Abstract
Parentage assessment in the potato (Solanum tuberosum L.), based on a reliable characterization of DNA varieties, can be a useful tool in validating pedigree information as well as for assigning potential parents to orphan varieties. The approach suggested in this study was to use the genetic profiles obtained on 577 cultivars using a set of 17 polymorphic simple sequence repeats (SSR) markers in conjunction with the pedigree information provided by either the literature or the breeders to set up reliable parentage methods. Kinship testing based on the simple exclusion method was developed with cultivated potatoes for which the genetic data of both parents was available in our database and proved to be hopeful in validating pedigree information. To determine parental assignment, two inferential methods, the maximum likelihood (LOD) and the genetic distance ranking (GDR), were set up and compared in order to highlight which one offered the most likely candidate parent to a chosen variety. Inferential analysis results revealed that the “alleged parent” had a higher probability of being ranked first using the LOD method. Finally, we discussed the relevance of this new original approach, particularly in relation to instances where the pedigree is either in doubt or lacking information for the cultivars.
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Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux RE (2001) Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome 44:50–62
Ashley MV (2010) Plant parentage, pollination, and dispersal: how DNA microsatellites have altered the landscape. Crit Rev Plant Sci 29:148–161. doi:10.1080/07352689.2010.481167
Ashley MV, Dow BD (1994) The use of microsatellite analysis in population biology: background, methods and potential applications. In: Schierwater B, Streit B, Wagner GP, DeSalle R (eds) Molecular ecology and evolution: approaches and applications. Experientia Supplementum, Birkhäuser Basel, pp 185–201. doi:10.1007/978-3-0348-7527-1_10
Baldwin SJ, Dodds KG, Auvray B, Genet RA, Macknight RC, Jacobs JME (2011) Association mapping of cold-induced sweetening in potato using historical phenotypic data. Ann Appl Biol 158:248–256. doi:10.1111/j.1744-7348.2011.00459.x
Berloo R, Hutten RCB, Eck HJ, Visser RGF (2007) An online potato pedigree database resource. Potato Res 50:45–57. doi:10.1007/s11540-007-9028-3
Bink M, Uimari P, Sillanpaa J, Janss G, Jansen C (2002) Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor Appl Genet 104:751–762. doi:10.1007/s00122-001-0796-x
Bradshaw JE, Hackett CA, Meyer RC, Milbourne D, McNicol JW, Phillips MS, Waugh R (1998) Identification of AFLP and SSR markers associated with quantitative resistance to Globodera pallida (Stone) in tetraploid potato (Solanum tuberosum subsp. tuberosum) with a view to marker-assisted selection. Theor Appl Genet 97:202–210. doi:10.1007/s001220050886
Braun A, Wenzel G (2004) Molecular analysis of genetic variation in potato (Solanum tuberosum L.). I. German cultivars and advanced clones. Potato Res 47:81–92. doi:10.1007/BF02731971
Broyles B, Wyatt R (1991) Effective pollen dispersal in a natural population of Asclepias exaltata: the influence of pollinator behavior, genetic similarity, and mating success. Am Nat 138:1239–1249. doi:10.1086/285280
Buteler MI, Labonte DR, Macchiavelli RE (1997) Determining paternity in polyploids: hexaploid simulation studies. Euphytica 96:353–361. doi:10.1023/A:1003096429238
Chakraborty R, Stivers DN (1996) Paternity exclusion by DNA markers: effects of paternal mutations. J Forensic Sci 41:671–677
Chakraborty R, Stivers DN, Zhong Y (1996) Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci. Mutat Res 354:41–48. doi:10.1016/0027-5107(96)00014-0
Côté MJ, Leduc L, Reid A (2013) Evaluation of simple sequence repeat (SSR) markers established in Europe as a method for the identification of potato varieties grown in Canada. Am Pot J 90:340–350. doi:10.1007/s12230-013-9310-7
