Czech J. Genet. Plant Breed., 2024, 60(1):42-49 | DOI: 10.17221/57/2023-CJGPB

Genomic SSR marker development in lentil (Lens culinaris Medik.) and assessment of cross-species/genera transferability to related legumesOriginal Paper

Melike Bakır ORCID...1*, ªehriban Demir1, Cebrail Yıldırım ORCID...2, Abdullah Kahraman3
1 Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Türkiye
2 Institute of Hemp Research, Yozgat Bozok University, Yozgat, Türkiye
3 Department of Field Crops, Faculty of Agriculture, Harran University, Sanliurfa, Türkiye

Simple sequence repeat (SSR) markers are valuable genetic and genomic research tools and are extensively used in major crops. However, a paucity of available molecular markers in lentils (Lens culinaris Medik.) has significantly hindered genomic studies in this vital legume crop. In this study, we developed 33 new SSR markers for lentils using an enriched genomic library and tested their polymorphism in 10 lentil cultivars. We found that 16 (48.5%) SSR markers were polymorphic. The expected heterozygosity values of the polymorphic SSR markers ranged from 0.095 to 0.820, while observed heterozygosity values varied between 0.100 and 1.00. In addition, we tested the transferability of 86 SSR markers, including the 33 newly developed ones, to other legume species. Transferability rates of lentil SSR markers to other species varied between 13.76% (Vicia sativa L.) and 2.58% (Phaseolus vulgaris L. and Trifolium pratense L.). These new SSR markers could be used in further molecular breeding, population genetics, and genetic mapping studies in lentils and other legume species.

Keywords: cross-transferability; genomic library; legumes; simple sequence repeats

Received: June 29, 2023; Revised: September 11, 2023; Accepted: September 13, 2023; Prepublished online: October 23, 2023; Published: November 27, 2023  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Bakır M, Demir ª, Yıldırım C, Kahraman A. Genomic SSR marker development in lentil (Lens culinaris Medik.) and assessment of cross-species/genera transferability to related legumes. Czech J. Genet. Plant Breed. 2024;60(1):42-49. doi: 10.17221/57/2023-CJGPB.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    Supplementary files:

