Orphan Crop: Lentil Enters the Genomics Era!

Authors

DOI:

https://doi.org/10.24925/turjaf.v13i5.1387-1403.7421

Keywords:

Lentil, crop wild relatives, molecular markers, genetic linkage map, QTL

Abstract

Lentil, an important crop, requires resilient and productive varieties to mitigate abiotic and biotic stresses associated with climate change. In this context, genetic materials derived from wild lentil genetic resources play a crucial role in genetic improvement and stress tolerance enhancement. Genetic diversity studies, genetic mapping, and advanced high-throughput sequencing technologies have facilitated the identification of adaptive genes, QTLs, and other valuable plant traits in response to stress factors. The integration of genomic technologies with plant breeding has led to significant advancements in lentil genomic research, including the development of dense genetic linkage maps, extensive genotyping, and QTL analyses. This review emphasizes recent advancements in genetic diversity, high-density genetic mapping, high-resolution QTL mapping, and the utilization of genomic tools for genetic improvement.

References

Abbo, S., & Ladizinsky, G. (1991). Anatomical aspects of hybrid embryo abortion in the genus Lens L. Botanical Gazette, 152, 316–320. https://doi.org/10.1086/337895

Abbo, S., & Ladizinsky, G. (1994). Genetical aspects of hybrid embryo abortion in the Lens L. Heredity, 72, 193–200. https://doi.org/10.1038/hdy.1994.26

Aldemir, S., Ateş, D., Temel, H. Y., Yağmur, B., Alsaleh, A., Kahriman, A., Ozkan, H., Vandenberg, A., & Tanyolac, M. B. (2017). QTLs for iron concentration in seeds of the cultivated lentil (Lens culinaris Medic.) via genotyping by sequencing. Turkish Journal of Agriculture and Forestry, 41(4), 243-255. https://doi.org/10.3906/tar-1610-33

Andeden, E. E., Baloch, F. S., Çakır, E., Toklu, F., & Özkan, 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

Arumuganathan, K., & Earle, E. D. (1991). Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9(3), 208-218. https://doi.org/10.1007/BF02672069

Asghar, M. J., Abbas, G., Shah, T. M., & Atta, B. M. (2010). Study of genetic diversity in some local and exotic lentil (L. culinaris Medik.) genotypes. Pakistan Journal of Botany, 42, 2681–2690.

Ates, D., Aldemir, S., Alsaleh, A., Erdogmus, S., Nemli, S., Kahriman, A., Ozkan, H., Vandenberg, A., & Tanyolac, B. (2018a). A consensus linkage map of lentil based on DArT markers from three RIL mapping populations. PLoS ONE, 13(1), e0191375. https://doi.org/10.1371/journal.pone.0191375

Ates, D., Aldemir, S., Yagmur, B., Kahraman, A., Ozkan, H., Vandenberg, A., & Tanyolac, M. B. (2018b). QTL mapping of genome regions controlling manganese uptake in lentil seed. G3: Genes, Genomes, Genetics, 8(5), 1409–1416. https://doi.org/10.1534/g3.118.200259

Ates, D., Sever, T., Aldemir, S., Yagmur, B., Temel, H. Y., Kaya, H. B., Kahraman, A., Ozkan, H., Vandenberg, A., & Tanyolac, M. B. (2016). Identification of QTLs controlling genes for Se uptake in lentil seeds. PLoS ONE, 11, e0149210. https://doi.org/10.1371/journal.pone.0154054

Bakır, 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. https://doi.org/10.1007/s10528-018-9893-2

Balfourier, F., Roussel, V., Strelchenko, P., Exbrayat-Vinson, F., Sourdille, P., Boutet, G., Koenig, J., Ravel, C., Mitrofanova, O., Beckert, M., & Charmet, G. (2007). A worldwide bread wheat core collection arrayed in a 384-well plate. Theoretical and Applied Genetics, 114(7), 1265-1275. https://doi.org/10.1007/s00122-007-0517-1

Baloch, F. S., Derya, M., Andeden, E. E., Alsaleh, A., Cömertpay, G., Kilian, B., & Özkan, H. (2015). Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species. Biochemical Systematics and Ecology, 58, 162-168. https://doi.org/10.1016/j.bse.2014.12.002

Batley, J., Barker, G., O'Sullivan, H., Edwards, K. J., & Edwards, D. (2003). Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology, 132(1), 84–91. https://doi.org/10.1104/pp.102.019422

