PLANT BIOLOGY
ANIMAL BIOLOGY
SUBSCRIPTION
E-SUBSCRIPTION
 
MAP
MAIN PAGE

 

 

 

 

Shalaeva T.V., Aniskina Yu.V., Kolobova O.S., Velishaeva N.S., Logvinov A.V., Mishchenko V.N., Shilov I.A. Investigation of the sugar beet (Beta vulgaris L. ssp. vulgaris) microsatellite loci structure to develop a technology for genetic analysis of sugar beet lines and hybrids. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2023, Vol. 58, № 3, p. 483-493.
(how to cite this article)

doi: 10.15389/agrobiology.2023.3.483eng

UDC: 635.112:631.522./524:577.2

Acknowledgements:
Сarried out as part of the state task “Development of crop genotyping technologies to accelerate and support breeding” (431-2022-0002).

 

INVESTIGATION OF THE SUGAR BEET (Beta vulgaris L. ssp. vulgaris) MICROSATELLITE LOCI STRUCTURE TO DEVELOP A TECHNOLOGY FOR GENETIC ANALYSIS OF SUGAR BEET LINES AND HYBRIDS

T.V. Shalaeva1 ✉, Yu.V. Aniskina1, O.S. Kolobova1, N.S. Velishaeva1, A.V. Logvinov2, V.N. Mishchenko2, I.A. Shilov1

1All-Russian Research Institute of Agricultural Biotechnology, 42, ul. Timiryazevskaya, Moscow, 127550 Russia, e-mail shalaeva.tv@mail.ru (✉ corresponding author), aniskina.julia@gmail.com, kolobus16@yandex.ru, nazife@mail.ru,
ishilov@rambler.ru;
2Pervomayskaya Selection and Experimental Station, 2a, ul. Timiryazeva, Gulkevichi, Gulkevichsky District, Krasnodar Krai, 352193 Russia, e-mail 1maybest@mail.ru, vlad.mischencko2012@yandex.ru

ORCID:
Aniskina Yu.V. orcid.org/0000-0002-3376-0263
Mishchenko V.N. orcid.org/0009-0007-3364-0505
Kolobova O.S. orcid.org/0000-0003-3172-8099
Shilov I.A. orcid.org/0000-0003-2448-6239
Velishaeva N.S. orcid.org/0000-0002-2755-3313

Final revision received January 15, 2023 
Accepted April 04, 2023

The quality control in the course of maintenance and reproduction of sugar beet (Beta vulgaris L. ssp. vulgaris) hybrid parent lines upon seed production is highly important. The method of microsatellite analysis seems to be very perspective tool to provide genotyping during breeding and seed production. Different research groups reported about microsatellite loci in the sugar beet genome. However, the implementation of this technique into the breeding process requires the development of robust and high-throughput technology of analysis. To develop a technology for obtaining stable DNA profiles, a more detailed study of the sugar beet genome microsatellite loci is required using a large set of verified breeding material. The sequencing a number of sugar beet genome regions containing microsatellite loci to clarify the nature of polymorphism as well as ability for providing the stable DNA profiles has been made in this study. Together with breeders (Pervomayskaya Selection and Experimental Station, Krasnodar Krai), a collection of 146 sugar beet plant samples was selected, including 28 male-sterile (MS) lines, 28 O-type lines, 82 pollinator lines, 6 hybrids of Russian selection (Azimut, Corvette, Pervomaisky, Rubin, Fregate, Uspekh) as well as Dobrava and Dorothea hybrids. Five plants of each sample were analyzed for 12 microsatellite loci, FDSB 502, FBSB 1001, FDSB 1033, Unigene 27833, Unigene 26753, Unigene 16898, Unigene 17623B, Unigene 15915, Unigene 17923, SB 04, SB 09, and SB 15. Allelic variants of each locus were amplified, cloned into the pAL2-T plasmid vector and sequenced. The results of sequencing the microsatellite loci FDSB 1001, FDSB 1033, Unigene 16898, Unigene 17623B, Unigene 26753, Unigene 17923, Unigene 27833, and SB 04 revealed that their length polymorphism is solely due to the different number of tandem repeats in the amplified DNA fragment. The locus Unigene 15915 was excluded from further work because of insertions and deletions in the flanking regions of microsatellite repeats (AC)n in its allelic variants. The polymorphism of allelic variants of the microsatellite loci SB 09, SB 15, and FDSB 502 is due to the complex (composite) repeats. Nevertheless, the SB 09 and SB 15 loci were approved for further study, since they produced stable DNA profiles. The allelic variants of the locus FDSB 502 contained the (TC)n(GAT)n(AAG)n sequence, which in some cases may complicate the analysis. To use this locus for the genetic analysis of sugar beet lines and hybrids, we propose the primers flanking only variable microsatellite repeatsб the (GAT)n and (AAG)n separately. The results we report here are prospective to develop a technology for the genetic analysis of sugar beet lines and hybrids as a reliable tool for both breeding and seed production.