    Download fileBakir_ESM.pdf

    File size: 148.22 kB

    References

    1. Almeida N.F., Leitao S.T., Caminero C., Torres A.M., Rubiales D., Patto M.C.V. (2014): Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies. Molecular Biology Reports, 41: 269-283. Go to original source... Go to PubMed...
    2. Andeden E.E., Baloch F.S., Çakir E., Toklu F., Özkan H. (2015): Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.). Plant Breeding, 134: 589-598. Go to original source...
    3. Arumuganathan K., Earle E.D. (1991): Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9: 208-218. Go to original source...
    4. Bahl P.N., Lal S., Sharma B.M. (1993): An overview of the production and problems in Southeast Asia. In: Erskine W., Saxena M.C. (eds.): Lentil in South Asia. Proc. Seminar on Lentils in South Asia, ICARDA. Aleppo.
    5. Bakir M. (2019): Transferability of newly developed genomic lentil SSR markers to Cicer species. Legume Research, 42: 479-484. Go to original source...
    6. Bakir M., Kahraman A. (2019): Development of new SSR (simple sequence repeat) markers for lentils (Lens culinaris Medik.) from genomic library enriched with AG and AC microsatellites. Biochemical Genetics, 57: 338-353. Go to original source... Go to PubMed...
    7. Bloor P.A., Barker F.S., Watts P.C., Noyes H.A., Kemp S.J. (2001): Microsatellite libraries by enrichment. Available at https://www.researchgate.net/profile/Stephen-Kemp-2/publication/228473909_Microsatellite_Library_by_Enrichment/links/0912f51012a1c27e39000000/Microsatellite-Library-by-Enrichment.pdf (accessed Aug 21, 2023).
    8. Botstein D., White R.L., Skolnick M., Davis R.W. (1980): Construction of genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32: 314-331.
    9. Choi H.K., Mun J.H., Kim D.J., Zhu H., Baek J.M., Mudge J., Roe B., Ellis N., Doyle J., Kiss G.B., Young N.D., Cook D.R. (2004): Estimating genome conservation between crop and model legume species. Proceedings of the National Academy of Sciences, 101: 15289-15294. Go to original source... Go to PubMed...
    10. Choudhary S., Sethy N.K., Shokeen B., Bhatia S. (2009): Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics, 118: 591-608. Go to original source... Go to PubMed...
    11. Cipriani G., Lot G., Huang W.G., Matarazzo M.T., Peterlunger E., Testolin R. (1999): AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: Isolation, characterisation and cross species amplification in Prunus. Theoretical and Applied Genetics, 99: 65-72. Go to original source...
    12. Cuc L.M., Mace E.S., Crouch J.H., Quang V.D., Long T.D., Varshney R.K. (2008): Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biology, 8: 55. Go to original source... Go to PubMed...
    13. Doyle J.J., Luckow M.A. (2003): The rest of the iceberg: Legume diversity and evolution in a phylogenetic context. Plant Physiology, 131: 900-910. Go to original source... Go to PubMed...
    14. Duran Y., Fratini R., Garcia P., De la Vega M.P. (2004): An intersubspecific genetic map of Lens. Theoretical and Applied Genetics, 108: 1265-1273. Go to original source... Go to PubMed...
    15. FAOSTAT (2023): Available at https://faost at3.fao.org/faost at-gatew ay/go/to/downl oad/Q/QC/E (accessed Aug 23, 2023).
    16. Gupta P.K., Balyan H.S., Sharma P.C., Ramesh B. (1996): Microsatellites in plants: A new class of molecular markers. Current Science, 70: 45-54.
    17. Gupta S., Kumari K., Sahu P.P., Vidapu S., Prasad M. (2012): Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italic (L.) P. Beauv.]. Plant Cell Reports, 31: 323-337. Go to original source... Go to PubMed...
    18. Hall T.A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
    19. Hamwieh A., Udupa S.M., Choumane W., Sarker A., Dreyer F., Jung C., Baum M. (2005): A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance. Theoretical and Applied Genetics, 110: 669-677. Go to original source... Go to PubMed...
    20. Hamwieh A., Udupa S.M., Sarkar A., Jung C., Baum M. (2009): Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breeding Science, 59: 77-86. Go to original source...
    21. Hendre P.S., Aggarwal R.K. (2007): DNA markers: Development and application for genetic improvement of coffee. In: Varshney R.K., Tuberosa R. (eds.): Genomics-Assisted Crop Improvement. Dordrecht, Springer: 399-434. Go to original source...
    22. Huang D., Zhang Y., Jin M., Li H., Song Z., Wang Y., Chen J. (2014): Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae). Molecular Ecology Resources, 14: 569-577. Go to original source... Go to PubMed...
    23. Huang X., Madan A. (1999): CAP3: A DNA sequence assembly program. Genome Resources, 9: 868-877. Go to original source... Go to PubMed...
    24. Jingade P., Bhosale L.V., Sanjayrao J.A., Rajanna R., Jain M., Ravikumar R.L. (2014): Characterization of microsatellite markers, their transferability to orphan legumes and use in determination of genetic diversity among chickpea (Cicer arietinum L.) cultivars. Journal of Crop Science and Biotechnology, 17: 191-199. Go to original source...
    25. Lefort F., Lally M., Thompson D., Douglas G.C. (1998): Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally Ireland. Silvae Genetica, 47: 5-6.