Bayaa, B., Erskine, W., & Hamdi, A. (1995). Evaluation of a wild lentil collection for resistance to vascular wilt. Genetic Resources and Crop Evolution, 42, 231–235. https://doi.org/10.1007/BF02431257

Bett, K., Ramsay, L., Sharpe, A., Cook, D., Penmetsa, R. V., & Verma, N. (2014). Lentil genome sequencing: Establishing a comprehensive platform for molecular breeding. In Proceedings of International Food Legumes Research Conference (IFLRC-VI) and ICCLG-VII (Vol. 19). (Saskatoon, SK: Crop Development Center).

Bhadauria, V., Ramsay, L., Bett, K. E., & Banniza, S. (2017). QTL mapping reveals genetic determinants of fungal disease resistance in the wild lentil species Lens ervoides. Scientific Reports, 7, 3231–3240. https://doi.org/10.1038/s41598-017-03463-9

Brown, A. H. D. (1989). Core collections: A practical approach to genetic resources management. Genome, 31, 818–824. https://doi.org/10.1139/g89-144

Cortinovis, G., Oppermann, M., Neumann, K., Graner, A., Gioia, T., Marsella, M., Alseekh, S., Fernie, A. R., Papa, R., Bellucci, E., & Bitocchi, E. (2021). Towards the development, maintenance, and standardized phenotypic characterization of single-seed-descent genetic resources for common bean. Current Protocols, 1, e133. https://doi.org/10.1002/cpz1.133

Dadu, R. H. R., Bar, I., Ford, R., Sambasivam, P., Croser, J., Ribalta, F., Kaur, S., Sudheesh, S., & Gupta, D. (2021). Lens orientalis contributes quantitative trait loci and candidate genes associated with ascochyta blight resistance in lentil. Frontiers in Plant Science, 12, 703283. https://doi.org/10.3389/fpls.2021.703283

de la Puente, R., Garcia, P., Polanco, C., & Perez de la Vega, M. (2013). An improved intersubspecific genetic map in Lens including functional markers. Spanish Journal of Agricultural Research, 11, 132–136. https://doi.org/10.5424/sjar/2013111-3283

Derya, M. (2012). SSR Markörleri Kullanılarak Mercimek Tür ve Çeşitlerinde Genetik Çeşitliliğe Dayalı Taksonomik İlişkinin Araştırılması. [Yayınlanmamış Yüksek Lisans Tezi]. Çukurova Universitesi

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. https://doi.org/10.3389/fgene.2020.00546

Dixit, G. P., Katiyar, P. K., Singh, B. B., & Kumar, S. (2009). Lentil varieties in india. all India coordinated research project on MULLaRP (Kanpur, India: IIPR), p13.

Durán, Y., Fratini, R., Garcia, P., & de la Vega, M. P. (2004). An intersubspecific genetic map of Lens. Theoretical and Applied Genetics, 108, 1265–1273. https://doi.org/10.1007/s00122-003-1542-3

El-Bouhssini, M., Sarker, A., Erskine, W., & Joubi, A. (2008). First sources of resistance to Sitona weevil (Sitona crinitus herbst.) in wild Lens species. Genetic Resources and Crop Evolution, 55, 1–4. https://doi.org/10.1007/s10722-007-9297-3

Erskine, W., Smartt, J., & Muehlbauer, F. J. (1994). Mimicry of lentil and the domestication of common vetch and grass pea. Economic Botany, 48, 326–332. https://doi.org/10.1007/BF02862334

Erskine, W., Chandra, S., Chaudhry, M., Malik, I. A., Sarker, A., Sharma, B., Tufail, M., & Tyagi, M. C. (1998). A bottleneck in lentil: widening its genetic base in South Asia. Euphytica, 101, 207–211. https://doi.org/10.1023/A:1018306723777

Eujayl, I., Baum, M., Powell, W., Erskine, W., & Pehu, E. (1998). A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines. Theoretical and Applied Genetics, 97(1–2), 83–89. https://doi.org/10.1007/s001220050869

FAO. (2024). Food and Agriculture Organization of the United Nations. FAOSTAT. http://www.fao.org/faostat/en/#data

