Hostname: page-component-cd9895bd7-gbm5v Total loading time: 0 Render date: 2024-12-20T14:42:33.708Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular variance and population structure of lentil (Lens culinaris Medik.) landraces from Mediterranean countries as revealed by simple sequence repeat DNA markers: implications for conservation and use

Published online by Cambridge University Press:  12 October 2017

Omar Idrissi ,
Angela R. Piergiovanni ,
Faruk Toklu ,
Chafika Houasli ,
Sripada M. Udupa ,
Ellen De Keyser ,
Patrick Van Damme  and
Jan De Riek
Omar Idrissi*
Affiliation:
Institut National de la Recherche Agronomique du Maroc (INRA), Regional Center of Settat P.B. 589, Settat 26000, Morocco
Angela R. Piergiovanni
Affiliation:
CNR – Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e Biorisorse Via G. Amendola 165/a, I-70126 Bari, Italy
Faruk Toklu
Affiliation:
Agricultural Faculty, Field Crops Department, Cukurova University, Adana, Turkey
Chafika Houasli
Affiliation:
Institut National de la Recherche Agronomique du Maroc (INRA), Regional Center of Settat P.B. 589, Settat 26000, Morocco
Sripada M. Udupa
Affiliation:
International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat, Morocco
Ellen De Keyser
Affiliation:
Institute for Agricultural and Fisheries Research (ILVO)-Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090 Melle, Belgium
Patrick Van Damme
Affiliation:
Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
Jan De Riek
Affiliation:
Institute for Agricultural and Fisheries Research (ILVO)-Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090 Melle, Belgium
*
*Corresponding author. E-mail: o.idrissi@yahoo.fr
Get access Rights & Permissions [Opens in a new window]

Abstract

The Mediterranean region has a rich history of domestication and cultivation of lentil (Lens culinaris Medik.). Landraces have been grown and repeatedly selected by local farmers under different agro-environments. Characterization of molecular variation and genetic differentiation helps to ensure enhanced valorization, conservation and use of these genetic resources. Nineteen Simple Sequence Repeat DNA markers were used for molecular variance analysis (AMOVA) and population structure assessment underlying 74 lentil landraces from four Mediterranean countries: Morocco, Italy, Greece and Turkey. Based on AMOVA, presence of population structure and genetic differentiation at different levels were evidenced. Genetic diversity among Turkish landraces was higher than that of other countries. These landraces were more homogeneous as shown by low genetic differentiation among individuals within each landrace. Whereas Moroccan landraces followed by Italian and Greek provenances showed higher diversity and differentiation among individuals within landraces. The wide genetic variability of these landraces could help to better adaptation to biotic and abiotic stresses. Moreover, they could provide useful alleles related to adaptive traits for breeding purposes. Based on structure analysis, we obtained indications of possible presence of two major gene pools: a northern gene pool composed of Turkish, Italian and Greek landraces, and a southern gene pool composed of Moroccan landraces. Our results could be of interest when designing future diversity studies, collection missions, conservation and core collection construction strategies on Mediterranean lentil landraces.

