Abstract
Knowledge of genetic diversity and population structure in breeding material could be of great importance for crop improvement. Inheritance of molecular markers has been proved to be a powerful tool for verifying or discovering the parentage of cultivars in several crops. The present study aimed to undertake an extended parentage analysis using a large sample of garden asparagus (Asparagus officinalis L.) cultivars based on single nucleotide polymorphism (SNP) markers. In the past, asparagus cultivars began to be classified according to the countries and towns where they were grown. Among them, Violet Dutch is one of the oldest asparagus cultivars, considered to be the genetic stock from which several modern cultivars were derived. Starting from Violet Dutch, the breeding programs branched in two directions, yielding Argenteuil and Braunschweiger varieties in France and Germany, respectively. These lines became very important in all breeding programs, replacing older populations and landraces. This could account for the narrow genetic basis of cultivated asparagus, but in fact very few molecular marker studies have confirmed this hypothesis to date. In the present paper, using a new set of 144 SNPs, genetic relationships were investigated within an important collection of anther donor asparagus genotypes and a large panel of Italian double haploids (DHs) extensively used in the Italian and international breeding programs over the last 30 years. The results were useful for confirming the narrow variability of modern asparagus germplasm and for comparing the pedigree notes with genetic analyses. The results of this work showed that the DH collection includes two main and distinct genetic backgrounds, likely derived from Argenteuil and Braunschweiger genetic stocks, as expected. Moreover, the genetic analyses showed that the cv. Mary Washington, previously indicated as being derived only from Argenteuil, has a mixed origin from the two main genetic stocks. In addition, the present study underlines how this cultivar plays a central role in the pedigree of many modern cultivars/hybrids, giving new impact to the pedigree notes already described taking into account the large number of DHs derived from Mary Washington.
Similar content being viewed by others
References
Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507–517
Astrego JJ (1951) Rassen-, selectie- en hiermede samenhangende problemen bij de aspergeteelt. Meded Dir Tuinb 14:657–671
Bailey LH (1942) The standard cyclopedia of horticulture. Macmillan Publishing Co, New York, pp 406–407
Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48
Benson BL, Takatori FH (1978) Meet UC 157. Am Veg Grower 26(5):8–9
Bohne F (1977) Mannliche Spargelpflanzen in Anbau. Gemuse 13(7):216–220
Boonen P (1987) The breeding and choice of asparagus in the Netherlands. Asparagus Res Newslett 5(2):37–42
Caruso M, Federici CT, Roose ML (2008) EST–SSR markers for asparagus genetic diversity evaluation and cultivar identification. Mol Breed 21:195–204
Cassens I, Mardulyn P, Milinkovitch MC (2005) Evaluating intraspecific ‘network’ construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach. Syst Biol 54:363–372
Clifford HT, Conran JG (1987) 2. Asparagus, 3. Protasparagus, 4. Myrsiphyllum. In: George AS (ed) Flora of Australia. Australian Government Publishing Service, Canberra, pp 159–164
Corriols L, Doré C, Rameau C (1990) Commercial release in France of Andreas, the first asparagus all-male F1 hybrid. Acta Hort 271:249–252
Corriols-Thévenin L (1979) Different methods in asparagus breeding. In: Reuther G (ed) Proceeding of the 5th international asparagus symposium. Eucarpia, Geisenheim, pp 8–20
Delbreil B, Guerche P, Jullien M (1993) Agrobacterium-mediated transformation of Asparagus officinalis L. long-term embryogenic callus and regeneration of transgenic plants. Plant Cell Rep 12:129–132
Denis JB, Rameau C (1994) Interpretation of performance of hybrids obtained from 43 asparagus parent genotypes. Agronomie 14:229–237
Doré C (1974) Production de plantes homozygotes mâles et femelles à partir d’anthères d’asperge cultivées in vitro. C R Acad Sci 278:2135–2138
Ellison JH (1986) Asparagus breeding. In: Bassett MJ (ed) Breeding vegetable crops. AVI Publishing Co, Westport, pp 521–569
Ellison JH, Kinelski JJ (1986) Greenwich, a male asparagus hybrid. HortScience 21:1249
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Falavigna A, Casali PE, Battaglia A (1999) Achievement of asparagus breeding in Italy. Acta Hort 479:67–74
Gao H, Williamson S, Bustamante CD (2007) A Markov Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176(3):1635–1651
Geoffriau E, Denoue D, Rameau C (1992) Assessment of genetic variation among asparagus (Asparagus officinalis L.) populations and cultivars: agromorphological and isozymic data. Euphytica 61:169–179
Greiner HD (1990) Asparagus breeding at the “Südwestdeutsche Saatzucht, Dr. Späth”, W. Germany. Acta Hort 271:63–67
Hamilton JP, Sim S, Stoffel K, Van Deynze A, Buell CR et al (2012) Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome 5:17–29. doi:10.3835/plantgenome2011.12.0033
Hanna GC (1952) Asparagus plant breeding. Calif Agric 6:6
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10:R32
Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KFX, Bauer E (2011) From RNA-seq to large-scale genotyping—genomics resources for rye (Secale cereale L.). BMC Plant Biol 11:131
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806
Jiang C, Sink KC (1997) RAPD and SCAR markers linked to the sex expression locus M in asparagus. Euphytica 94:329–333
Jiang C, Lewis ME, Sink KC (1997) Combined RAPD and RFLP molecular linkage map of asparagus. Genome 40(1):69–76
Kanno A, Kubota S, Ishino K (2014) Conversion of a male-specific RAPD marker into an STS marker in Asparagus officinalis L. Euphytica 197:39–46
Khandka DK, Nejidat A, Golan-Goldhirsh A (1996) Polymorphism and DNA markers for asparagus cultivars identified by random amplified polymorphic DNA. Euphytica 887:39–44
Kidner AW (1947) Asparagus. Faber and Faber Ltd, London, p 168
Knaflewski M (1996) Genealogy of asparagus cultivars. Acta Hort 415:87–91
Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer KA (2003) Graner, Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 270:24–33
Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118:979–992
Lužný J (1979) The history of asparagus as a vegetable, the tradition of its growing in Czechoslovakia (CSSR) and the prospect of its further propagation and breeding. In: Reuther G (ed) Proceedings of the 5th international asparagus symposium. Eucarpia, Geisenheimpp, pp 82–86
Marks GE (1979) Hermaphrodites, do they have a role in asparagus breeding. In: Reuther G (ed) Proceedings of the 5th international asparagus symposium. Eucarpia, Geisenheim, pp 39–41
Mercati F, Riccardi P, Leebens-Mack J, Abenavoli MR, Falavigna A, Sunseri F (2013) Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.). Plant Sci 203–204:115–123
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
Nakayama H, Ito T, Hayashi Y, Sonoda T, Fukuda T, Ochiai T, Kameya T, Kanno A (2006) Development of sex-linked primers in garden asparagus (Asparagus officinalis L.). Breed Sci 56(499):327–330
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539
Polzin T, Daneschmand SV (2003) On Steiner trees and minimum spanning trees in hypergraphs. Oper Res Lett 31:12–20
Pritchard JK, Wen W (2003) Documentation for structure software: version 2. http://pritch.bsd.uchicago.edu. Accessed 5 Sept 2012
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Qiao Y, Falavigna A (1990) An improved in vitro anther culture method for obtaining doubled-haploid clones of asparagus. Acta Hort 271:145–150
Qiu F, Guo L, Wen TJ, Liu F, Ashlock DA, Schnable PS (2003) DNA sequence-based bar codes for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources. Plant Physiol 133:475–481
Reamon-Büttner SM, Jung C (2000) AFLP-derived STS markers for the identification of sex in Asparagus officinalis L. Theor Appl Genet 100:432–438
Reuther G (1984) Asparagus. In: Sharp WR, Evans DA, Amminato PV, Yamada Y (eds) Handbook of plant cell culture, vol 2. Macmillan Publishing Co, New York, pp 211–242
Riccardi P, Casali PE, Mercati F, Falavigna A, Sunseri F (2011) Genetic characterization of asparagus doubled haploids collection and wild relatives. Sci Hort 130:691–700
Riccardi P, Leebens-Mack J, Cifarelli R, Falavigna A, Sunseri F (2012) EST libraries development in Asparagus officinalis for SNPs discovery. Acta Hort (ISHS) 950:127–132
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Scholten CTJ, Boonen PHG (1996) Asparagus breeding in the Netherlands. Acta Hort 415:67–70
Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7:e40563
Skiebe K, Stein M, Gottwald J, Wolterstorff B (1991) Breeding of polyploid asparagus (Asparagus officinalis L.). Plant Breed 106:99–106
Sneep J (1953) The significance of andromonoecy for the breeding of Asparagus officinalis L. Euphytica 2:89–95
Spada A, Caporali E, Marziani G, Portaluppi P, Restivo FM, Tassi F, Falavigna A (1998) A genetic map of Asparagus officinalis based on integrated RFLP, RAPD and AFLP molecular markers. Theor Appl Genet 97:1083–1089
Stajner N, Bohanec B, Javornik B (2002) Genetic variability of economically important asparagus species as revealed by genome size analysis and rDNA ITS polymorphisms. Plant Sci 162:931–937
Sturtevant EL (1980) History of garden vegetables. Am Nat 24:719–744
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolution art distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Telgmann-Rauber A, Jamsari A, Kinney MS, Pires JC, Jung C (2007) Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus. Mol Genet Genomics 278:221–234
Thévenin L (1967) Les problèmes d’amélioration chez Asparagus officinalis L. I. Biologie et amélioration. Ann Amélior Plantes 17:33–66
Thévenin L, Doré C (1976) L’amelioration de l’asperge et son atout majeur, la culture in vitro. Ann Amélior Plantes 26:655–674
Van Den Broek JH, Boonen PH (1990) Today’s asparagus breeding in the Netherlands. Acta Hort 271:33–338
Author information
Authors and Affiliations
Corresponding author
Additional information
Francesco Mercati and Paolo Riccardi contributed equally to this study and should be considered co-first authors.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Mercati, F., Riccardi, P., Harkess, A. et al. Single nucleotide polymorphism-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification. Mol Breeding 35, 59 (2015). https://doi.org/10.1007/s11032-015-0217-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11032-015-0217-5