Journals / Turkish Journal Of Field Crops / 2026 / Volume: 30 Issue: 1

Transferability of Genomic SSR Markers in Lens Species for Genus Characterization and Lentil (Lens culinaris Medik.) Breeding

Pages
—
Publication Date
2025-06-23
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

The identified polymorphic markers provide a valuable resource for exploring the genetic diversity of wild lentil relatives and the breeding of beneficial agronomic traits into new lentil cultivars.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Simple sequence repeats (SSRs) are pivotal for germplasm characterization and crop improvement.
📊
Key Findings & Data:A total of 100 SSR loci were analyzed in 21 accessions representing all the Lens genus using PowerMarker software v3.25, which identified 41 polymorphic loci.
💡
Conclusion & Impact:The identified polymorphic markers provide a valuable resource for exploring the genetic diversity of wild lentil relatives and the breeding of beneficial agronomic traits into new lentil cultivars.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:SSR · Lentil · Transferability

Abstract

Simple sequence repeats (SSRs) are pivotal for germplasm characterization and crop improvement. However, lentil breeding faces challenges due to the limited availability of markers. This study assessed the transferability of genomic SSR markers developed in cultivated lentils to wild Lens species. A total of 100 SSR loci were analyzed in 21 accessions representing all the Lens genus using PowerMarker software v3.25, which identified 41 polymorphic loci. These loci generated 219 alleles, with an average of 5.34 per locus and a polymorphic information content (PIC) value of 0.61. Notably, 52.2% of the polymorphic loci were shared among all Lens species. Transferability rates varied across species: 41% for Lens nigricans, 40% for Lens culinaris subsp. tomentosus, 39% for Lens culinaris subsp. orientalis, 34% for Lens culinaris subsp. odemensis, 34% for Lens ervoides, and 31% for Lens lamottei. The identified polymorphic markers provide a valuable resource for exploring the genetic diversity of wild lentil relatives and the breeding of beneficial agronomic traits into new lentil cultivars.

🔖

Cite This Article

Koboyi, B. W., Keklik, M., Doğanay, Ö., Bakır, M. (2025). Transferability of Genomic SSR Markers in Lens Species for Genus Characterization and Lentil (Lens culinaris Medik.) Breeding. Turkish Journal Of Field Crops, Volume: 30 Issue: 1. https://doi.org/10.17557/tjfc.1623413

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (69)