    26. Li C., Zheng Y., Liu Y., Lin F., Huang P. (2021): Development of genomic SSR for the subtropical hardwood tree Dalbergia hupeana and assessment of their transferability to other related species. Forests, 12: 804. Go to original source...
    27. Liu K., Muse S.V. (2005): PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21: 2128-2129. Go to original source... Go to PubMed...
    28. Min X., Zhang Z., Liu Y., Wei X., Liu Z., Wang Y., Liu W. (2017): Genome-wide development of microRNA-based SSR markers in Medicago truncatula with their transferability analysis and utilization in related legume species. International Journal of Molecular Sciences, 18: 2440. Go to original source...
    29. Muehlbauer F.J. (1991): Use of introduced germplasm in cool season food legume cultivar development. In: Shands H.L., Wiesner L.E. (eds.): Use of Plant Introductions in Cultivar Development. Part 2. Crop Science Society of America, Social Publication: 49-73. Go to original source...
    30. Nei M. (1973): Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 70: 3321-3323. Go to original source... Go to PubMed...
    31. Oliveira E.J., Pádua J.G., Zucchi M.I., Vencovsky R., Vieira M.L.C. (2006): Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29: 294-307. Go to original source...
    32. Parida S.K., Kalia S.K., Sunita K., Dalal V., Hemaprabha G., Selvi A., Pandit A., Singh A., Gaikwad K., Sharma T.R., Srivastava P.S., Singh N.K., Mohapatra T. (2009): Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theoretical and Applied Genetics, 118: 327-338. Go to original source... Go to PubMed...
    33. Peakall R., Gilmore S., Keys W., Morgante M., Rafalski A. (1998): Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants. Molecular Biology and Evolution, 15: 1275-1287. Go to original source... Go to PubMed...
    34. Powell W., Mackray G.C., Provan J. (1996): Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1: 215-222. Go to original source...
    35. Reddy M.R.K., Rathour R., Kumar N., Katoch P., Sharma T.R. (2010): Cross-genera legume SSR markers for analysis of genetic diversity in Lens species. Plant Breeding, 129: 514-518. Go to original source...
    36. Rehman S., Altaf C.H.M. (1994): Karyotipic studies in Lens culinaris Medic, ssp. Macrosperma Cv. Laird X Precoz. Pakistan Journal of Botany, 26: 347-352.
    37. Roa A.C., Chavarriaga-Aguirre P., Duque M.C., Maya M.M., Bonierbale M.W., Iglesias C., Tohme J. (2000): Cross species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: Allelic polymorphism and degree of relationship. American Journal of Botany, 87: 1647-1655. Go to original source...
    38. Rossetto M. (2001): Sourcing of SSR markers from related plant species. In: Henry R.J. (ed.): Plant Genotyping: the DNA Fingerprinting of Plants. Wallingford, CAB International: 211-224. Go to original source...
    39. Saha G.C., Sarker A., Chen W., Vandemark G.J., Muehlbauer F.J. (2010): Inheritance and linkage map positions of genes conferring resistance to Stemphylium blight in lentil. Crop Science, 50: 1831-1839. Go to original source...
    40. Satya P., Paswan P.K., Ghosh S., Majumdar S., Ali N. (2016): Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species. 3 Biotech, 6: 65. Go to original source... Go to PubMed...
    41. Singh D., Singh C.K., Tribuvan K.U., Tyagi P., Taunk J., Tomar R.S.R., Kumari S., Tripathi K., Kumar A., Gaikwad K., Yadav R.K., Pal M. (2020): Development, characterization, and cross species/genera transferability of novel EST-SSR markers in lentil, with their molecular applications. Plant Molecular Biology Reporter, 38: 114-129. Go to original source...
    42. Squirrell J., Hollingsworth P.M., Woodhead M., Russell J., Lowe A.J., Gibby M., Powell W. (2003): How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology, 12: 1339-1348. Go to original source... Go to PubMed...
    43. Tamura K., Dudley J., Nei M., Kumar S. (2007): MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24: 1596-1599. Go to original source... Go to PubMed...
    44. Techen N., Arias R.S., Glynn N.C., Pan Z., Khan I.A., Scheffler B.E. (2010): Optimized construction of microsatellite-enriched libraries. Molecular Ecology Resources, 10: 508-515. Go to original source... Go to PubMed...
    45. Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S., McCouch S.R. (2001): Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Research, 11: 1441-1452. Go to original source... Go to PubMed...
    46. Verma P., Sharma T.R., Srivastava P.S., Abdin M.Z., Bhatia S. (2014): Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers. Molecular Biology Reports, 41: 5607-5625. Go to original source... Go to PubMed...
    47. Wang L.X., Chen H.L., Bai P., Wu J.X., Wang S.H., Blair M.W., Cheng X.Z. (2015): The transferability and polymorphism of mung bean SSR markers in rice bean germplasm. Molecular Breeding, 35: 1-10. Go to original source...
    48. You F.M., Huo N., Gu Y.Q., Luo M.C., Ma Y., Hane D., Lazo G.R., Dvorak J., Anderson O.D. (2008): BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics, 9: 253. Go to original source... Go to PubMed...
    49. Zucchi M.I., Brondani R.V., Pinheiro J.B., Brondani C., Vencovsky R. (2002): Transferability of microsatellite markers from Eucalyptus spp. to Eugenia dysenterica (Myrtaceae family). Molecular Ecology Notes, 2: 512-514. Go to original source...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content