Genetic diversity assessment in pea cultivars and lines using the SSR analysis

Background. Pea is the main leguminous crop in the Republic of Bashkortostan and widespread all over the world. The key role in the breeding of new pea cultivars is played by source material representing the phenotypic and genotypic diversity of Pisum sativum L., searched for in plant genetic resources collections. SSR markers are successfully used to study the DNA polymorphism of various genetic objects, including pea. However, the distribution of a number of microsatellite alleles in the genotypes of specific lines and cultivars of this valuable pulse crop remains practically unexplored.

Materials and methods. Molecular genetic polymorphism was studied in 40 pea cultivar accessions of different ecological and geographical origin from the Vavilov Institute’s genebank of plant genetic resources or developed at regional breeding centers. Microsatellite analysis was performed using 5 SSR markers from the genomic library of microsatellites (Agrogene®, France).

Results. All markers delivered good electrophoretic profiles and helped to amplify a number of alleles per locus varying from 2 (AB53) to 9 (AA355). The total number of alleles was 26, while the average number of alleles per locus was 5.2. The polymorphism information content (PIC) varied from 0.39 for locus AB53 to 0.82 for locus AA355, with the mean value of 0.60. The set of SSR markers used in the work made it possible to individualize each of the studied pea genotypes. The measured genetic distances were used to draw a dendrogram showing the distribution of genotypes according to their genetic relationship.

Conclusion. Through studying the source material for pea breeding by the SSR analysis the data were obtained that provide additional information about the genetic structure of the collection and the polymorphism of the studied cultivar accessions. The results of genotyping pea cultivars and lines can be used for their genetic identification or to select parental pairs for hybridization. 

1. Abdel-Mawgood A.L., Ahmed M.M.M., Ali B.A. Application of molecular markers for hybrid maize (Zea mays L.) identification. Journal of Food, Agriculture and Environment. 2006;4(2):176-178.

2. Awadalla P., Ritland K. Microsatellite variation and evolution in the Mimulus guttatus species complex with contrasting mating systems. Molecular Biology and Evolution. 1997;14(10):1023-1034. DOI: 10.1093/oxfordjournals.molbev.a025708

3. Boronnikova S.V. Molecular marking and genetic certification resource and rare species of plants for the purpose of optimization of preservation of their genofunds. Agrarian Bulletin of the Urals. 2009;2(56):57-59. [in Russian]

4. Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics. 1980;32(3):314-331.

5. Davletov F.A. Breeding of non-shattering pea cultivars under the conditions of the Southern Urals (Selektsiya neosypayushchikhsya sortov gorokha v usloviyakh Yuzhnogo Urala). Ufa: Gilem; 2008. [in Russian]

6. Davletov F.A., Gainullina K.P. The influence of meteorological conditions on the hybridization results. Agrarian Bulletin of the Urals. 2011;4(83):5-6. [in Russian]

7. Davletov F.A., Gainullina K.P., Ashiev A.R. Peculiarities of growth and development of pea’s varieties and lines of different morphotypes in the conditions of South Urals. Grain Economy of Russia. 2011;5:22-31. [in Russian]

8. Davletov F.A., Gainullina K.P., Ashiev A.R. Variability of the duration of vegetative period of field pea (Pisum sativum L.) in the Cis-Ural steppe of the Republic of Bashkortostan. Herald of the Academy of Sciences of the Republic of Bashkortostan. 2014;19(3):49-59. [in Russian]

9. De Haan H. The breeding of peas in the Netherlands. Euphytica. 1954;3:188-194. DOI: 10.1007/BF00055592

10. Dribnokhodova O.P., Gostimsky S.A. Allele polymorphism of microsatellite loci in pea (Pisum sativum L.) lines, varieties, and mutants. Russian Journal of Genetics. 2009;45(7):900-906. [in Russian]

11. Dyachenko E.A., Ryzhova N.N., Kochieva E.Z., Vish nyakova M.A. Molecular genetic diversity of the pea (Pisum sativum L.) from the Vavilov Research Institute collection detected by the AFLP analysis. Russian Journal of Genetics. 2014;50(9):1040-1049. [in Russian] DOI: 10.7868/S0016675814090045

12. Gainullina K.P., Davletov F.A. Creation and introduction in agricultural industry of high-producing technological pea cultivar Pamyati Hangil’dina. In: Current state, traditions and innovative technologies in the development of the agro-industrial complex. Part 1 (Sovremennoye sostoyaniye, traditsii i innovatsionnyye tekhnologii v razvitii APK. Chast 1). Proceedings of the International Scientific and Practical Conference in the Framework of the XXVIII International Specialized Exhibition “Agrocomplex-2018”; March 14–26, 2018; Ufa. Ufa: Bashkir SAU; 2018. p.29- 33. [in Russian] URL: https://elibrary.ru/download/elibrary_34987801_24170663.pdf [дата обращения: 10.04.2020]