Demeke T, Lynch DR, Kawchuk LM, Kozub GC, Armstrong JD (1996) Genetic diversity of potato determined by random amplified polymorphic DNA analysis. Plant Cell Rep 15:662–667. doi:10.1007/BF00231920
Devlin B, Roeder K, Ellstrand NC (1988) Fractional paternity assignment: theoretical development and comparison to other methods. Theor Appl Genet 76:369–380. doi:10.1007/BF00265336
D’hoop BB, Paulo MJ, Kowitwanich K, Sengers M, Visser RGF, Van Eck HJ, van Eeuwijk FA (2010) Population structure and linkage disequilibrium unravelled in tetraploid potato. Theor Appl Genet 121:1151–1170. doi:10.1007/s00122-010-1379-5
Double MC, Cockburn A, Barry SC, Smouse PE (1997) Exclusion probabilities for single-locus paternity analysis when related males compete for matings. Mol Ecol 6:1155–1166. doi:10.1046/j.1365-294X.1997.00291.x
Dow B, Ashley M (1996) Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Mol Ecol 5:615–627. doi:10.1111/j.1365-294X.1996.tb00357.x
Ellstrand NC (1984) Multiple paternity within the fruits of the wild radish, Raphanus sativus. Am Nat 123:819–828. doi:10.1086/284241
Ellstrand NC, Devlin B, Marshall DL (1989) Gene flow by pollen into small populations: data from experimental and natural stands of wild radish. Proc Natl Acad Sci U S A 86:9044–9047. doi:10.1073/pnas.86.22.9044
Esselink GD, Nybom H, Vosman B (2004) Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method. Theor Appl Genet 109:402–408. doi:10.1007/s00122-004-1645-5
Feingold S, Lloyd J, Norero N, Bonierbale M, Lorenzen J (2005) Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet 111:456–466. doi:10.1007/s00122-005-2028-2
Ge J, Eisenberg A, Yan J, Chakraborty R, Budowle B (2011) Pedigree likelihood ratio for lineage markers. Int J Legal Med 125:519–525. doi:10.1007/s00414-010-0514-9
Gerber S, Mariette S, Streiff R, Bodenes C, Kremer A (2000) Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis. Mol Ecol 9:1037–1048. doi:10.1046/j.1365-294x.2000.00961.x
Ghislain M, Spooner DM, Rodriguez F, Villamon F, Nunez J, Vasquez C, Waugh R, Bonierbale M (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108:881–890. doi:10.1007/s00122-003-1494-7
Ghislain M, Nunez J, Ma RH, Pignataro J, Guzman F, Bonierbale M, Spooner D (2009) Robust and highly informative microsatellite-based genetic identity kit for potato. Mol Breed 23:377–388. doi:10.1007/s11032-008-9240-0
Grattapaglia D, Ribeiro VJ, Rezende GD (2004) Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus. Theor Appl Genet 109:192–199. doi:10.1007/s00122-004-1617-9
Gunn PR, Trueman K, Stapleton P, Klarkowski DB (1997) DNA analysis in disputed parentage: the occurrence of two apparently false exclusions of paternity, both at short tandem repeat (STR) loci, in the one child. Electrophoresis 18:1650–1652. doi:10.1002/elps.1150180930
Hackett CA, Luo ZW (2003) TetraploidMap: construction of linkage map in a Autotetraploid Species. J Hered 94:358–359. doi:10.1093/jhered/esg066
Hamrick JL, Schnabel A (1985) Understanding the genetic structure of plant populations: some old problems and a new approach. In: Gregorius HR (ed) Population genetics in forestry. Lecture notes in biomathematics. Springer, Berlin, pp 50–70. doi:10.1007/978-3-642-48125-3_4
Haynes KG, Douches DS (1993) Estimation of the coefficient of double reduction in the cultivated tetraploid potato. Theor Appl Genet 85:857–862. doi:10.1007/BF00225029
Hosaka K, Mori M, Ogawa K (1994) Genetic relationships of Japanese potato cultivars assessed by RAPD analysis. Am Pot J 71:535–546. doi:10.1007/BF02851325
Isenegger DA, Taylor PWJ, Ford R, Franz P, McGregor GR, Hutchinson JF (2001) DNA fingerprinting and genetic relationships of potato cultivars (Solanum tuberosum L.) commercially grown in Australia. Aust J Agric Res 52:911–918. doi:10.1071/AR00161
Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 44:223–270. doi:10.5169/seals-268384
Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Mol Ecol 12:2511–2523. doi:10.1046/j.1365-294X.2003.01928.x
Junge A, Brinkmann B, Fimmers R, Madea B (2006) Mutations or exclusion: an unusual case in paternity testing. Int J Legal Med 120:360–363. doi:10.1007/s00414-005-0045-y
Karaagac E, Yilma S, Cuesta-Marcos A, Vales MI (2014) Evaluation of simple sequence repeat (SSR) markers established in Europe as a method for the identification of potato varieties grown in Canada. Am Pot J 91:195–203. doi:10.1007/s12230-013-9338-8
Kawchuk LM, Lynch DR, Thomas J, Penner B, Sillito D, Kulcsar F (1996) Characterization of Solanum tuberosum simple sequence repeats and application to potato culiwar identification. Am Pot J 73:325–335. doi:10.1007/BF02849164
Krauss SL (1994) Restricted gene flow within the morphologically complex species Persoonia mollis (Proteaceae): contrasting evidence from the mating system and pollen dispersal. Heredity 73:142–154. doi:10.1038/hdy.1994.113
Lewis P, Snow A (1992) Deterministic paternity exclusion using RAPD markers. Mol Ecol 1:155–160. doi:10.1111/j.1365-294X.1992.tb00171.x
Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465. doi:10.1046/j.1365-294X.2002.01643.x
Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2000) Predicting parental genotypes and gene segregation for tetrasomic inheritance. Theor Appl Genet 100:1067–1073. doi:10.1007/s001220051388
Malosetti M, van der Linden CG, Vosman B, van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175:879–889. doi:10.1534/genetics.105.054932
Marshall TC, Slate J, Kruuk LE, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655. doi:10.1046/j.1365-294x.1998.00374.x
Mather K (1936) Segregation and linkage in autotetraploids. J Genetics 32:287–314. doi:10.1007/BF02982683
McGregor CE, Lambert CA, Greyling MM, Louw JH, Warnich L (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144. doi:10.1023/A:1003925620546
Meagher TR (1986) Analysis of paternity within a natural population of Chamaelirium luteum. 1. Identification of most-likely male parents. Am Nat 128:199–215. doi:10.1086/284554
Meagher T, Thompson E (1986) The relationship between single parent and parent pair genetic likelihoods in genealogy reconstruction. Theor Popul Biol 29:87–106. doi:10.1016/0040-5809(86)90006-7
Milbourne D, Meyer R, Bradshaw J, Baird E, Bonar N, Provan J, Powell W, Waugh R (1997) Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136. doi:10.1023/A:1009633005390
Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245. doi:10.1007/s004380050809
Milligan B, McMurry C (1993) Dominant vs. codominant genetic markers in the estimation of male mating success. Mol Ecol 2:275–283. doi:10.1111/j.1365-294X.1993.tb00020.x
Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci 43:1235–1248. doi:10.2135/cropsci2003.1235
Moisan-Thiery M, Marhadour S, Kerlan MC, Dessenne N, Perramant M, Gokelaere T, Hingrat Y (2005) Potato cultivar identification using simple sequence repeats markers (SSR). Potato Res 48:191–200. doi:10.1007/BF02742376
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70:3321–3323. doi:10.1073/pnas.70.12.3321
Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273. doi:10.1073/pnas.76.10.5269
Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084. doi:10.1007/BF00224052
Reid A, Hof L, Esselink D, Vosman B (2009) Potato cultivar genome analysis. In: Burns R(ed) Humana Press, a part of Springer Science + Business Media, Totowa, NJ, New York, N.Y., pp 295–308. doi:10.1007/978-1-59745-062-1_23
Reid A, Hof L, Felix G, Rucker B, Tams S, Milczynska E, Esselink D, Uenk G, Vosman B, Weitz A (2011) Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU Common Catalogue. Euphytica 182:239–249. doi:10.1007/s10681-011-0462-6
Rios D, Ghislain M, Rodriguez F, Spooner DM (2007) What is the origin of the European potato? Evidence from Canary Island Landraces. Crop Sci 47:1271–1280. doi:10.2135/cropsci2006.05.0336