  1. Ahmad, M., Fautrier, A. G., Burritt, D. J., & McNeil, D. L. (1997). Genetic diversity and relationships in Lens species and their F1 interspecific hybrids as determined by SDS‐PAGE, New Zealand Journal of Crop and Horticultural Science, 25(2), 99-108. https://doi.org/10.1080/01140671.1997.9513995
  2. Andeden, E. E., Baloch, F. S., Cakır, E., Toklu, F., & Ozkan, H. (2015). Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.). Plant Breeding, 134(5), 589-598. https://doi.org/10.1111/pbr.12296
  3. Ates, D. (2019). Genetic diversity in lentil landraces revealed by diversity array technology (DArT). Turkish Journal of Field Crops, 24(2), 252-260. https://doi.org/10.17557/tjfc.656511
  4. Bakir, M. (2019). Transferability of newly developed genomic lentil SSR markers to Cicer species. Legume Research-An International Journal, 42(4), 479-484. https://doi.org/10.18805/LR-466
  5. 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. Biochem Genet 57, 338–353. https://doi.org/10.1007/s10528- 018-9893-2
  6. Bakir, M., Demir, S., Yildirim, C., & Kahraman, A. (2024). Genomic SSR marker development in lentil (Lens culinaris Medik.) and assessment of cross-species/genera transferability to related legumes. Czech Journal of Genetics and Plant Breeding, 60(1). http://dx.doi.org/10.17221/57/2023-CJGPB
  7. Begna, T., & Yesuf, H. (2021). Genetic mapping in crop plants. Open J. Plant Sci. 6(1): 019-026. DOI: https://dx.doi.org/10.17352/ojps.000028
  8. Bett KE, Cook DR (2016) KnowPulse. (Accessed on July 01, 2021); Available online: https://knowpulse.usask.ca/ Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331
  9. Cevik, S., ÜNYAYAR, S., & ERGÜL, A. (2015). Genetic relationships between cultivars of Cicer arietinum and its progenitor grown in Turkey determined by using the SSR markers. Turkish Journal of Field Crops, 20(1). https://doi.org/10.17557/.87839
  10. Caracuta, V., Vardi, J., Paz, Y., & Boaretto, E. (2017). Farming legumes in the pre-pottery Neolithic: new discoveries from the site of Ahihud (Israel). PLoSOne 12:e0177859. https://doi.org/10.1371/journal.pone.0177859
  11. 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.de. https://doi.org/10.1007/s00122-008-0923- z
  12. Datta, S., Mahfooz, S., Singh, P., Choudhary, A. K., Singh, F., & Kumar, S. (2010). Cross-genera amplification of informative microsatellite markers from common bean and lentil for the assessment of genetic diversity in pigeonpea. Physiol.Mol. Biol. Plants 16: 123-134. https://doi.org/10.1007/s12298-010-0014-x
  13. Datta, S., Mahfooz, S., Sahil, P., Choudhary, A. K., Chaturvedi, S. K., & Nadarajan, N. (2013). Conservation of microsatellite regions across legume genera increases marker repertoire in pigeonpea. Australian Journal of Crop Science, 7(13), 1990-1997.
  14. Daudi, H., Shimelis, H., Mathew, I., Oteng‐Frimpong, R., Ojiewo, C., & Varshney, R. K. (2021). Genetic diversity and population structure of groundnut (Arachis hypogaea L.) accessions using phenotypic traits and SSR markers: implications for rust resistance breeding. Genetic Resources and Crop Evolution, 68, 581-604. https://doi.org/10.1007/s10722-020-01007-1
  15. de Oliveira, J. C., da Silva, A. L. D., & da Silva, L. M. et al. (2023). Novel Microsatellite Markers Derived from Arachis pintoi Transcriptome Sequencing for Cross-Species Transferability and Varietal Identification. Plant Mol Biol Rep. https://doi.org/10.1007/s11105-023-01402-9
  16. Demir, S., & Bakir, M. (2022). Development of new ssr markers by screening libraries enriched with AG and AC repeats with TG and TC repeats in lentil. European Journal of Science and Technology, (41), 54-58. https://doi.org/10.31590/ejosat.1075391
  17. Dhull, S. B., Kinabo, J., & Uebersax, M. A. (2022). Nutrient profile and effect of processing methods on the composition and functional properties of lentils (Lens culinaris Medik): a review. Legume Science 5, e156. https://doi.org/10.1002/leg3.156