Keywords

AMOVAgenetic differentiationMediterranean lentil landracesSSR markers
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 3 , June 2018 , pp. 249 - 259
Copyright
Copyright © NIAB 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Akeroyd, J (1999) Conserving the Mediterranean flora: a way forward. Plant Talk 18: 23–28.Google Scholar
Bacchi, M, Leone, M, Mercati, F, Preiti, G, Sunseri, F and Monti, M (2010) Agronomic evaluation and genetic characterization of different accessions in lentil (Lens culinaris Medik.). Italian Journal of Agronomy 4: 303–314.Google Scholar
Benbrahim, N, Taghouti, M, Zouahri, A and Gaboun, F (2017) On-farm conservation of Zaer lentil landrace in context of climate change and improved varieties competition. Universal Journal of Agricultural Research 5(1): 27–38. doi: 10.13189/ujar.2017.050104.Google Scholar
Bhatty, RS (1988) Composition and quality of lentil (Lens culinaris Medik): a review. Canadian Institute of Food Science and Technology Journal 21: 144–160.Google Scholar
Carbonaro, M, Nardini, M, Maselli, P and Nucara, A (2015) Chemico-physical and nutritional properties of traditional legumes (lentil, Lens culinaris L., and grass pea, Lathyrus sativus L.) from organic agriculture: an explorative study. Organic Agriculture 5: 179–187. doi: 10.1007/s13165-014-0086-y.CrossRefGoogle Scholar
Coyne, C and McGee, R (2013) Lentil. In: Singh, M, Upadhyaya, HD and Bisht, IS (eds) Genetic and Genomic Resources of Grain Legume Improvement. London, UK: Elsevier Inc., pp. 157–180. doi: 10.1016/B978-0-12-397935-3.00013-X.Google Scholar
Cubero, JI, Pérez de la Vega, M and Fratini, R (2009) Origin, phylogeny, domestication and spread. In: Erskine, W, Muehlbauer, F, Sarker, A and Sharma, B (eds) The Lentil: Botany, Production and Uses. London, UK: CABI Publishing, pp. 13–33.Google Scholar
Davis, SD, Heywood, VH and Hamilton, AC (1994) Centres of Plant Diversity. A Guide and Strategy for their Conservation. Vol. 1: Europe, Africa and the Middle East. Cambridge, UK: IUCN Publications Unit.Google Scholar
Dikshit, HK, Singh, A, Singh, D, Aski, MS, Prakash, P, Jain, N, Meena, S, Kumar, S and Sarker, A (2015) Genetic diversity in Lens species revealed by EST and genomic simple sequence repeat analysis. PLoS ONE 10: e0138101. doi: 10.1371/journal.pone.0138101.Google Scholar
Duran, Y and Perez De La Vega, M (2004) Assessment of genetic variation and species relationships in a collection of Lens using RAPD and ISSR. Spanish Journal of Agricultural Research 2: 538–544.Google Scholar
Erskine, W (1997) Lessons for breeders from landraces of lentil. Euphytica 93: 107–112.Google Scholar
Erskine, W, Myveci, K and Izgin, N (1981) Screening a world lentil collection for cold tolerance. LENS Newsletter 8: 5–8.Google Scholar
Erskine, W, Adham, Y and Holly, L (1989) Geographic distribution of variation in quantitative traits in a world lentil collection. Euphytica 43: 97–103.Google Scholar
Erskine, W, Ellis, RH, Summerfield, RJ, Roberts, EH and Hussain, A (1990) Characterization of responses to temperature and photoperiod for time to flowering in a world lentil collection. Theoretical and Applied Genetics 80: 193–199.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x.Google Scholar
Excoffier, L, Laval, G and Schneider, S (2005) ARLEQUIN ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1, 47–50, Online.Google Scholar
Faratini, R, Perez De La Vega, M and Cubero, JI (2011) Lentil origin and domestication. In: Rubiales, D (ed.) Grain Legumes, vol. 57. Córdoba, Spain: Magazine of the European Association for Grain Legumes Research, pp. 5–8.Google Scholar