Keywords: Beta vulgaris, sugar beet, fingerprinting, microsatellite analysis, DNA-profile.

 

REFERENCES

  1. Panella L. Sugar beet as an energy crop. Sugar Techno, 2010, 12: 288-293 CrossRef
  2. Tayyab M., Wakeel A., Mubarak M.U., Artyszak A., Ali S., Hakki E.E., Mahmood K., Song B., Ishfaq M. Sugar Beet Cultivation in the Tropics and Subtropics: Challenges and Opportunities. Agronomy, 2023, 13(5): 1213 CrossRef
  3. Balkov I.Ya. Selektsiya sakharnoy svekly na geterozis [Selection of sugar beet for heterosis]. Moscow, 1978 (in Russ.).
  4. Logvinov V.A. V sbornike: Selektsiya i agrotekhnika sakharnoy svekly na Severnom Kavkaze [In: Selection and agrotechnics of sugar beet in the North Caucasus]. Kiev, 1982: 41-46 (in Russ.).
  5. Suslov V.I., Logvinov V.A., Mishchenko V.N., Suslov A.V., Logvinov A.V. Trudy Kubanskogo gosudarstvennogo universiteta, 2010, 5: 62-67 (in Russ.).
  6. Balkov I.Ya., Karakotov S.D., Logvinov A.V., Logvinov V.A, Mishchenko V.N. Еvolyutsiya sakharnoy svekly: ot ogorodnykh form – do sovremennykh rentabel’nykh gibridov [The evolution of sugar beet: from garden forms to modern cost-effective hybrids]. Moscow, 2017 (in Russ.).
  7. Lukow T., Dunfield P.F., Liesack W. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiology Ecology, 2000, 32(3): 241-247 CrossRef
  8. Snigir’ E.A., Pyshnaya O.N., Kochieva E.Z., Ryzhova N.N. AFLP-analysis of varietal polymorphysm in Capsicum annuum L.Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2013, 1: 53-60 CrossRef
  9. Fedulova T.P., Fedorin D.N., Nalbandyan A.A., Bogomolov M.A. Sakhar, 2019, 5: 50-53 CrossRef (in Russ.).
  10. Feng S., Zhu Y., Yu C., Jiao K., Jiang M., Lu J., Shen C., Ying Q., Wang H. Development of species-specific SCAR Markers Based on a SCoT analysis to authenticate Physalis (Solanaceae) species. Frontiers in Genetics, 2018, 9: 192 CrossRef
  11. Kishor D. S., Alavilli H., Lee S.-C., Kim J.-G., Song K. Development of SNP markers for white immature fruit skin color in cucumber (Cucumis sativus L.) using QTL-seq and marker analyses. Plants, 2021, 10(11), 2341 CrossRef
  12. Gawroński P., Pawełkowicz M., Tofil K., Uszyński G., Sharifova S., Ahluwalia S., Tyrka M., Wędzony M., Kilian A., Bolibok-Brągoszewska H. DArT markers effectively target gene space in the rye genome. Frontiers in Plant Science, 2016, 7: 1600 CrossRef
  13. Kolobova O.S., Malyuchenko O.P., Shalaeva T.V., Shanina E.P., Shilov I.A., Alekseev Ya.I., Velishaeva N.S. Vavilovskiy zhurnal genetiki i selektsii, 2017, 21(1): 124-127 CrossRef (in Russ.).
  14. Möhring S., Salamini F., Schneider K. Multiplexed, linkage group-specific SNP marker sets for rapid genetic mapping and fingerprinting of sugar beet (Beta vulgaris L.). Molecular Breeding, 2004, 14: 475–488 CrossRef
  15. Stevanato P., Broccanello C., Biscarini F., Del Corvo M., Sablok G., Panella L., Concheri, G. High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes. Plant Molecular Biology Reporter, 2013 CrossRef
  16. Tehseen M.M., Zheng Y., Wyatt N.A., Bolton M.D., Yang S., Xu S.S., Li X., Chu C. Development of STARP marker platform for flexible SNP genotyping in sugar beet. Agronomy, 2023, 13: 1359 CrossRef
  17. Padi F.K., Ofori A., Takrama J., Djan E., Opoku S.Y., Dadzie A.M., Zhang D. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao. Tree Genetics & Genomes, 2015, 11(3) CrossRef