  18. Dikshit, H. K., Singh, A., Singh, D., Aski, M. S., Prakash, P., Jain, N.,. & Sarker, A. (2015). Genetic diversity in Lens species revealed by EST and genomic simple sequence repeat analysis. PloS one, 10(9), e0138101. https://doi.org/10.1371/journal.pone.0138101
  19. Dissanayake, R., Braich, S., Cogan, N. O., Smith, K., & Kaur, S. (2020). Characterization of genetic and allelic diversity amongst cultivated and wild lentil accessions for germplasm enhancement. Frontiers in Genetics, 11, 546.
  20. FAOSTAT (2023) FAOSTAT. https://www.fao.org/faostat/en/#data/QCL. Accessed 18 June 2023 Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5 c. Joseph Felsenstein.
  21. Ferguson, M. E., Robertson, L. D., Ford-Lloyd, B. V., Newbury, H. J., & Maxted, N. (1998). Contrasting genetic variation amongst lentil landraces from different geographical origins. Euphytica, 102, 265-273.
  22. Gupta, D., Taylor, P. W. J., Inder, P., Phan, H. T. T., Ellwood, S. R., Mathur, P. N.,. & Ford, R. (2012). Integration of EST-SSR markers of Medicago truncatula into intraspecific linkage map of lentil and identification of QTL conferring resistance to ascochyta blight at seedling and pod stages. Molecular breeding, 30, 429-439. https://doi.org/10.1007/s11032-011-9634-2
  23. Gutierrez-Gonzalez, J. J., García, P., Polanco, C., González, A. I., Vaquero, F., Vences, F. J.,. & Sáenz de Miera, L. E. (2022). Multi-species transcriptome assemblies of cultivated and wild lentils (Lens sp.) provide a first glimpse at the lentil pangenome. Agronomy, 12(7), 1619. https://doi.org/10.3390/agronomy12071619
  24. Hamwieh, A., Udupa, M., Sarker, A., Jung, C., & Baum, M. (2009). Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breed Sci. 59: 77–86.
  25. Hoffman, D. L., Muehlbauer, F. J., & Ladizinsky, G. (1988). Morphological variation in Lens (Leguminosae). Systematic Botany, 13(1), 87–96. https://doi.org/10.2307/2419244
  26. 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(3), 191-199.
  27. Koboyi, B. W., & Bakir, M. (2024). Integration of Novel SSR Markers into The Lentil (Lens culinaris Medik.) Genome. Turkish Journal of Field Crops, 29(1), 40-45. https://doi.org/10.17557/tjfc.1415823
  28. Konda, A. K., & Annapragada, H. (2024). Structural and functional genomic resources. In the Lentil Genome (pp. 195-216). Academic Press. https://doi.org/10.1016/B978-0-443-19409-2.00010-7
  29. Koul, P. M., Sharma, V., Rana, M., Chahota, R. K., Kumar, S., & Sharma, T. R. (2017). Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers. 3 Biotech 7:83. https://doi.org/10.1007/s13205-017- 0683-z
  30. Kumar, J., Srivastava, E., Singh, M., Kumar, S., Nadarajan, N., & Sarker, A. (2014). Diversification of indigenous gene-pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris). Physiol. Mol. Biol. Plants 20, 125–132. https://doi.org/10.1007/s12298-013-0214-2
  31. Lefort,F., Lally, M., Thompson, D., & Douglas, G.C. (1998). Morfolojical traits microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. Robur L.) At Tuallynally, Ireland. Silvae Genetica, 47, 5-6.
  32. Li, J. (2023). Draft genome assembly, organelle genome sequencing and diversity analysis of marama bean (Tylosema esculentum), the green gold of Africa (Doctoral dissertation, Case Western Reserve University).
  33. Liber, M., Oliveira, H. R., Duarte, I., & Maia, A. T. (2021). The history of lentil (Lens culinaris ssp. culinaris) domestication and spread as revealed by genotyping-bysequencing of wild and landrace accessions. Front. Plant Sci. 12. https://doi.org/10.3389/fpls.2021.628439
  34. Liu, K., & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. https://doi.org/10.1093/bioinformatics/bti282
  35. Mehandi, S., & Mishra, S. P. (2023). Genetic diversity and population structure analyses in mungbean (Vigna radiata L. Wilczek). J Food Chem Nanotechnol, 9(S1), S316-S322.
  36. Muehlbauer, F. J., & McPhee, K.E. (2005). Lentil (Lens culinaris Medik.). In: Singh R. J., Jauhar P. P., editors. Genetic Resources, Chromosome Engineering, and Crop Improvement: Grain Legumes. Taylor & Francis. pp. 268–280.
  37. Nei, M. (1973). The theory and estimation of genetic distance. Genetic Structure of Populations (ed. Morton, N. E.), pp. 45–54.
