Genotypic clustering of 51 soybean cultivars and wild forms using SSR-markers

Cover Page

Cite item

Abstract

Soybean cultivars are characterized mainly by morphological and biochemical traits. However, researchers encounter difficulties when trying to use these parameters in cultivar identification and differentiation, making it difficult to work with closely related cultivar lines. Microsatellite markers or SSRs (simple sequence repeats) are an excellent tool for variety identification and differentiation, revealing the degree of genetic relatedness and copyright protection. The aim of the research was to obtain molecular genetic formulas for cultivated and wild soybean varieties with subsequent identification of their genetic relatedness. The object of the study was 51 samples of soybean (39 cultivars and 12 wild forms). Genomic DNA was isolated from the studied samples and then amplified. The obtained amplicons were separated in 2% agarose gel and the length of the fragments was detected in two replications. Nine microsatellite loci (Satt1, Satt2, Satt5, Satt9, Soyhsp176, Satt681, Sat_263, Satt141, Satt181) were used for molecular genetic characterization. Results demonstrating the length of each locus were analyzed by the UPGMA algorithm to record genetic relatedness or remoteness. The molecular genetic formulae of the studied samples were obtained, which can be further used to compile genetic passports. Based on the UPGMA algorithm, 51 soybean genotypes were grouped into 13 main clusters. Most of the soybean wild forms growing in the Amur Region demonstrated genetic proximity due to belonging to three closely located clusters. However, the soybean wild form from the Khabarovsk Territory (Dikaya soya 31) and one of the forms from the Amur Region (KZ-6337) were genetically distant from other groups of soybean wild forms. These results indicate the adequacy of the use of 9 SSR locuses for identification tasks, identification of relatedness and further passportization of soybeans.

Full Text

Table 1
Optimum annealing temperature

 Locus

 Annealing temperature, °C

 Actual

 Calculated

 Satt1

 60

 60

 Satt2

 60

 63

 Satt5

 55

 58

 Satt9

 45

 61

 Soyhsp176

 60

 67

 Satt681

 58

 65

 Sat_263

 65

 56

 Satt141

 63

 60

 Satt181

 63

 50

Source: compiled by O.N. Bondarenko, A.A. Penzin based on experimental data.

Table 2
The molecular genetic formulas of 51 soy genotype obtained by microsatelite analysis

 № 

 Soy culivar / wild form

 Formula*

 1

 Kruzhevnitsa

 А137B154C150D206H115 J244K135L148M225

 2

 Sentyabrinka

 A145B154C136D200H115J244K135L210M208

 3

 Vereteika

 A137B154C150D212H115J244K135L187M225

 4

 Lidiya

 A137B154C150D186H115J244K135L187M208

 5

 Umka

 A137B154C136D159H115J244K135L187M225

 6

 Dauriya

 A145B154C150D168H115J244K135L187M218

 7

 Zolushka

 A154B154C160D176H115J244K135L210M208

 8

 Lazurnaya

 A145B154C150D154H115J244K135L210M185

 9

 Topaz

 A145B154C136D138H115J244K135L210M170

 10

 Olimp

 A145B154C160D186H115J244K135L210M218

 11

 Lyana

 A145B146C160D154H115J244K135L210M185

 12

 Grei

 A137B146C160D186H115J244K165L210M218

 13

 VNIIS18

 A145B146C160D186H115J244K156L210M208

 14

 Alpetra

 A145B146C160D186H120J244K165L210M208

 15

 Zolotnitsa

 A137B154C160D212H115J244K156L210M170

 16

 Apis

 A125B154C160D212H115J244K156L210M208

 17

 Luchistaya

 A125B146C160D212H115J244K156L210M208

 18

 Tisei

 A125B146C160D206H115J244K180L210M208

 19

 Pepelina

 A137B154C160D168H115J244K156L210M208

 20

 Charodeika

 A154B163C160D186H115J200K165L210M208

 21

 Persona

 A125B146C160D212H105J220K135L187M175

 22

 Statnaya

 A125B146C165D212H105J228K135L187M170

 23

 Evgeniya

 A145B154C175D212H105J228K135L187M205

 24

 Zhuravushka

 A145B154C160D220H105J220K135L187M208

 25

 Bonus

 A137B137C175D200H105J244K156L187M195

 26

 Lebedushka

 A137B146C160D120H105J220K145L187M208

 27

 Kukhanna

 A137B146C185D120H105J244K135L187M208

 28

 MK 100

 A137B146C185D206H115J244K135L187M208

 29

 Nevesta

 A137B146C185D186H115J244K156L187M208

 30

 Nega 1

 A137B146C175D168H115J244K145L187M195

 31

 Oktyabr 70

 A145B146C185D154H115J244K135L187M208

 32

 Gratsiya

 A137B146C165D148H115J244K135L187M185

 33

 Intriga

 A137B146C185D200H115J244K135L187M195

 34

 Lastochka

 A145B154C185D212H105J244K156L210M185

 35

 Tatiana

 A137B137C160D212H105J256K156L187M208

 36

 Garmoniya

 A154B146C175D212H115J244K135L187M218

 37

 Sonata

 A154B146C175D212H115J244K135L187M208

 38

 Kitrossa

 A154B146C175D176H115J244K135L187M225

 39

 Alena

 A154B137C150D168H115J200K135L187M185

 40

 Dikaya soya 31

 A137B154C185D120H126J228K135L187M170

 41

 KZ‑6337

 A108B146C160D186H115J200K135L148M170

 42

 KBl‑29 [3]