  18. Zhang J., Yang J., Fu S., Ren J., Zhang X., Xia C., Zhao H., Yang K., Wen C. Comparison of DUS testing and SNP fingerprinting for variety identification in cucumber Horticultural Plant Journal, 2022, 8(5): 575-582 CrossRef
  19. Yang Y., Lyu M., Liu J. et al. Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars. BMC Plant Biol, 2022, 22: 522 CrossRef
  20. Li J., Chang X., Huang Q., Liu P., Zhao X., Li F., Wang Y., Chang C. Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China. Frontiers in Plant Science, 2023, 14:1080691 CrossRef
  21. Laurent V., Devaux P., Thiel T., Viard F., Mielordt S., Touzet P., Quillet M.C. Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome. Theoretical and Applied Genetics, 2007, 115(6): 793-805 CrossRef
  22. Smulders M., Esselink D., Everaert I., De Riek J., Vosman B. Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers. BMC Genetics, 2010, 11: 41 CrossRef
  23. Fugate K.K., Fajardo D., Schlautman B., Ferrareze J.P., Bolton M.D., Campbell L.G., Wiesman E., Zalapa J. Generation and characterization of a sugarbeet transcriptome and transcript-based SSR markers. The Plant Genome, 2014, 7(2) CrossRef
  24. McGrath J.M., Trebbi D., Fenwick A., Panella L., Schulz B., Laurent V., Barnes S., Murray S.C. An open-source first-generation molecular genetic map from a sugar beet ½ table beet cross and its extension to physical mapping. The Plant Genome, 2007, 1: 27-44 CrossRef
  25. Richards C.M., Brownson M., Mitchell S.E., Kresovich S., Panella L. Polymorphic microsatellite markers for inferring diversity in wild and domesticated sugar beet (Beta vulgaris). Molecular Ecology Notes, 2004, 4(5): 243-245 CrossRef
  26. Srivastava S., Pathak A. D., Kumar R., Joshi B.B. Genetic diversity of sugar beet genotypes evaluated by microsatellite DNA markers. Journal of Environmental Biology, 2017, 38: 777-783 CrossRef
  27. Shilov I.A., Aniskina Yu.V., Shalaeva T.V., Kolobova O.S., Velishaeva N.S., Mishchenko V.N., Logvinov A.V. Sakhar, 2020, 8: 27-31 CrossRef (in Russ.).
  28. Nalbandyan A.A., Khusseyn A.S. V sbornike: Zakonomernosti i tendentsii razvitiya nauki v sovremennom obshchestve [In: Patterns and trends in the development of science in modern society]. Ufa, 2016: 30-32 (in Russ.).
  29. Nalbandyan A.A., Khusseyn A.S., Fedulova T.P., Cherepukhina I.V., Kryukova T.I., Rudenko T.S. Sakhar, 2019, 11: 36-39 (in Russ.).
  30. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 1987, 19: 11-15.
  31. Maniatis T., Frich Е., Sеmbruk Dzh. Metody geneticheskoy inzhenerii. Molekulyarnoe klonirovanie [Methods of genetic engineering. Molecular cloning]. Moscow, 1984 (in Russ.).
  32. Aniskina Yu.V., Malinovskaya E.V., Shalaeva T.V., Mitsurova V.S., Rodionova D.A., Kharchenko P.N., Shilov I.A. Biotekhnologiya, 2018, 34(2): 54-69 CrossRef (in Russ.).
  33. Sekridova A.V., Shilov I.A., Kislin E.N., Malyuchenko O.P., Kharchenko P.N. Biotekhnologiya, 2021, 37(3): 85-95 CrossRef (in Russ.).
  34. Shilov I.A., Velishaeva N.S., Aniskina Yu.V., Kolobova O.S., Shalaeva T.V., Borisenko O.M., Demurin Ya.N., Frolov S.S. Dostizheniya nauki i tekhniki APK, 2023, 37(1): 10-15 CrossRef (in Russ.).

 

back

 


CONTENTS

 

 

Full article PDF (Rus)

Full article PDF (Eng)