  38. Honolulu: University of Hawaii Press.Google ScholarPubMed Ningwal, R., Tripathi, M. K., Tiwari, S., Asati, R., Yadav, R. K., Tripathi, N., & Yasin, M. (2023). Identification of polymorphic SSR marker and diversity analysis in a set of desi chickpea genotypes. In Biological Forum-An International Journal (Vol. 15, No. 3, pp. 45-51).
  39. Odeny, D. A., Jayashree, B., Ferguson, M., Hoisington, D., Crouch, J., & Gebhardt, C. (2007). Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breeding, 126(2), 130-136. https://doi.org/10.1111/j.1439- 0523.2007.01324.x
  40. Ozkan, G., Haliloglu, K., Turkoglu, A., Ozturk, H. I., Elkoca, E., & Poczai, P. (2022). Determining genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from Türkiye using SSR markers. Genes, 13(8), 1410. https://doi.org/10.3390/genes13081410
  41. Peng, J. H., & Lapitan, N. L. (2005). Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct. Integr. Genomics 5: 80-96. https://doi.org/10.1007/s10142-004-0128-8
  42. Polanco, C., de Miera, L. E. S., González, A. I., García, P. G., Fratini, R., Vaquero, F., Vences, F. J., & De La Vega, M. P. (2019). Construction of a high-density interspecific (Lens culinaris × L. odemensis) genetic map based on functional markers for mapping morphological and agronomical traits, and QTLs affecting resistance to Ascochyta in lentil. PLoS ONE, 14, e0214409. https://doi.org/10.1371/journal.pone.0214409
  43. Rajendra, D., Ashutosh, S., Krishna Hari, D., & Madhav Prasad, P. (2019). Molecular characterization of high concentration of iron (Fe) and zinc (Zn) biofortified nepalese lentil (Lens culinaris Medikus Subspecies culinaris) accessions and their genetic diversity analysis through using simple sequence repeat (SSR) markers. BAOJ Biotech, 5, 041.
  44. Rajpal, V. R., Singh, A., Kathpalia, R., Thakur, R. K., Khan, M. K., Pandey, A.,. & Raina, S. N. (2023). The prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. Frontiers in Plant Science, 14, 1127239. https://doi.org/10.3389/fpls.2023.1127239
  45. 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(5), 514-518. https://doi.org/10.1111/j.1439-0523.2009.01723.x
  46. Renfrew, J. M. (1973). Palaeoethnobotany. Columbia Univ. Press, New York.
  47. Rubiales, D., & Fondevilla, S. (2012). Future prospects for Ascochyta blight resistance breeding in cool season food legumes. Frontiers in Plant Science, 3, 27. https://doi.org/10.3389/fpls.2012.00027
  48. Saidi, A., Sarvmeili, J., & Pouresmael, M. (2022). Genetic diversity study in lentil (Lens culinaris Medik.) Germplasm: a comparison of CAAT Box Derived Polymorphism (CBDP) and simple sequence repeat (SSR) markers. Biologia, 77(10), 2793- 2803. https://doi.org/10.1007/s11756-022-01089-5
  49. Saıdou, M., Wang, C., Alam, M. A., Chen, C., & Jı, W. (2016). Genetic analysis of powdery mildew resistance gene using SSR markers in common wheat originated from wild emmer (Triticum dicoccoides Thell). Turkish Journal of Field Crops, 21(1), 10-15. https://doi.org/10.17557/tjfc.83589
  50. Saxena, S., Kaila, T., Chaduvula, P. K., Singh, A., Singh, N. K., & Gaikwad, K. (2019). Novel chloroplast microsatellite markers in pigeonpea ('Cajanus cajan'L. Millsp.) and their transferability to wild'Cajanus' species. Australian Journal of Crop Science, 13(2), 185-191.
  51. Schuelke, M. (2000). An economic method for the fuorescent labelling of PCR fragments. Nat Biotechnol 18:233–234 Sharma S. K., Knox, M. X., & Ellis, T. H. N. (1996). AFLP analysis of the diversity and phylogeny of Lens and its comparison with RAPD analysis. Theor. Appl. Genet. 93: 751–758.
  52. Singh, A., Dikshit, H. K., Singh, D., Jain, N., Aski, M., Sarker, A., & Sharma, T. R. (2016). Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species. The Journal of Agricultural Science, 154(7), 1254-1269. https://doi.org/10.1017/S0021859615001252
  53. Singh, B., Malhotra, N., & Gupta, D. (2018). Widening the genetic base of cultivated gene pool following introgression from wild Lens taxa. Plant Breed. 137, 447–485. doi: 10.1111/pbr.12615
