Phenotyping and SSR markers as a tool for identification of duplicates in lettuce germplasm

https://doi.org/10.17221/68/2018-CJGPBCitation:Sochor M., Jemelková M., Doležalová I. (2019): Phenotyping and SSR markers as a tool for identification of duplicates in lettuce germplasm. Czech J. Genet. Plant Breed., 55: 110-119.
supplementary materialdownload PDF

In total, 117 individual samples from 39 accessions of Lactuca sativa were selected from the Czech national collection of lettuce with the aim to quantify and compare patterns of genetic and phenotypic variability within and among lettuce accessions and to propose a rapid, reliable and inexpensive method for verification of possible duplicates. We focused on phenotypic evaluation and SSR genotyping, and studied their ability to distinguish between individual accessions. Phenotypic data revealed that no two accessions shared the exactly same phenotype and no accession exhibited variability in the characters studied. Variability in SSR markers was very low as ten of twenty scorable SSR loci exhibited no variation and the remaining ten provided 48 alleles in total. Although neither phenotypic nor SSR data alone can serve as evidence for unambiguous duplicate confirmation, their combination increases the resolution power of the method considerably. The obtained data on cultivated lettuce indicate weak, but significant correlation (R2 = 0.34, P = 0.01) between the two data sets.

References:
Babic Vojka, Nikolic Ana, Andjelkovic Violeta, Kovacevic Dragan, Filipovic Milomir, Vasic Vladimir, Mladenovic-Drinic Snezana (2016): UPOV morphological versus molecular markers for maize inbred lines variability determination. Chilean journal of agricultural research, 76, 417-426  https://doi.org/10.4067/S0718-58392016000400004
 
Barcaccia G. (2009): Molecular markers for characterizing and conserving crop plant germplasm. In: Jain S.M., Brar D.S. (eds.): Molecular Techniques in Crop Improvement. 2nd Ed. Dordrecht, Springer Netherlands: 231–254.
 
BLACKET M. J., ROBIN C., GOOD R. T., LEE S. F., MILLER A. D. (2012): Universal primers for fluorescent labelling of PCR fragments-an efficient and cost-effective approach to genotyping by fluorescence. Molecular Ecology Resources, 12, 456-463  https://doi.org/10.1111/j.1755-0998.2011.03104.x
 
Bortiri E., Heuvel B. Vanden, Potter D. (2006): Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy. Plant Systematics and Evolution, 259, 53-71  https://doi.org/10.1007/s00606-006-0427-8
 
Daunay M.C., Allender C., Astley D., Bas N., van Dooijeweert W., van Treuren R., Branca F., Díez M.J., Geoffriau E., Keller E.R.J., Kotlińska T., Smékalová K., Engels J., Maggioni L. (2011): MORE EFFICIENT CONSERVATION AND USE OF VEGETABLE GENETIC RESOURCES IN EUROPE: ECPGR ACHIEVEMENTS AND PERSPECTIVES. Acta Horticulturae, , 405-417  https://doi.org/10.17660/ActaHortic.2011.918.52
 
del Rio A. H., Bamberg J. B., Huaman Z. (2006): Genetic equivalence of putative duplicate germplasm collections held at CIP and US potato genebanks. American Journal of Potato Research, 83, 279-285  https://doi.org/10.1007/BF02872164
 
Doležalová I. (2014): Genetic resources of leafy vegetables with respect to the genus Lactuca L. In: Petrželová I., Doležalová I., Sapáková E., Horák M. (eds.): Genetic Resources of Vegetable and Special Crops. Folia Universitas Agriculturae et Silviculturae Mendelianae Brunensis, 7: 32–45.
 
Donelli Gianfranco, Vuotto Claudia, Mastromarino Paola (2013): Phenotyping and genotyping are both essential to identify and classify a probiotic microorganism. Microbial Ecology in Health & Disease, 24, -  https://doi.org/10.3402/mehd.v24i0.20105
 
FAO (2010): The state of ex situ conservation. Chapter 3. In: The Second Report on the State of the World’s Plant Genetic Resources for Food and Agriculture. Rome, FAO: 54–90.
 
Frankel R., Galun E. (1977): Pollination Mechanisms, Reproduction and Plant Breeding. Berlin, Heidelberg, New York, Springer-Verlag.
 
Garcia Antonio A. F., Benchimol Luciana L., Barbosa Antônia M. M., Geraldi Isaias O., Souza Jr. Cláudio L., Souza Anete P. de (2004): Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology, 27, 579-588  https://doi.org/10.1590/S1415-47572004000400019
 
Gaut Brandon S. (2015): Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution. Molecular Biology and Evolution, 32, 1661-1671  https://doi.org/10.1093/molbev/msv105
 
George R.A.T. (1999): Vegetable Seed Production. 2nd Ed. Wallingford, CABI Publishing.
 
Hong Jee-Hwa, Kwon Yong-Sham, Choi Keun-Jin, Mishra Raghvendra Kumar, Kim Doo Hwan (2013): Identification of Lettuce Germplasms and Commercial Cultivars Using SSR Markers Developed from EST. Korean Journal of Horticultural Science and Technology, 31, 772-781  https://doi.org/10.7235/hort.2013.13055
 
Hong Jee-Hwa, Kwon Yong-Sham, Mishra Raghvendra Kumar, Kim Doo Hwan (2015): Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test. American Journal of Plant Sciences, 06, 113-125  https://doi.org/10.4236/ajps.2015.61013
 
Irish Brian M., Goenaga Ricardo, Zhang Dapeng, Schnell Raymond, Brown J. Steve, Motamayor Juan Carlos (2010): Microsatellite Fingerprinting of the USDA-ARS Tropical Agriculture Research Station Cacao ( L.) Germplasm Collection. Crop Science, 50, 656-  https://doi.org/10.2135/cropsci2009.06.0299
 
Jones C.J., Edwards K.J., Castaglione S., Winfield M.O., Sala F., van de Wiel C., Bredemeijer G., Vosman B., Matthes M., Daly A., Brettschneider R., Bettini P., Buiatti M., Maestri E., Malcevschi A., Marmiroli N., Aert R., Volckaert G., Rueda J., Linacero R., Vazquez A., Karp A. (1997): Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding, 3: 381–390. https://doi.org/10.1023/A:1009612517139
 
Kesseli Rick, Ochoa Oswaldo, Michelmore Richard (1991): Variation at RFLP loci in Lactuca spp. and origin of cultivated lettuce ( L . sativa ). Genome, 34, 430-436  https://doi.org/10.1139/g91-065
 
Kovach W.L. (2010): MVSP – A MultiVariate Statistical Package for Windows, Ver. 3.2. Pentraeth, Wales, Kovach Computing Services.
 
Lebeda A., Ryder E.J., Grube R., Doležalová I., Křistková E. (2007): Lettuce (Asteraceae; Lactuca spp.). In: Singh R.J. (ed.): Genetic Resources, Chromosome Engineering, and Crop Improvement. Vol. 3. Vegetable Crops. Boca Raton, CRC Press, Taylor and Francis Group: 377–472.
 
Lipman E., Jongen M.W.M, van Hintum T.J.L., Gass T., Maggioni L. (1997): Central Crop Databases: Tools for Plant Genetic Resources Management. Rome, Wageningen, International Plant Genetic Resources Institute.
 
Lund B., Ortiz R., Skovgaard I., Waugh R., Andersen S. (2003): Analysis of potential duplicates in barley gene bank collections using re-sampling of microsatellite data. Theoretical and Applied Genetics, 106, 1129-1138  https://doi.org/10.1007/s00122-002-1130-y
 
Majeský Ľuboš, Vašut Radim J., Kitner Miloslav (2015): Genotypic diversity of apomictic microspecies of the Taraxacum scanicum group (Taraxacum sect. Erythrosperma). Plant Systematics and Evolution, 301, 2105-2124  https://doi.org/10.1007/s00606-015-1218-x
 
MEIRMANS PATRICK G., VAN TIENDEREN PETER H. (2004): genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794  https://doi.org/10.1111/j.1471-8286.2004.00770.x
 
Michelmore R.W. (2014): Genetic variation in lettuce. In: California Leafy Greens Research Program, Davis, The Genome Center and The Department of Plant Sciences, University of California, Apr 1, 2013–Mar 31, 2014.
 
PAETKAU D., STROBECK C. (1994): Microsatellite analysis of genetic variation in black bear populations. Molecular Ecology, 3, 489-495  https://doi.org/10.1111/j.1365-294X.1994.tb00127.x
 
Peakall R., Smouse P. E. (2012): GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics, 28, 2537-2539  https://doi.org/10.1093/bioinformatics/bts460
 
Rao N.K., Hanson J., Dulloo M.E., Ghosh K., Nowell D., Larinde M. (2006): Manual of Seed Handling in Genebanks. Handbooks for Genebanks No. 8. Rome, Bioversity International.
 
Rasheed Awais, Hao Yuanfeng, Xia Xianchun, Khan Awais, Xu Yunbi, Varshney Rajeev K., He Zhonghu (2017): Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. Molecular Plant, 10, 1047-1064  https://doi.org/10.1016/j.molp.2017.06.008
 
Rauscher Gilda, Simko Ivan (2013): Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes. BMC Plant Biology, 13, 11-  https://doi.org/10.1186/1471-2229-13-11
 
Rebourg C, Gouesnard B, Charcosset A (): Large scale molecular analysis of traditional European maize populations. Relationships with morphological variation. Heredity, 86, 574-587  https://doi.org/10.1046/j.1365-2540.2001.00869.x
 
Richerzhagen C. (2010): Protecting Biological Diversity. The Effectiveness of Access and Benefit-sharing Regimes. New York, Abingdon, Taylor & Francis.
 
Šarhanová Petra, Sharbel Timothy F., Sochor Michal, Vašut Radim J., Dančák Martin, Trávníček Bohumil (2017): Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers. Annals of Botany, 120, 317-328  https://doi.org/10.1093/aob/mcx033
 
Selkoe Kimberly A., Toonen Robert J. (2006): Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters, 9, 615-629  https://doi.org/10.1111/j.1461-0248.2006.00889.x
 
Simko Ivan (2009): Development of EST-SSR Markers for the Study of Population Structure in Lettuce (Lactuca sativa L.). Journal of Heredity, 100, 256-262  https://doi.org/10.1093/jhered/esn072
 
Simko Ivan, Eujayl Imad, van Hintum Theo J.L. (2012): Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Science, 184, 54-62  https://doi.org/10.1016/j.plantsci.2011.12.009
 
Smýkal P., Bačová-Kerteszová N., Kalendar R., Corander J., Schulman A. H., Pavelek M. (2011): Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theoretical and Applied Genetics, 122, 1385-1397  https://doi.org/10.1007/s00122-011-1539-2
 
Spooner D., van Treuren R., de Vicente M.C. (2005): Molecular Markers for Genebank Management. IPGRI Technical No. 10. Rome, International Plant Genetic Resources Institute.
 
Thomson R.C., Whitaker T.W., Bohn G.W., van Horn C.W. (1958): Natural cross-pollination in lettuce. American Society for Horticultural Science, 72: 403–409.
 
Valière Nathaniel (2002): gimlet: a computer program for analysing genetic individual identification data. Molecular Ecology Notes, 2, 377-379  https://doi.org/10.1046/j.1471-8286.2002.00228.x-i2
 
van Hintum Theo J. L., Knüpffer Helmut (1995): Duplication within and between germplasm collections. Genetic Resources and Crop Evolution, 42, 127-133  https://doi.org/10.1007/BF02539516
 
van Hintum T.J.L., Boukema I.W. (1999): Genetic resources of leafy vegetables, In: Lebeda A., Křístková E. (eds.): Eucarpia Leafy Vegetables '99, Proc. Eucarpia Meeting on Leafy Vegetables Genetics and Breeding, Olomouc, June 8–10, 1999: 59–72.
 
van Treuren R., van Hintum T.J.L. (2001): Identification of intra-accession genetic diversity in selfing crops using AFLP markers: Implications for collection management. Genetic Resources and Crop Evolution, 48: 287–295. https://doi.org/10.1023/A:1011272130027
 
van Treuren R., van Hintum T.J.L. (2003): MARKER-ASSISTED REDUCTION OF REDUNDANCY IN GERMPLASM COLLECTIONS: GENETIC AND ECONOMIC ASPECTS. Acta Horticulturae, , 139-149  https://doi.org/10.17660/ActaHortic.2003.623.15
 
van Treuren R., van Soest L. J. M., van Hintum Th. J. L. (2001): Marker-assisted rationalisation of genetic resource collections: a case study in flax using AFLPs. Theoretical and Applied Genetics, 103, 144-152  https://doi.org/10.1007/s001220100537
 
van Treuren R., de Groot E. C., Boukema I. W., van de Wiel C. C. M., van Hintum Th. J. L. (2010): Marker-assisted reduction of redundancy in a genebank collection of cultivated lettuce. Plant Genetic Resources, 8, 95-105  https://doi.org/10.1017/S1479262109990220
 
Wang Shuzhen, Wang Bincai, Liu Jie, Ren Jin, Huang Xingxue, Zhou Guolin, Wang Aihua (2017): Novel polymorphic EST-based microsatellite markers characterized in lettuce (Lactuca sativa). Biologia, 72, -  https://doi.org/10.1515/biolog-2017-0154
 
Washburn Jacob D., Bird Kevin A., Conant Gavin C., Pires J. Chris (2016): Convergent Evolution and the Origin of Complex Phenotypes in the Age of Systems Biology. International Journal of Plant Sciences, 177, 305-318  https://doi.org/10.1086/686009
 
Waycott W, Fort S B, Ryder E J, Michelmore R W (1999): Mapping morphological genes relative to molecular markers in lettuce (Lactuca sativa L.). Heredity, 82, 245-251  https://doi.org/10.1038/sj.hdy.6884730
 
supplementary materialdownload PDF

© 2019 Czech Academy of Agricultural Sciences