 A145B176C175D120H126J244K165L210M208

 43

 KA‑14133

 A145B176C175D120H126J244K165L210M208

 44

 KA‑32

 A125B176C175D120H126J244K165L210M208

 45

 KBel‑72

 A145B176C160D120H126J244K165L210M208

 46

 KBl‑243

 A145B176C175D120H126J244K165L210M208

 47

 KA 3464

 A137B176C175D138H115J244K135L210M208

 48

 KT‑156 [4]

 A137B176C175D138H115J244K135L210M208

 49

 KZ‑5784

 A137B176C175D138H115J244K135L210M208

 50

 KBl‑90

 A125B176C175D186H115J244K135L210M208

 51

 KBl‑77

 A154B176C175D138H115J244K2135L210M208

Note. *Lokus code A — Satt1, B — Satt2, C — Satt5, D — Satt9, H — Soyhsp176, J — Satt681, K — Sat_263, L — Satt141, M — Satt181.
Source: compiled by A.A. Ivaniy, A.A. Penzin, O.N. Bondarenko, P.D. Timkin based on experimental data.

Fig. 1. Electrophoregram of DNA amplification products by cultivars: 2–3 — Persona; 4–5 — Statnaya; 7–8 — Evgeniya; 9–10 — Zhuravushka; 12–13 — Bonus; 14–15 — Lebedushka;
17–18 — Kukhanna using Satt181 locus
Source: compiled by A.A. Ivaniy, A.A. Blinova, A.E. Gretchenko based on experimental data.

 

Fig. 2. Dendrogram for 51 soybean genotype (39 cultivars and 12 wild forms)
Source: compiled by A.A. Ivaniy based on experimental data.

 

×

About the authors

Alena A. Ivaniy

Russian Research Institute of Soybean

Author for correspondence.
Email: iaa@vniisoi.ru
ORCID iD: 0009-0004-7304-7771

Junior Researcher, Laboratory of Biotechnology

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Andrey A. Penzin

Russian Research Institute of Soybean

Email: paa@vniisoi.ru
ORCID iD: 0000-0002-8578-9818
SPIN-code: 1467-9500

Research Associate, Laboratory of Biotechnology

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Olga N. Bondarenko

Russian Research Institute of Soybean

Email: ton@vniisoi.ru
ORCID iD: 0000-0002-5051-7695
SPIN-code: 1592-0588

Research Associate, Laboratory of Biotechnology

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Anastasia A. Blinova

Russian Research Institute of Soybean

Email: baa@vniisoi.ru
ORCID iD: 0000-0002-7234-0595
SPIN-code: 8575-0595

Researcher, Head of the biotechnology laboratory

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Alina E. Gretchenko

Russian Research Institute of Soybean

Email: gae@vniisoi.ru
ORCID iD: 0000-0003-3930-5672
SPIN-code: 3750-4348

Researcher, Laboratory of plant physiology and biochemistry

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Lyubov E. Ivachenko

Russian Research Institute of Soybean

Email: ivachenko-rog@yandex.ru
ORCID iD: 0000-0003-4870-2223
SPIN-code: 4641-4820