  54. Singh, D., Singh, C. K., Taunk, J., Jadon, V., Pal, M., & Gaikwad, K. (2019). Genome wide transcriptome analysis reveals vital role of heat responsive genes in regulatory mechanisms of lentil (Lens culinaris Medikus). Scientific reports, 9(1), 12976. https://doi.org/10.1038/s41598-019-49496-0
  55. Singh, M., Kumar, S., Basandrai, A. K., Basandrai, D., Malhotra, N., Saxena, D. R., Gupta, D., Sarker, A., & Singh, K. (2020). Evaluation and identification of wild lentil accessions for enhancing genetic gains of cultivated varieties. PLoS One, 15(3), e0229554. https://doi.org/10.1371/journal.pone.0229554
  56. Singh, M., Kumar, S., Mehra, R., Sood, S., Malhotra, N., Sinha, R., Jamwal, S., & Gupta, V. (2022). Evaluation and identification of advanced lentil interspecific derivatives resulted in the development of early maturing, high yielding, and disease-resistant cultivars under Indian agro-ecological conditions. Frontiers in Plant Science, 13, 936572. https://doi.org/10.3389/fpls.2022.936572
  57. Sharma, R., Chaudhary, L., & Kumar, M. (2023). Microsatellites based assessment of genetic diversity and population structure of indian lentil (Lens culinaris Medik.) genotypes. Biologia, 78(9), 2317-2328.
  58. 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. https://doi.org/10.1093/molbev/msm092
  59. Tantasawat, P., Trongchuen, J., Prajongjai, T., Jenweerawat, S., & Chaowiset, W. (2011). SSR analysis of soybean (Glycine max L. Merr.) genetic relationship and variety identification in Thailand. Australian J. Crop Sci. 5: 283-290
  60. Tiwari, K. K., Thakkar, N. J., Dharajiya, D.T. et al. (2021). Genome-wide microsatellites in amaranth: development, characterization, and cross-species transferability. 3 Biotech 11, 395. https://doi.org/10.1007/s13205-021-02930-5
  61. Topu, M., Sesiz, U., Bektas, H., Toklu, F., & Ozkan, H. (2023). Next-generation-sequencing-based simple sequence repeat (SSR) marker development and linkage mapping in lentil (Lens culinaris L.). Life, 13(7), 1579. https://doi.org/10.3390/life13071579
  62. Varshney, R. K., Graner, A., & Sorrells, M.E. (2005). Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48-55. https://doi.org/10.1016/j.tibtech.2004.11.005
  63. Verma, P., Sharma, T., Srivastava, P., 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: 1–19. https://doi.org/10.1007/s11033-014-3431-z
  64. Wong, M. M., Gujaria-Verma, N., Ramsay, L., Yuan, H. Y., Caron, C., Diapari, M., Vandenberg, A., & Bett, K. E., (2015). Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PlosONE 10 (3), E0122025. https://doi.org/10.1371/journal.pone.0122025
  65. Zhao, D., Sapkota, M., Lin, M., Beil, C., Sheehan, M., Greene, S., & Irish, B. M. (2024). Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine. Frontiers in Plant Science, 15, 1339298. https://doi.org/10.3389/fpls.2024.1339298
  66. Dikshit, H. K., Singh, A., Singh, D., Aski, M. S., Prakash, P., Jain, N.,. & Sarker, A. (2015). Genetic diversity in Lens species revealed by EST and genomic simple sequence repeat analysis. PloS one, 10(9), e0138101. https://doi.org/10.1371/journal.pone.0138101
  67. Gupta, D., Taylor, P. W. J., Inder, P., Phan, H. T. T., Ellwood, S. R., Mathur, P. N.,. & Ford, R. (2012). Integration of EST-SSR markers of Medicago truncatula into intraspecific linkage map of lentil and identification of QTL conferring resistance to ascochyta blight at seedling and pod stages. Molecular breeding, 30, 429-439. https://doi.org/10.1007/s11032-011-9634-2
  68. Gutierrez-Gonzalez, J. J., García, P., Polanco, C., González, A. I., Vaquero, F., Vences, F. J.,. & Sáenz de Miera, L. E. (2022). Multi-species transcriptome assemblies of cultivated and wild lentils (Lens sp.) provide a first glimpse at the lentil pangenome. Agronomy, 12(7), 1619. https://doi.org/10.3390/agronomy12071619
  69. Rajpal, V. R., Singh, A., Kathpalia, R., Thakur, R. K., Khan, M. K., Pandey, A.,. & Raina, S. N. (2023). The prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. Frontiers in Plant Science, 14, 1127239. https://doi.org/10.3389/fpls.2023.1127239