Ferguson, M and Erskine, W (2001) The genetic diversity of legumes species in the Mediterranean: lens. In: Maxted, N and Bennett, SJ (eds) Plant Genetic Resources of Legumes in the Mediterranean. Dordrecht, The Netherlands: Kluwer Academic Publishers, pp. 125–133.Google Scholar
Ferguson, ME, Robertson, LD, Ford-Lloyd, BV, Newbury, HJ and Maxted, N (1998) Contrasting genetic variation amongst lentil landraces from different geographical origins. Euphytica 102: 265–273.Google Scholar
Gepts, P (2006) Plant genetic resources conservation and utilization: the accomplishments and future of a societal insurance policy. Crop Science 46: 2278–2292.Google Scholar
Grusak, MA (2009) Nutritional and health-beneficial quality. In: Erskine, W, Muehlbauer, FJ, Sarker, A and Sharma, B (eds) The Lentil: Botany, Production and Uses. Oxfordshire: CAB International, pp. 368–390.Google Scholar
Grusak, MA and Coyne, CJ (2009) Variation for seed minerals and protein concentrations in diverse germplasm of lentil. In: Paper presented at North America Pulse Improvement Association, 20th Biennial Meeting, Fort Collins.Google Scholar
Hamwieh, A, Udupa, SM, Choumane, W, Sarker, A, Dreyer, F, Jung, C and 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.CrossRefGoogle ScholarPubMed
Hamwieh, A, Udupa, SM, Sarker, A, Jung, C and Baum, M (2009) Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breeding Science 59: 77–86.Google Scholar
Heywood, VH (1995) The Mediterranean flora in the context of world diversity. Ecologia Mediterranea 21: 11–18.Google Scholar
Idrissi, O, Udupa, SM, Houasli, Ch, De Keyser, E, Van Damme, P and 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. doi: 10.1111/pbr.12261.Google Scholar
Idrissi, O, Udupa, SM, De Keyser, E, Van Damme, P and De Riek, J (2016) Functional genetic diversity analysis and identification of associated simple sequence repeats and amplified fragment length polymorphism markers to drought tolerance in lentil (Lens culinaris ssp. Culinaris Medicus) landraces. Plant MolBiol Report 34(3): 659–680. doi: 10.1007/s11105-015-0940-4.Google Scholar
Khazaei, H, Caron, CT, Fedoruk, M, Diapari, M, Vandenberg, A, Coyne, CJ, McGee, R and Bett, KE (2016) Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world's agro-ecological zones. Frontiers in Plant Science 7: 1093. doi: 10.3389/fpls.2016.01093.Google Scholar
Ladizinsky, G (1979) The origin of lentil and its wild gene pool. Euphytica 28: 179–187.Google Scholar
Lombardi, M, Materne, M, Cogan, NO, Rodda, M, Daetwyler, HD, Slater, AT, Forster, JW and 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: 150. doi: 10.1186/ s12863-014-0150-3.Google Scholar
Maxim, A (2010) Conservation of genetic diversity in culture plants. Pro Environment 3: 50–53.Google Scholar
Maxted, N and Bennett, SJ (2001) Legume diversity in the Mediterranean region. In: Maxted, N and Bennett, SJ (eds) Plant Genetic Resources of Legumes in the Mediterranean. Dordrecht, The Netherlands: Kluwer Academic Publishers, pp. 51–75.Google Scholar
Mayer, JE, Pfeiffer, WH and Beyer, P (2008) Biofortified crops to alleviate micronutrient malnutrition. Current Opinion in Plant Biology 11: 166–170.Google Scholar
Muehlbauer, FJ and Tullu, A (1997) Lens culinaris Medik. West Lafayette: Center for New Crops and Plant Products, Purdue University. Available at http://www.hort.purdue.edu/newcrop/cropfactsheets/lentil.html (Last accessed 5 May 2017).Google Scholar
Piergiovanni, AR and Taranto, G (2003) Geographic distribution of genetic variation in lentil collection as revealed by SDS-PAGE fractionation of seed storage proteins. Journal Genetic and Breeding 57: 39–46.Google Scholar