Doctor of Biological Sciences, Leading Researcher, Laboratory of Biotechnology

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

Pavel D. Timkin

Russian Research Institute of Soybean

Email: tpd@vniisoi.ru
ORCID iD: 0000-0001-6655-1049
SPIN-code: 2729-2815

Junior Researcher, Laboratory of Biotechnology

19 Ignatievskoye Shosse, Blagoveshchensk, Amur region, 675027, Russian Federation

References

  1. Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, et al. Plant Variety and cultivar identification: advances and prospects. Critical Reviews in Biotechnology. 2013;33(2):111-125. doi: 10.3109/07388551.2012.675314
  2. Kim YH, Park HM, Hwang TY, Lee SK, Choi MS, Jho S, et al. Variation block-based genomics method for crop plants. BMC Genomics. 2014;15(1):477. doi: 10.1186/1471-2164-15-477
  3. Gautam AK, Verma RK, Avasthi S, Sushma, Bohra Y, Devadatha B, et al. Current insight into traditional and modern methods in fungal diversity estimates. Journal of Fungi. 2022;8(3):226. doi: 10.3390/jof8030226 EDN: SXJPCZ
  4. Oliveira M, Azevedo L. Molecular markers: An overview of data published for fungi over the last ten years. Journal of Fungi. 2022;8(8):803. doi: 10.3390/jof8080803 EDN: JRTUAE
  5. Hou X, Li L, Peng Z, Wei B, Tang S, Ding M, et al. A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. The Plant Journal. 2010;63(5):880-888. doi: 10.1111/j.1365-313x.2010.04277.x
  6. Chaudhary R, Maurya GK. Restriction fragment length polymorphism. In: Vonk J, Shackelford TK. (eds.) Encyclopedia of Animal Cognition and Behavior. Cham, Switzerland: Springer; 2019. doi: 10.1007/978-3-319-47829-6_175-1
  7. Atoui A, El Khoury A. PCR-RFLP for Aspergillus species. In: Moretti A, Susca A. (eds.) Mycotoxigenic Fungi. Methods in Molecular Biology, volume 1542. New York, USA: Humana Press; 2017. p.313-320. doi: 10.1007/978-1-4939-6707-0_20
  8. Ibrahimi M, Brhadda N, Ziri R, Fokar M, Iraqi D, Gaboun F, et al. Analysis of genetic diversity and population structure of Moroccan date palm (Phoenix dactylifera L.) using SSR and DAMD molecular markers. Journal of Genetic Engineering and Biotechnology. 2023;21(1):66. doi: 10.1186/s43141-023-00516-7 EDN: JYOHAN
  9. Abugalieva SI, Zatybekov AK, Enuarbek SN, et al. Izuchenie geneticheskogo raznoobraziya i pasportizatsiya sortov soi Glycine max (L.) Merr. [Study of genetic diversity and certification of soybean varieties Glycine max (L.) Merr.]. Almaty; 2017. (In Russ.).
  10. Zatybekov AK, Turuspekov YT, Doszhanova BN, Abugalieva SI. A study of the genetic diversity in the world soybean collection using microsatellite markers associated with fungal disease resistance. Proceedings on applied botany, genetics and breeding. 2020;181(3):81-90. doi: 10.30901/2227-8834-2020-3-81-90 EDN: MMIRVY
  11. Ivaniy AA, Penzin AA. Comparative analysis of the yield of DNA released by a set of DNA-extran 3 when working with seeds and seedlings. In: Agro-industrial complex: problems and development prospects: conference proceedings. Blagoveshchensk; 2023. p.58-62. (In Russ.). doi: 10.22450/9785964205385_1_58 EDN: DPUUAN
  12. Ramazanova SA. Identification of soybean (Glycine max L.) cultivars using microsatellite DNA loci. Maslichnye kul’tury. Nauchno-tekhnicheskii byulleten’ Vserossiiskogo nauchno-issledovatel’skogo instituta maslichnykh kul’tur. 2016;(2):63-67. (In Russ.). EDN: WXSKMT
  13. Kumar SP, Susmita C, Sripathy KV, Agarwal DK, Pal G, Singh AN, et al. Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers. Molecular Biology Reports. 2021;49(3):2129-2140. doi: 10.1007/s11033-021-07030-4
  14. Mukuze C, Tukamuhabwa P, Maphosa M, Dari S, Dramadri IO, Obua T, et al. Genetic diversity analysis among soybean genotypes using SSR markers in Uganda. Afr J Biotech. 2020;19(7):439-448. doi: 10.5897/ AJB2020.17152 EDN: ZRJMEW
  15. Bondarenko ON, Blinova AA, Ivachenko LE, Lavrentieva SI. Selection of microsatellite DNA loci for creating molecular genetic passports of wild forms and varieties of Amur soybean breeding. Vestnik of the Far East branch of the Russian Academy of Sciences. 2022;(2):37-48. (In Russ.). doi: 10.37102/08697698_2022_222_02_3 EDN: TJLSZW

Supplementary files

Supplementary Files
Action
1. Fig. 1. Electrophoregram of DNA amplification products by cultivars: 2–3 — Persona; 4–5 — Statnaya; 7–8 — Evgeniya; 9–10 — Zhuravushka; 12–13 — Bonus; 14–15 — Lebedushka; 17–18 — Kukhanna using Satt181 locus
Source: compiled by A.A. Ivaniy, A.A. Blinova, A.E. Gretchenko based on experimental data.

Download (133KB)
2. Fig. 2. Dendrogram for 51 soybean genotype (39 cultivars and 12 wild forms)
Source: compiled by A.A. Ivaniy based on experimental data.

Download (100KB)

Copyright (c) 2025 Ivaniy A.A., Penzin A.A., Bondarenko O.N., Blinova A.A., Gretchenko A.E., Ivachenko L.E., Timkin P.D.

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies