EVALUATION OF GENETIC DIVERSITY OF SOYBEANACCESSIONS USING SSR MARKERS
Main Article Content
Authors
A.A. Amangeldiyeva
1 Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan
2Al-Farabi Kazakh National University, 71 Al-Farabi Avenue, Almaty 050040, Kazakhstan
R.S. Yerzhebayeva
Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan
S.V. Didorenko
Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan
Abstract
Soybean (Glycine max L.) is an important legume crop used to meet the protein and oil demands of many populations worldwide. Assessing the genetic diversity of soybean accessions is crucial for expanding the genetic base and improving the efficiency of breeding programs. The aim of this study was to evaluate the genetic diversity of 188 soybean accessions using 15 polymorphic SSR markers to determine the degree of their genetic differentiation and their potential for use in breeding. As a result of the study, a total of 55 alleles were identified, with an average of 2.68 alleles per locus. The polymorphic information content (PIC) ranged from 0.35 (Satt385) to 0.74 (Satt409), with an average of 0.61. The expected heterozygosity (He) ranged from 0.35 (Satt385) to 0.74 (Satt409), with an average value of 0.60. Furthermore, a phylogenetic Neighbor-Joining (NJ) dendrogram based on the binary allele data revealed three main clusters, each of which was divided into two subclusters. In addition, the analysis of molecular genetic data using the UPGMA method allowed the identification of two and one main clusters at different levels of genetic distance (0.21; 0.22). The obtained clusters reflect various relationships between local and foreign genotypes, indicating both the preservation of the local gene pool and its expansion through the inclusion of foreign cultivars. The information on genetic diversity among soybean genotypes obtained in this study will assist breeders in selecting parental lines for future breeding programs.
Keywords
soybean, SSR marker, genetic diversity, allele, genotype, cluster analysis
Article Details
References
Chander S., Garcia-Oliveira A.L., Gedil M., Shah T., Otusanya G.O., Asiedu R., Chigeza G. Genetic diversity and population structure of soybean lines adapted to sub-Saharan Africa using single nucleotide polymorphism (SNP) markers // Agronomy. – 2021. – Vol. 11(604)
Khojely D.M., Ibrahim S.E., Sapey E., Han T. History, current status, and prospects of soybean production and research in sub-Saharan Africa // Crop. J. – 2018. – Vol. 6. – P. 226–235.
Lukanda M.M., Dramadri I.O., Adjei E.A., Arusei P., Gitonga H.W., Wasswa P., Edema R., Ssemakula M.O., Tukamuhabwa P., Tusiime G. Genetic Diversity and Population Structure of Ugandan Soybean (Glycine max L.) Germplasm Based on DArTseq // Plant Mol. Biol. Rep. – 2023. – Vol.41. -P. 417–426.
Sivabharathi R., Muthuswamy A., Anandhi K., Karthiba L. Genetic Diversity Studies of Soybean [Glycine max (L.) Merrill] Germplasm Accessions using Cluster and Principal Component Analysis // Legume Res.Int. J. – 2023. – Vol. 1 (6)
Abebe A.T., Kolawole A.O., Unachukwu N., Chigeza G., Tefera H., Gedil M. Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers // Plant Genet. Resour. – 2021. – Vol.19. – P. 20–28.
Hymowitz T., Shurtleff W.R. Debunking Soybean Myths and Legends in the Historical and Popular Literature // Crop Sci. – 2005. – Vol. 45. – P. 473–476.
Walling J.G., Shoemaker R., Young N., Mudge J., Jackson S. Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps // Genetics. - 2006. – Vol. 172. – P. 1893–1900.
Mazkirat Sh, Babissekova D.I., Didorenko S.V., Kulakhmetova Zh.E., Bulatova K.M. Use of codominant protein and DNA markers in identification of F1 hybrid progenies in soybean // Experimental Biology. – 2023. – Vol. (95). – P. 84-94.
Rahman S.U., McCoy E., Raza G., Ali Z., Mansoor S., Amin I. Improvement of soybean; a way forward transition from genetic engineering to new plant breeding technologies // Molecular Biotechnology. – 2023. – Vol.65. – P. 162-180, Crossref 00456-6.
Tasma I.M., Yani N.P.M.G., Purwaningdyah R. Satyawan D., Nugroho K., Lestari P., Trijatmiko K.R. and Mastur M. Genetic diversity analysis and F2 population development for breeding of long juvenile trait in soybean // Jurnal AgroBiogen. – 2018. – Vol. 14(1). – P. 11-22.
Mawasid F.P. Syukur M., Trikoesoemaningtyas T., Wibisono, K. Evaluation to select tomato genotypes with big fruit and verification of genetic advance // Current Applied Science and Technology. – 2023. – Vol. 23(3). Crossref.
Dama H., Aisyah S.I., Sudarsono S., Dewi A.K., Wibisono K. Identification, selection, and response of radiation induced towuti mutant rice (Oryza sativa L.) in drought stress conditions // Atom Indonesia. – 2022. – Vol. 48(2). – P. 107-114, Crossref.
Nugroho K., Terryana R.T., Reflinur N., Asadi N., Lestari P. The genetic diversity analysis of introduced soybean cultivars using microsatellite markers // Informatika Pertanian. – 2017. – Vol. 26(2). – P. 121-132, Crossref.
Kujane K., Sedibe M.M., Mofokeng M.A. Assessment of genetic diversity among soybean (Glycine max (L.) Merr.) genotypes making use of agromorphological based on nutritional quality traits // Appl. Ecol. Environ. Res. – 2021. – Vol. 19. – P.3703–3716.
