Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers

Authors

  • Mohammad ANISUZZAMAN Universiti Putra Malaysia, Malaysia
  • Mohammad Rafiqul ISLAM Bangladesh Rice Research Institute, Bangladesh
  • Hasina KHATUN Bangladesh Rice Research Institute, Bangladesh
  • Mohammad Amdadul HAQUE Bangladesh Agricultural Research Institute, Bangladesh
  • Mahammad Shariful ISLAM Bangladesh Agricultural Research Institute, Bangladesh
  • Mohammad Shamim AHSAN Bangladesh Agricultural Research Institute, Bangladesh

DOI:

https://doi.org/10.14720/aas.2022.118.4.2500

Keywords:

molecular diversity, SSR markers, polymorphic information content, rice

Abstract

Rice crop improvement is determined by the degree of genetic variability and the heritability of favorable genes. A total of twenty-five SSR markers were used to measure the level of polymorphism and genetic variation among the 65 rice genotypes. Twenty-one of the twenty-five SSRs were discovered to be polymorphic, whereas the rest were determined to be monomorphic. A total of 91 alleles were found in 21 SSR markers, with an average of 4.00 alleles which ranged from 3 (RM335, RM551, RM538 RM190, RM242 and RM270) to 7 (RM263). The average PIC value was 0.62 ranging from 0.28 (RM 270) to 0.76 (RM 481). The rice genotypes were divided into nine primary clusters by a dendrogram based on NTSYS software’s UPGMA analysis. The cluster analysis revealed that these genotypes were divided into nine clusters where cluster IB-1a has the most genotypes (31) followed by cluster IB-1b (24).The genotype BR24 and Utri as well as Pukhi and WANGI PUTEH had the highest dissimilarity coefficient values indicating genotype diversity. These accessions have a lot of genetic diversity among the constituents; thus, they could be used directly in a hybridization program to improve yield-related parameters.

Author Biographies

  • Mohammad ANISUZZAMAN, Universiti Putra Malaysia, Malaysia
    Faculty of Agriculture and Senior Scientific Officer
  • Mohammad Rafiqul ISLAM, Bangladesh Rice Research Institute, Bangladesh
    Plant Breeding Division and Senior Scientific Officer
  • Hasina KHATUN, Bangladesh Rice Research Institute, Bangladesh
    Plant Breeding Division and Senior Scientific Officer
  • Mohammad Amdadul HAQUE, Bangladesh Agricultural Research Institute, Bangladesh
    Pomology division and Senior Scientific Officer
  • Mahammad Shariful ISLAM, Bangladesh Agricultural Research Institute, Bangladesh
    On-Farm Research Division and Senior Scientific Officer
  • Mohammad Shamim AHSAN, Bangladesh Agricultural Research Institute, Bangladesh
    Plant Physiology Division and Senior Scientific Officer

References

Anderson, J. A., Churchill, G. A., Autrique, J. E., Tanksley, S. D., & Sorrells, M. E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36(1), 181–186. https://doi.org/10.1139/93-024

Ashraf, H., Husaini, A. M., Ashraf Bhat, M., Parray, G., Khan, S., & Ganai, N. A. (2016). SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India. Physiology and Molecular Biology of Plants, 22(4), 547–555. https://doi.org/10.1007/s12298-016-0377-8

Becerra, V., Paredes, M., Ferreira, M. E., Gutiérrez, E., & Díaz, L. M. (2017). Assessment of the genetic diversity and population structure in temperate japonica rice germplasm used in breeding in Chile, with SSR markers. Chilean Journal of Agricultural Research, 77(1), 15–26. https://doi.org/10.4067/S0718-58392017000100002

Bohra, A., Jha, R., Pandey, G., Patil, P. G., Saxena, R. K., Singh, I. P., Singh, D., Mishra, R. K., Mishra, A., Singh, F., Varshney, R. K., & Singh, N. P. (2017). New hypervariable SSR markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [Cajanus cajan (L.) Millspaugh]. Frontiers in Plant Science, 8(March), 1–15. https://doi.org/10.3389/fpls.2017.00377

Brumlop, S., & Finckh, M. R. (2011). Applications and potentials of marker assisted selection (MAS) in plant breeding: final report of the F+ E project” Applications and Potentials of Smart Breeding”(FKZ 350 889 0020)-on behalf of the Federal Agency for Nature Conservation.

Buzatti, R. S. de O., Pfeilsticker, T. R., Muniz, A. C., Ellis, V. A., Souza, R. P. de, Lemos-Filho, J. P., & Lovato, M. B. (2019). Disentangling the environmental factors that shape genetic and ghenotypic leaf trait variation in the tree Qualea grandiflora across the Brazilian Savanna. Frontiers in Plant Science, 10(December), 1–14. https://doi.org/10.3389/fpls.2019.01580

Dhama, Nishat, Saini, R. K., Kumar, R., Chaudhary, D. P., Maurya, B. K., Sharma, M., Sen, M., Kumar, D., Malik, P., & Kumar, P. (2018). Analysis of genetic diversity in rice (Oryza Sativa L .) cultivars using SSR. Bulletin of Environmental Pharmacology and Life Science, 7(3), 1–7.

Doyle, J. J., & Doyle, J. L. (1987). Doyle plant DNA extract. Phytochemical Bulletin, 19(1), 11–15.

Gedil, M., & Menkir, A. (2019). An integrated molecular and conventional breeding scheme for enhancing genetic gain in maize in Africa. Frontiers in Plant Science, 10(November), 1–17. https://doi.org/10.3389/fpls.2019.01430

Hernández, H. G., Tse, M. Y., Pang, S. C., Arboleda, H., & Forero, D. A. (2013). Optimizing methodologies for PCR-based DNA methylation analysis. BioTechniques, 55(4), 181–197. https://doi.org/10.2144/000114087

Huang, M., Xie, F. M., Chen, L. Y., Zhao, X. Q., Jojee, L., & Madonna, D. (2010). Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers. Rice Science, 17(4), 257–268. https://doi.org/10.1016/S1672-6308(09)60025-1

Hue, H. T., Nghia, L. T., Minh, H. T., Anh, L. H., Trang, L. T. T., & Khanh, T. D. (2018). Evaluation of genetic diversity of local-colored rice landraces using SSR markers. International Letters of Natural Sciences, 67, 24–34. https://doi.org/10.18052/www.scipress.com/ilns.67.24

Koskey, G., Mburu, S. W., Kimiti, J. M., Ombori, O., Maingi, J. M., & Njeru, E. M. (2018). Genetic characterization and diversity of Rhizobium isolated from root nodules of mid-altitude climbing bean (Phaseolus vulgaris L.) varieties. Frontiers in Microbiology, 9(MAY), 1–12. https://doi.org/10.3389/fmicb.2018.00968

Linda, M., Arshiya N., & Maria A. P. (2009).Assessing plant genetic diversity by molecular tools. Jounal of MDPIDiversity, 1, 19-35; https://doi.org/10.3390/d1010019

McCouch, S. R., Temnykh, S., Lukashova, A., Coburn, J., DeClerck, G., Cartinhour, S., Harrington, S., Thomson, M., Septiningsih, E., Semon, M., Moncada, P., & Jimin, L. (2008). Microsatellite markers in rice: abundance, diversity, and applications. In: Rice Genetics IV. IRRI. Manila, Philippines (pp. 117–135). https://doi.org/10.1142/9789812814296_0008

Nachimuthu, V. V., Raveendran, M., Duraialaguraja, S., Sivakami, R., Pandian, B. A., Ponniah, G., Gunasekaran, K., Swaminathan, M., K K, S., & Sabariappan, R. (2015). Analysis of population structure and genetic diversity in rice germplasm using SSR markers: An initiative towards association mapping of agronomic traits in Oryza sativa L. Rice, 8(1). https://doi.org/10.1186/s12284-015-0062-5

Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N., Özkan, H., Chung, G., & Baloch, F. S. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology and Biotechnological Equipment, 32(2), 261–285. https://doi.org/10.1080/13102818.2017.1400401

Osekita, O., Akinyele, B., & Odiyi, A. (2015). Evaluation of exotic rice varieties for genetic parameters in a Nigerian agro-ecology. International Journal of Plant & Soil Science, 5(6), 350–358. https://doi.org/10.9734/ijpss/2015/12828

Pathak, P., Singh, S. K., Korada, M., Habde, S., Singh, D. K., Khaire, A., & Kumar Majhi, P. (2020). Genetic characterization of local rice (Oryza sativa L.) genotypes at morphological and molecular level using SSR markers. Journal of Experimental Biology and Agricultural Sciences, 8(2), 148–156. https://doi.org/10.18006/2020.8(2).148.156

Rohlf Fj. (1987). NTSYS-pc Version. 2.02i Numerical Taxonomy and Multivariate Analysis System. Applied Biostatistics Inc., Exeter Software, Setauket, New York. https://doi.org/10.2307/2684761

Sahagun-castellanos, J. (1985). Efficiency of augmented designs for selection. In Doctoral dissertation. Iowa State University.

Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., Rabaiolli, S. M. dos S., & Stefanel, C. M. (2020). Determining the polymorphism information content of a molecular marker. Gene, 726, 144175. https://doi.org/10.1016/j.gene.2019.144175

Singh, A., Saini, R., Singh, J., Arya, M., Ram, M., Pallavi, Mukul, & Singh, P. K. (2014). Genetic diversity studies in rice (Oryza sativa L.) using microsatellite markers. International Journal of Agriculture, Environment and Biotechnology, 8(1), 143. https://doi.org/10.5958/2230-732x.2015.00019.4

Singh, N., Choudhury, D. R., Tiwari, G., Singh, A. K., Kumar, S., Srinivasan, K., Tyagi, R. K., Sharma, A. D., Singh, N. K., & Singh, R. (2016). Genetic diversity trend in Indian rice varieties: An analysis using SSR markers. BMC Genetics, 17(1), 1–13. https://doi.org/10.1186/s12863-016-0437-7

Siva, R., Kumar, K., & Rajasekaran, C. (2013). Genetic diversity study of important Indian rice genotypes using biochemical and molecular markers. African Journal of Biotechnology, 12(10), 1004–1009. https://doi.org/10.5897/AJB10.797

Sonkar, S., Singh, S. K., Vennela, P. R., & Singh, D. K. (2016). Molecular marker based genetic diversity analysis in rice genotypes (Oryza sativa L.) using SSR markers. International Journal of Agriculture, Environment and Biotechnology, 9(1), 45–51. https://doi.org/10.5958/2230-732X.2016.00007.3

Sun, P., Jia, H., Yue, Z., Li, J., Li, J., Zhang, J., Lu, M., & Hu, J. (2020). Genetic identification of 91 poplar cultivars based on SSR markers. Nordic Journal of Botany, 38(6). https://doi.org/10.1111/njb.02504

Tarang, A., Kordrostami, M., Shahdi Kumleh, A., Hosseini Chaleshtori, M., Forghani Saravani, A., Ghanbarzadeh, M., & Sattari, M. (2020). Study of genetic diversity in rice (Oryza sativa L.) cultivars of Central and Western Asia using microsatellite markers tightly linked to important quality and yield related traits. Genetic Resources and Crop Evolution, 67(6), 1537–1550. https://doi.org/10.1007/s10722-020-00927-2

Thomson, M. J., de Ocampo, M., Egdane, J., Rahman, M. A., Sajise, A. G., Adorada, D. L., Tumimbang-Raiz, E., Blumwald, E., Seraj, Z. I., Singh, R. K., Gregorio, G. B., & Ismail, A. M. (2010). Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice, 3(2–3), 148–160. https://doi.org/10.1007/s12284-010-9053-8

Toppo, A., Rastogi, N., Sarawgi, A., & Saxena, R. R. (2018). Molecular characterization of rice accessions using microsatellite markers. Indian Journal of Plant Genetic Resources, 31(3), 310. https://doi.org/10.5958/0976-1926.2018.00036.0

Uba, C. U., Oselebe, H. O., Tesfaye, A. A., & Abtew, W. G. (2021). Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers. PloS One, 16(7), e0253600. https://doi.org/10.1371/journal.pone.0253600

Xu, Y., Li, P., Zou, C., Lu, Y., Xie, C., Zhang, X., Prasanna, B. M., & Olsen, M. S. (2017). Enhancing genetic gain in the era of molecular breeding. Journal of Experimental Botany, 68(11), 2641–2666. https://doi.org/10.1093/jxb/erx135

Yadav, M. K., Aravindan, S., Ngangkham, U., Shubudhi, H. N., Bag, M. K., Adak, T., Munda, S., Samantaray, S., & Jena, M. (2017). Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS ONE, 12(4), 1–19. https://doi.org/10.1371/journal.pone.0176236

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Published

30. 12. 2022

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Original Scientific Article

How to Cite

ANISUZZAMAN, M., ISLAM, M. R., KHATUN, H., HAQUE, M. A., ISLAM, M. S., & AHSAN, M. S. (2022). Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers. Acta Agriculturae Slovenica, 118(4), 1–13. https://doi.org/10.14720/aas.2022.118.4.2500

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