Porras-Hurtado, L, Ruiz, Y, Santos, C, Phillips, Ch, Carracedo, Á and Lareu, MV (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in Genetics 4: 98. doi: 10.3389/fgene.2013.00098.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Pritchard, JK, Wen, X and Falush, D (2010) Documentation for structure software: Version 2.3. Department of Human Genetics University of Chicago, Department of Statistics University of oxford. http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf (Last accessed 26 April 2017).Google Scholar
Sandhu, JS and Singh, S (2007) History and origin. In: Yadav, SS, McNeil, D and Stevenson, PhC (eds) Lentil: An Ancient Crop for Modern Times. Dordrecht, The Netherlands: Springer, pp. 1–9.Google Scholar
Sarker, A, Erskine, W, Bakr, MA, Rahman, MM, Yadav, NK, Ali, A and Saxena, MC (2002) Role of lentil human nutrition in the Asian region. In: Paper presented at Joint CLAN Steering Committee Meeting, 10–12 Nov., ICRISAT, Patancheru.Google Scholar
Schmidt, K (2011) Göbeklitepe: a neolithic site in Southeastern Anatolia. In: Steadman, SR and McMahon, G (eds) The Oxford Handbook of Ancient Anatolia. Oxford: Oxford University Press, pp. 917–933.Google Scholar
Shahzad, Z, Rouached, H and Rakha, A (2014) Combating mineral malnutrition through iron and zinc biofortification of cereals. Comprehensive Reviews in Food Science and Food Safety 13: 329–346.Google Scholar
Singh, M, Bisht, IS, Kumar, S, Dutta, M, Bansal, KC, Karale, M, Sarker, A, Amri, A, Kumar, S and Datta, SK (2014) Global wild annual lens collection: a potential resource for lentil genetic base broadening and yield enhancement. PLoS ONE 9(9): e107781. doi: 10.1371/journal.pone.0107781.Google Scholar
Sonnante, G and Pignone, D (2001) Assessment of genetic variation in a collection of lentil using molecular tools. Euphytica 120: 301–307.Google Scholar
Sonnante, G and Pignone, D (2007) The major Italian landraces of lentil (Lens culinaris Medik.): their molecular diversity and possible origin. Genetic Resources and Crop Evolution 54: 1023–1031.Google Scholar
Sonnante, G, Galasso, I and Pignone, D (2003) ITS sequence analysis and phylogenetic inference in the genus Lens mill. Annals of Botany 91: 49–54.Google Scholar
Toklu, F, Karaköy, T, Hakli, E, Bicer, T, Brandolini, A, Kilian, B, Özkan, H (2009) Genetic variation among lentil (Len sculinaris Medik) landraces from Southeast Turkey. Plant Breeding 128: 178–186.Google Scholar
Torricelli, R, Donato, DF, Nicoletta, FV, Gianfranco, V, Fabio, V and Luigi, R (2011) Characterization of the lentil landrace Santo Stefano di Sessanio from Abruzzo, Italy. Genetic Resources and Crop Evolution 59: 261–276.Google Scholar
Viscosi, V, Lalicicco, M, Rocco, M, Trupiano, D, Arena, S, Chiatante, D, Scaloni, A and Scippa, GS (2010) Lentils biodiversity: the characterization of two local landraces. In: Nimis, PL, Vignes Lebbe, R (eds) Tools for Identifying Biodiversity: Progress and Problems, ISBN 978-88-8303-295-0.EUT. UK: Cambridge University Press, pp. 327–331.Google Scholar
White, PJ and Broadley, MR (2009) Biofortification of crops with seven mineral elements often lacking in human diets – iron, zinc, copper, calcium, magnesium, selenium and iodine. New Phytologist Journal 182: 49–84.Google Scholar
Wright, S (1978) Evolution and the Genetics of Populations. Vol. 4. Variability Within and Among Natural Populations. Chicago: University of Chicago Press, 590 p.Google Scholar
Yadav, SS, Stevenson, PhC, Rizvi, AH, Manohar, M, Gailing, S and Mateljan, G (2007) Uses and consumption. In: Yadav, SS, McNeil, D and Stevenson, PC (eds) Lentil: An Ancient Crop for Modern Times. Dordrecht, The Netherlands: Springer, pp. 33–46.Google Scholar
Zaccardelli, M, Lupo, F, Piergiovanni, AR, Laghetti, G, Sonnante, G, Daminati, MG, Sparvoli, F and Lioi, L (2011) Characterization of Italian lentil (Lens culinaris Medik.) germplasm by agronomic traits, biochemical and molecular markers. Genetic Resources and Crop Evolution 59: 727–738.Google Scholar