Fedoruk, M. J., Vandenberg, A., & Bett, K. E. (2013). Quantitative trait loci analysis of seed quality characteristics in lentil using single nucleotide polymorphism markers. Plant Genome,6,plantgenome2013.05.0012.https://doi.org/10.3835/plantgenome2013.05.0012

Ferguson, M. E., Maxted, N., van Slageren, M., & Robertson, L. D. (2000). A re-assessment of the taxonomy of Lens Mill. (Leguminosae, Papilionoideae, Vicieae). Botanical Journal of the Linnean Society, 133, 41–59. https://doi.org/10.1111/j.1095-8339.2000.tb01536.x

Ford, R., & Taylor, P. W. J. (2003). Construction of an intraspecific linkage map of lentil (Lens culinaris ssp. culinaris). Theoretical and Applied Genetics, 107(5), 910-916. https://doi.org/10.1007/s00122-003-1326-9

Frankel, O.H. (1984). Genetic Perspectives of Germplasm Conservation Genetic Manipulation Impact on Man & Society. Cambridge: Cambridge University Press, 161–170.

Fratini, R., & Ruiz, M. L. (2006). Interspecific hybridization in the Lens applying in vitro embryo rescue. Euphytica, 150, 271–280. https://doi.org/10.1007/s10681-006-9118-3

Fratini, R., & Ruiz, M. L. (2011). Wide crossing in lentil through embryo rescue. In T. A. Thorpe & E. C. Young (Eds.), Plant embryo culture (s. 131–139). Humana Press. https://doi.org/10.1007/978-1-61737-988-8_11

Fratini, R., Durán, Y., Garcı́a, P., & Pérez de la Vega, M. (2007). Identification of quantitative trait loci (QTL) for plant structure, growth habit and yield in lentil. Spanish Journal of Agricultural Research, 5, 348–356. https://doi.org/10.5424/sjar/2007053-255

Fratini, R., Ruiz, M. L., & de la Vega, M. P. (2004). Intra-specific and inter-subspecific crossing in lentil (Lens culinaris Medik.). Canadian Journal of Plant Science, 84, 981–986. https://doi.org/10.4141/P03-20

Gap Bölge Kalkınma İdaresi Başkanlığı. (2018). http://www.gap.gov.tr/tarim-sayfa-15.html

García-García, P., Vaquero, F., Vences, F. J., Sáenz de Miera, L. E., Polanco, C., González, A. I., Horres, R., Krezdorn, N., Rotter, B., Winter, P., & Pérez de la Vega, M. (2019). Transcriptome profiling of lentil in response to Ascochyta lentis infection. Spanish Journal of Agricultural Research, 17(4), e0703-e0703. https://doi.org/10.5424/sjar/2019174-14982

Gela, T., Ramsay, L., Haile, T. A., Vandenberg, A., & Bett, K. (2021b). Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome-wide association study. Plant Genome, 14, e20131. https://doi.org/10.1002/tpg2.20131

Gela, T. S., Koh, C. S., Caron, C. T., Chen, L. A., Vandenberg, A., & Bett, K. E. (2021a). QTL mapping of lentil anthracnose (Colletotrichum lentis) resistance from Lens ervoides accession IG 72815 in an interspecific RIL population. Euphytica, 217, 1–11. https://doi.org/10.1007/s10681-021-02804-0

Gorim, L. Y., & Vandenberg, A. (2017). Evaluation of wild lentil species as genetic resources to improve drought tolerance in cultivated lentil. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.01129

Guerra‐García, A., Gioia, T., von Wettberg, E., Logozzo, G., Papa, R., Bitocchi, E., & Bett, K. E. (2021). Intelligent characterization of lentil genetic resources: evolutionary history, genetic diversity of germplasm, and the need for well‐represented collections. Current Protocols, 1(5), e134. https://doi.org/10.1002/cpz1.134

Gujaria-Verma, N., Vail, S. L., Carrasquilla-Garcia, N., Penmetsa, R. V., Cook, D. R., Farmer, A. D., Vandenberg, A., & Bett, K. E. (2014). Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea. Frontiers in Plant Science, 5. https://doi.org/10.3389/fpls.2014.00676

Gupta, D., & Sharma, S. K. (2005). Embryo-ovule rescue technique overcoming post-fertilization barriers in interspecific crosses of Lens. Journal of Lentil Research, 2, 27–30.