13. Govorov L.I. Pea (Gorokh). In: Cultivated Flora of the USSR (Kulturnaya flora SSSR). Moscow; Leningrad: Selkhozgiz; 1937. [in Russian]

14. Guchetl S.Z., Chelyustnikova T.A., Antonova T.S., Ra ma sanova S.A. Microsatellite loci as markers for identification and certification of sunflower lines and hybrids of VNIIMK breeding. Oil Crops. Scientific and Technical Bulletin of VNIIMK. 2007;137(2):27-32. [in Russian]

15. Guyomarc’h H., Sourdille P., Charmet G., Edwards K., Bernard M. Characterisation of polymorphic microsatellite markers from Aegilops tauschii and transferability to the D-genome of bread wheat. Theoretical and Applied Genetics. 2002;104:1164-1172. DOI: 10.1007/s00122-001-0827-7

16. Jain S., Kumar A., Mamidi S., McPhee K. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers. Molecular Biotechnology. 2014;56(10):925- 938. DOI: 10.1007/s12033-014-9772-y

17. Khlestkina E.K. Molecular markers in genetic studies and breeding. Vavilov Journal of Genetics and Breeding. 2013;17(4/2):1044-1054. [in Russian]

18. Lihacheva L.I., Gimaletdinova V.S. Selection evaluation of promising varieties of peas in the conditions of Middle Ural. Legumes and Groat Crops. 2014;11(3):20- 24. [in Russian].

19. Loridon K., McPhee K., Morin J., Dubreuil P., Pilet-Nayel M.L., Aubert G. et al. Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theoretical and Applied Genetics. 2005;111:1022-1031. DOI: 10.1007/s00122-005-0014-3

20. Ma Y., Coyne C.J., Grusak M.A., Mazourek M., Cheng P., Main D. et al. Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC Plant Biology. 2017;17:43. DOI: 10.1186/s12870-016-0956-4

21. Makasheva R.Kh. Pea (Gorokh). In: Cultivated Flora of the USSR (Kulturnaya flora SSSR). Leningrad: Kolos; 1979. [in Russian]

22. Popolzukhin P.V., Gaidar A.A., Vasilevskii V.D. The role of the sowing schedule in the growing of cultivated pea seeds of various morphotypes in the southern forest-steppe of Western Siberia (Rol sroka poseva v vyrashchivanii semyan sortov gorokha posevnogo razlichnogo morfotipa v yuzhnoi lesostepi Zapadnoy Sibiri). In: Leguminous crops – a developing trend in Russia (Zernobobovye kultury – razvivayushcheyesya napravleniye v Rossii). Omsk: Omsk SAU; 2016. p.100-104. [in Russian] URL: https://elibrary.ru/ download/elibrary_26340635_29221627.pdf [дата обращения: 10.04. 2020].

23. Qu J., Liu J. A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data. BMC Research Notes. 2013;6:403. DOI: 10.1186/1756-0500-6-403

24. Shelepina N.V., Shchurov A.Y. National economic significance and features of the chemical composition of pea grain (Narodnokhozyaystvennoye znacheniye i osobennosti khimicheskogo sostava zerna gorokha). Nauchnye zapiski OrelGIET = Scientific Notes of Orel State University of Economic and Trade. 2010;1:537-539. [in Russian]

25. Singh A.K., Rai R., Singh B.D., Chand R., Srivastava C.P. Validation of SSR markers associated with rust (Uromyces fabae) resistance in pea (Pisum sativum L.). Physiology and Molecular Biology of Plants. 2015;21(2):243–247. DOI: 10.1007/s12298-015-0280-8

26. Sulimova G.E. DNA-markers in genetic studies: types of markers, their characteristics and application. Advances in Current Biology. 2004;124(3):260-271. [in Russian]

27. Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research. 1989;17(16):6463-6471. DOI: 10.1093%2Fnar%2F17.16.6463

28. Yang T., Fang L., Zhang X., Hu J., Bao S., Hao J. et al. Highthroughput development of SSR markers from pea (Pisum sativum L.) based on next generation sequencing of a purified Chinese commercial variety. PLoS One. 2015;10(10):e0139775. DOI: 10.1371/journal.pone.0139775

29. Zhang Z., Deng Y., Tan J., Hu S., Yu J., Xue Q. A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Research. 2007;14(1):37-45. DOI: 10.1093/dnares/dsm005