Teklu D.H., Shimelis H., Tesfaye A., Shayanowako A.I.T. Analyses of genetic diversity and population structure of sesame (Sesamum indicum L.) germplasm collections through seed oil and fatty acid compositions and SSR markers // J. Food Compos. Anal. – 2022. – Vol. 110. – P. 104-545.
Chander S., Garcia-Oliveira A.L., Gedil M., Shah T., Otusanya G.O., Asiedu R., Chigeza G. Genetic diversity and population structure of soybean lines adapted to sub-Saharan Africa using single nucleotide polymorphism (SNP) markers // Agronomy. - 2021. – Vol. 11. – P. 604.
Mondini L., Noorani A., Pagnotta M.A. Assessing plant genetic diversity by molecular tools // Diversity. – 2009. – Vol. 1(1). – P.19–35.
Tantasawat P., Trongchuen J., Prajongjai T., Jenweerawat S., Chaowiset W. SSR Analysis of Soybean (Glycine max(L.) Merr.) Genetic Relationship and Variety Identification in Thailand // Australian Journal of CropScience. – 2011. -Vol. 5(3). – P.283–90. URL. 279676194009468.
Alemu A., Feyissa T., Letta T., Abeyo B. Genetic diversity and population structure analysis based on the high density SNP markersin Ethiopian durumwheat(Triticum turgidumssp. durum) // BMC Genetics. – 2020. – Vol. 21(1). – P. 1–12.
Vigna l. A., Milan D., San Cristobal M., Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics // Genetics Selection Evolution. -2022. – Vol. 34(3). – P.275–305. Crossref. 1186/1297-9686-34-3-275
Guan R., Chang R., Li Y., Wang L., Liu Z., Qiu L.Genetic diversity comparison between Chinese and Japanese soybeans(Glycine max(L.) Merr.) revealed by nuclear SSRs // Genetic ResourcesCrop Evolution. – 2010. – Vol.57(2). – P.229–42.
Zhang C., Peng B., Zhang W., Wang S., Sun H., Dong Y.,et.al. Application of SSR markers for puritytesting of commercial hybrid soybean (Glycine max L.) // Journal of Agricultural Science Technology. – 2014. – Vol. 16 (6). – P.1389–96.
Wang L., Guan R., Zhangxiong L., Chang R., Qiu L. Genetic diversity of Chinese cultivated soybean revealed by SSR markers //CropScience. – 2006. – Vol.46(3). – P. 1032–8.
Doyle J.J., Doyle J.L. Arapid DNA isolation procedure for small quantities of fresh leaf tissue. 1987.
Cregan P.B., Jarvik T., Bush A.L., Shoemaker R.C., Lark K.G., Kahler A.L., Kaya N., Vantoai T.T., Lohnes D.G., Chung J., Specht J.E. An integrated genetic linkage map of the soybean genome // Crop Sci. – 1999. – Vol. 39(5). – P.1464-1490.
Gerardo Domingo Lucio Cervigni, Ivan Schuster, Everaldo Gonçalves de Barros Maur´ılio Alves Moreira. Two microsatellite markers flanking a dominant gene for resistance to soybean cyst nematode race // Euphytica. – 2004. – Vol. 135. – P. 99–105.
Khatab I.A., Morsy A.R., Fares W.M. Kumamaru T. Genetic Diversity of Soybean Genotypes revealed by Agro–morphological // J. Fac. Agr., Kyushu Univ. – 2016. – Vol. 61 (1). – P. 79–87.
Rani R., Raza G., Tung M.H., Rizwan M., Ashfaq H., Shimelis H., et al. (2023) Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSRand EST-SSR markers //PLoS ONE. – 2023. – Vol. 18(5): e0286099. Crossref. pone.0286099
Keitumetse K., Moosa M. S., Alina M. Genetic diversity analysis of soybean (Glycine max (L.) Merr.) genotypes making use of SSR markers // AJCS. – 2019. – Vol. 13(07). – P.1113-1119 (2019) doi: 10.21475/ajcs.19.13.07.p1638
Ghimire N.H., Dhakal K. H., Pandey M.P., Joshi B.K., Khanal B. Assessment of Agronomic Traits and Molecular Diversity Using SSR Markers in Soyabean, (Glycine Max (L.) Merr. Accessions in Nepal // Agronomy Journal of Nepal. – 2024. – Vol.8(1). – P. 119-134 ISSN: 2091-0649. Crossref
Kimura M., Crow J. The number of alleles that can be maintained in a finite population // Genetics. – 1964. – Vol. 49(4). – P. 725-738. doi:10.1093/ genetics/49.4.725.
Lewontin R. The apportionment of human diversity // Evol. Biol. – 1972. Crossref 9063-3_14
Peakall R., Smouse P. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update // Bioinformatics bioinformatics. – 2012. doi:10.1093/ https://biology assets.anu.edu.au/GenAlEx/Download://biol ogy-asset.
Botstein D., White R.L., Skalnick M.H., Davies R.W. (1980) Construc tion of a genetic linkage map in man using restriction fragment length polymorphism // Am J Hum Genet. – 1980. – Vol. 32. – P. 314–331.
Zatybekov A., Yermagambetova M., Genievskaya Y., Didorenko S., Abugalieva S. Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers // Plants. - 2023. – Vol. 12. – P. 34-45. Crossref 10.3390/plants12193445.