Gupta, D., & Sharma, S. K. (2006). Evaluation of wild Lens taxa for agromorphological traits, fungal diseases and moisture stress in northwestern Indian hills. Genetic Resources and Crop Evolution, 53, 1233–1241. https://doi.org/10.1007/s10722-005-2932-y

Gupta, D., Taylor, P. W. J., Inder, P., Phan, H. T. T., Ellwood, S. R., Mathur, P. N., Sarker, A., & Ford, R. (2012a). 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

Gupta, D. S., Cheng, P., Sablok, G., Thavarajah, P., Coyne, C. J., Kumar, S., Baum, M., & McGee, R. J. (2016). Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information. The Crop Journal, 4(5), 425–433. https://doi.org/10.1016/j.cj.2016.06.012.

Gupta, M., Verma, B., Kumar, N., Chahota, R. K., Rathour, R., Sharma, S. K., Bhatia, S., & Sharma, T. R. (2012b). Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. Journal of Genetics, 91, 279–287. https://doi.org/10.1007/s12041-012-0180-4

Hamdi, A., Küsmenoĝlu, I., & Erskine, W. (1996). Sources of winter hardiness in wild lentil. Genetic Resources and Crop Evolution, 43, 63–67. https://doi.org/10.1007/BF00126942

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. https://doi.org/10.1007/s00122-004-1892-5

Hansen, J., & Renfrew, J. M. (1978). Paleolithic-Neolithic seed remains at Franchthi cave, Greece. Nature, 271, 349–352. https://doi.org/10.1038/271349a0

Havey, M. J., & Muehlbauer, F. J. (1989). Linkages between restriction fragment length, isozyme, and morphological markers in lentil. Theoretical and Applied Genetics, 77(3), 395–401. https://doi.org/10.1007/BF00305835

Helbaek, H. (1969). Plant collecting, dry-farming and irrigation agriculture in prehistoric Deh Luran. In F. Hole, K. V. Flannery, & J. A. Neely (Eds.), Prehistory and human ecology of the Deh Luran Plain (pp. 383–426). Memoirs Museum Anthropology No. 1. University of Michigan, Ann Arbor, USA.

Idrissi, O., Udupa, S. M., De Keyser, E., McGee, R. J., Coyne, C. J., Saha, G. C., Muehlbauer, F. J., Van Damme, P., & De Riek, J. (2016). Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.01174

Idrissi, O., Udupa, S. M., Houasli, C., De Keyser, E., Van Damme, P., & De Riek, J. (2015). Genetic diversity analysis of Moroccan lentil (Lens culinaris Medik.) landraces using simple sequence repeat and amplified fragment length polymorphisms reveals functional adaptation towards agro-environmental origins. Plant Breeding, 134, 322–332. https://doi.org/10.1111/pbr.12261

Kahraman, A., Demirel, U., Ozden, M., & Muehlbauer, F. J. (2010). Mapping of QTLs for leaf area and the association with winter hardiness in fall-sown lentil. African Journal of Biotechnology, 9, 8515–8519. https://doi.org/10.5897/AJB10.57

Kahraman, A., Kusmenoglu, I., Aydin, N., Aydogan, A., Erskine, W., & Muehlbauer, F. J. (2004). QTL mapping of winter hardiness genes in lentil. Crop Science, 44, 13–22. https://doi.org/10.2135/cropsci2004.1300

Kahraman, A., Temel, H. Y., Aydogan, A., & Tanyolac, M. B. (2015). Major quantitative trait loci for flowering time in lentil. Turkish Journal of Agriculture and Forestry, 39, 588–595. https://doi.org/10.3906/tar-1408-16

Kaur, S., Cogan, N. O., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., & Forster, J. W. (2011). Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 12(1), 265. https://doi.org/10.1186/1471-2164-12-265

Kaur, S., Cogan, N. O., Stephens, A., Noy, D., Butsch, M., Forster, J. W., & Materne, M. (2014). EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance. Theoretical and Applied Genetics, 127(3), 703–713. https://doi.org/10.1007/s00122-013-2252-0

Khazaei, H., Caron, C. T., Fedoruk, M., Diapari, M., Vandenberg, A., Coyne, C. J., McGee, R., & Bett, K. E. (2016). Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world’s agro-ecological zones. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.01093

Khazaei, H., Fedoruk, M., Caron, C. T., Vandenberg, A., & Bett, K. E. (2018). Single nucleotide polymorphism markers associated with seed quality characteristics of cultivated lentil. The Plant Genome, 11(1), 1–7. https://doi:10.3835/plantgenome2017.06.0051