Rodzen JA, Famula TR, May B (2004) Estimation of parentage and relatedness in the polyploid white sturgeon (Acipenser transmontanus) using a dominant marker approach for duplicated microsatellite loci. Aquaculture 232:165–182. doi:10.1016/S0044-8486(03)00450-2
Schnabel A (1998) Parentage analysis in plants: mating systems, gene flow, and relative fertilities. In: Carvalho GR (ed) Advances in molecular ecology. Ios Press, The Netherlands, pp 173–189
Schneider K, Douches DS (1997) Assessment of PCR-based simple sequence repeats to fingerprint North American potato cultivars. Am Pot J 74:149–160. doi:10.1007/BF02851594
Simko I, Haynes KG, Jones RW (2004) Mining data from potato pedigrees: tracking the origin of susceptibility and resistance to Verticillium dahliae in North American cultivars through molecular marker analysis. Theor Appl Genet 108:225–230. doi:10.1007/s00122-003-1448-0
Slater AT, Wilson GM, Cogan NO, Forster JW, Hayes BJ (2014) Improving the analysis of low heritability complex traits for enhanced genetic gain in potato. Theor Appl Genet 127:809–820. doi:10.1007/s00122-013-2258-7
Smouse PE, Meagher TR (1994) Genetic analysis of male reproductive contributions in Chamaelirium luteum (L.) Gray (Liliaceae). Genetics 136:313–322
Snow AA, Lewis PO (1993) Reproductive traits and male fertility in plants: empirical approaches. Annu Rev Ecol Syst 24:331–351. doi:10.1146/annurev.es.24.110193.001555
Song YS, Hepting L, Schweizer G, Hartl L, Wenzel G, Schwarzfischer A (2005) Mapping of extreme resistance to PVY (Ry (sto)) on chromosome XII using anther-culture-derived primary dihaploid potato lines. Theor Appl Genet 111:879–887. doi:10.1007/s00122-005-0010-7
Sun G, Wang-Pruski G, Mayich M, Jong H (2003) RAPD and pedigree-based genetic diversity estimates in cultivated diploid potato hybrids. Theor Appl Genet 107:110–115. doi:10.1007/s00122-003-1215-2
Tarn TR, Tai GCC, De Long H, Murphy AM, Seabrook JEA (1992) Breeding potatoes for long-day, temperate climates. Plant breeding reviews. Wiley, New York, pp 217–332. doi:10.1002/9780470650363.ch8
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471. doi:10.1093/nar/17.16.6463
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138. doi:10.1093/nar/12.10.4127
Veilleux RE, Shen LY, Paz MM (1995) Analysis of the genetic composition of anther-derived potato by randomly amplified polymorphic DNA and simple sequence repeats. Genome 38:1153–1162. doi:10.1139/g95-153
Acknowledgments
We gratefully acknowledged Maarten Vossen (Agrico Research BV), Sjefke Allefs (Agrico Research BV), Maurice Schehr (HZPC Holland BV), Guus Heselmans (C. Meijer BV), Hervé van den Wyngaert (Binst Breeding Selection), Jens Kr. Ege Olsen (LKF Vandel, Danespo A/S), Sylvie Marhadour (FN3PT), Eric Bonnel (Germicopa SAS), Olivier Mahieu (CARAH asbl), and Peter Oldenkamp (KWS Potato BV) for providing the plant material and associated information used in the present study. This research was fully supported by the Haute Ecole Provinciale de Hainaut-CONDORCET, 17 Chemin du Champ de Mars, 7000 Mons, Wallonia, Belgium. The help of Jeromy Hrabovecky, Michel Van Koninckxloo, Cathy Jean, Kelly Hall, Jonathan Spanoghe, Juan Leopoldo Delitte, and Mickael Venard is kindly acknowledged.
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In this study, the maximum likelihood method was carried out according to the formulas used for the dominant markers described in Gerber et al. (2000), which have been successfully applied following polyploid model (Rodzen et al. 2004).
The LOD formulas were written in MATLAB V5 software (The Math Works Inc., Natick, MA, USA), as follows:
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Spanoghe, M., Marique, T., Rivière, J. et al. Investigation and Development of Potato Parentage Analysis Methods Using Multiplexed SSR Fingerprinting. Potato Res. 58, 43–65 (2015). https://doi.org/10.1007/s11540-014-9271-3
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DOI: https://doi.org/10.1007/s11540-014-9271-3