carvalho, C., Guedes-Pinto, P., Igrejas, G., Stephenson, P., Schwaraacher, T. and Heslop-Harrison, J.S. (2004). High levels of genetic diversity throughout the range of the Portuguese wheat landrace 'Barbela. Annals of Botany, 94: 699-705. [DOI:10.1093/aob/mch194]
24. Roldan-Ruiz, F.A., Gilliland, T.J., Dubreuil, P., Dillmann, C. and Lallemand, J. (2001). A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theoretical and Applied Genetics, 103: 1138-1150. [DOI:10.1007/s001220100571]
25. Saghai Mroof, M.A., Biyashev, R.M., Yang, G.P., Zhang, Q. and Allard, R.W. (1994). Extraordinarily polymorphic DNA in barely species diversity, chromosomal location, and population dynamics, Proceedings of the National Academy of Sciences of the United States of America, 91: 5466-5570.‌ [DOI:10.1073/pnas.91.12.5466]
26. Salehi Lisar, S.Y. and Bakhshayeshan Agdam, H. (2016). Drought Stress in Plants: Causes, Consequences, and Tolerance. Springer, Cham, CH. [DOI:10.1007/978-3-319-28899-4_1]
27. Shayan, S., Moghaddam Vahed, M., Norouzi, M., Mohammadi, S.A., Toorchi, M. and Molaei, B. (2017). Inheritance of Agronomical and Physiological Traits in the Progeny of Moghan3 and Arg Bread Wheat Varieties Cross. Plant Genetic Researches, 4: 43-60 (In Persian). [DOI:10.29252/pgr.4.2.43]
28. Switzer, R.C., Merril, C.R. and Shifrin, S. (1979). A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gel. Analytical Biochemistry, 98: 231-237. [DOI:10.1016/0003-2697(79)90732-2]
29. Tavala, R., Aalami, A., Sabouri, H. and Sabouri, A. (2015). Evaluation of haplotype and allelic diversity of SSR markers linked to major effect QTL on chromosome 9 controlling drought tolerance in rice. Cereal Research, 5: 107-119 (In Persian).
30. Valizadeh Soumeh, Z., Samizadeh Lahiji, H. and Rabiei, B. (2014). Assessment of morphologic and genetic diversity of rice varieties using SSR markers associated with drought tolerance characteristics. Cereal Research, 4: 89-101 (In Persian).
31. Vikram, P., Swamy, B.P.M., Dixit, S.H., Trinidad, J., Cruz, M.T.S., Maturan, P.C., Amante, M. and Kumar, A. (2016). Linkages and Interactions Analysis of Major Effect Drought Grain Yield QTLs in Rice. PLOS ONE, DOI:10.1371/journal.pone.0151532. [DOI:10.1371/journal.pone.0151532]
32. Vikram, P., Swamy, B.M., Dixit, S.H., Ahmed, H.U., Cruz, M.T.S., Singh, A.K. and Kumar, A. (2011). qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with aconsistent effect in multiple elite genetic backgrounds. BMC Genetics, 12: 1-15. [DOI:10.1186/1471-2156-12-89]
33. Yashitol, T.M., Sandarm, R., biradar, S. and Thirumuragau, K. (2004). Sequence specific PCR marker for disting uishing rmice line at the basis of wild abortive cytoplasm for their congatc maintir lin. Crop Science, 44: 920-924. [DOI:10.2135/cropsci2004.9200]
34. Zali, H., Hasanloo, T., Sofalian, O., Asghari, A. and Zeinalabedini, M. (2016). Drought stress effect on physiological parameter and amino acids accumulations in canola. Journal of Crop Breeding, 8: 191-203 (In Persian). [DOI:10.29252/jcb.8.18.191]
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Badirdast H, Salehi-Lisar S Y, Sabouri H, Movafeghi A, Gholamalalipour Alamdari E. Identification of Informative Alleles Controlling Rice Traits under Flooding and Drought Stress Conditions‌‌. pgr 2018; 5 (1) :39-54
URL: http://pgr.lu.ac.ir/article-1-121-en.html


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Volume 5, Issue 1 (2018) Back to browse issues page
پژوهش های ژنتیک گیاهی Plant Genetic Researches
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