Khazaei, H., Podder, R., Caron, C. T., Kundu, S. S., Diapari, M., Vandenberg, A., & Bett, K. E. (2017). Marker–trait association analysis of iron and zinc concentration in lentil (Lens culinaris Medik.) seeds. The Plant Genome, 10(2), 1–8. https://doi.org/10.3835/plantgenome2017.02.0007

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

Kroc, M., Tomaszewska, M., Czepiel, K., Bitocchi, E., Oppermann, M., Neumann, K., Guasch, L., Bellucci, E., Alseekh, S., Graner, A., Fernie, A. R., Papa, R., & Susek, K. (2021). Towards development, maintenance, and standardized phenotypic characterization of single-seed-descent genetic resources for lupins. Current Protocols, 1, e191. https://doi.org/10.1002/cpz1.19

Kumar, J., Basu, P. S., Gupta, S., Dubey, S., Gupta, D. S., & Singh, N. P. (2018a). Physiological and molecular characterisation for high temperature stress in Lens culinaris. Functional Plant Biology, 45(4), 474–487. https://doi.org/10.1071/FP17211

Kumar, J., Basu, P. S., Srivastava, E., Chaturvedi, S. K., Nadarajan, N., & Kumar, S. (2012). Phenotyping of traits imparting drought tolerance in lentil. Crop and Pasture Science, 63(6), 547-554. https://doi.org/10.1071/CP12168

Kumar, J., Gupta, S., Biradar, R. S., Gupta, P., Dubey, S., & Singh, N. P. (2018b). Association of functional markers with flowering time in lentil. Journal of Applied Genetics, 59(1), 9–21. https://doi.org/10.1007/s13353-017-0419-0

Kumar, J., Gupta, S., Gupta, D. S., & Singh, N. P. (2018c). Identification of QTLs for agronomic traits using association mapping in lentil. Euphytica, 214(4), 75. https://doi.org/10.1007/s10681-018-2155-x

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 ssp. culinaris). Physiology and Molecular Biology of Plants, 20, 125–132. https://doi.org/10.1007/s12298-013-0214-2

Kumar, S., Rajendran, K., Kumar, J., Hamwieh, A., & Baum, M. (2015). Current knowledge in lentil genomics and its application for crop improvement. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.00078

Kupicha, F.K. (1981). Vicieae. Advances in legume systematics, part 1, 377-381

Ladizinsky, G., Braun, D., Goshen, D., & Muehlbauer, F. J. (1984). The biological species of the Lens l. Botanical Gazette, 145, 253–261. https://doi.org/10.1086/337454

Ladizinsky, G. (1979). The origin of lentil and its wild gene pool. Euphytica, 28, 179–187. https://doi.org/10.1007/BF00029189

Ladizinsky, G. (1993). Wild lentils. Critical Reviews in Plant Sciences, 12, 169–184. https://doi.org/10.1080/07352689309701900

Li, Z. C., Zhang, H. L., Cao, Y. S., Qiu, Z. E., Wei, X. H., Tang, S. X., Yu, P., & Wang, X. K. (2003). Studies on the sampling strategy for primary core collection of Chinese indigence. Acta Agron Sin 29:20–24

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-by-sequencing of wild and landrace accessions. Frontiers in Plant Science, 12. https://doi: 10.3389/fpls.2021.628439

Lombardi, M., Materne, M., Cogan, N. O., Rodda, M., Daetwyler, H. D., Slater, A. T., Forster, J. W., & Kaur, S. (2014). Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers. BMC Genetics, 15(1), 150. https://doi: 10.1186/s12863-014-0150-3

Mahmoodi, R., Dadpour, M. R., Hassani, D., Zeinalabedini, M., Vendramin, E., Micali, S., & Nahandi, F. Z. (2019). Development of a core collection in Iranian walnut (Juglans regia L.) germplasm using the phenotypic diversity. Scientia Horticulturae, 249, 439-448. https://doi: 10.1016/j.scienta.2019.02.017

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21.05.2025

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Topu, M. (2025). Orphan Crop: Lentil Enters the Genomics Era!. Turkish Journal of Agriculture - Food Science and Technology, 13(5), 1387–1403. https://doi.org/10.24925/turjaf.v13i5.1387-1403.7421

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