Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm

Abstract

Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A. comosus accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. ‘Cayenne’, ‘Spanish’, ‘Queen’) was not well supported by the present study. These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

References

[1] Food and Agriculture Organization of the United Nations. Statistical databases. United Nations: FAO, 2014. Available at http://faostat.fao.org/site/567/DesktopDefault.aspx?PageID=567#ancor (accessed December 31, 2014).

[2] Baker KF, Collins JL . Notes on the distribution and ecology of Ananas and Pseudananas in South America. Am J Bot 1939; 26: 697-702.

[3] Pearsall DM . The origins of plant cultivation in South America. In: Cowan CW, Watson PJ, editors. The Origins of Agriculture: An International Perspective. Washington, DC: Smithsonian Institution Press; 1992, pp 173-205.

[4] Bartholomew DP, Paull RE, Rohrbach KG (eds). The Pineapple: Botany, Production and Uses. Wallingford: CABI Publishing; 2003.

[5] Purseglove JW . Tropical Crops. Monocotyledons. London: Longman; 1972. pp 75-91.

[6] Loison-Cabot C . Origin, phylogeny and evolution of pineapple species. Fruits 1992; 47: 25-32.

[7] Coppens d’Eeckenbrugge G, Leal F . “ Chapter 2: Morphology, Anatomy, and Taxonomy”. In: Bartholomew DP, Paull RE, Rohrbach KG, editors. The Pineapple: Botany, Production, and Uses. Wallingford: CABI Publishing; 2003. pp 13-32.

[8] Coppens d’Eeckenbrugge G, Sanewski GM, Smith MK et al. Ananas. In: Kole C editor. Wild Crop Relatives: Genomic and Breeding Resources, Tropical and Subtropical Fruits. Berlin and Heidelberg: Springer-Verlag; 2011, pp 21-41.

[9] Morrison SE . Journals and Other Documents of the Life and Voyages of Christopher Columbus. New York: Heritage Press; 1973.

[10] Collins JL . The Pineapple, Botany, Utilisation, Cultivation. London: Leonard Hill Ltd; 1960. p294.

[11] Bartholomew DP, Hawkins RA, Lopez JA . Hawaii pineapple: the rise and fall of an industry. HortScience 2012; 47: 1390-1398.

[12] Hidayat T, Abdullah FI, Kuppusamy C, Samad AA, Wagiran A . Molecular identification of Malaysian pineapple cultivar based on internal transcribed spacer region. APCBEE Procedia 2012; 4: 146-151.

[13] Sripaoraya S, Marchant R, Power JB, Davey MR . Herbicide-tolerant transgenic pineapple (Ananas comosus) produced by microprojectile bombardment. Ann Bot 2001; 88: 597-603.

[14] Zhang J, Liu J, Ming R . Genomic analyses of the CAM plant pineapple. J Exp Bot 2014; 65: 3395-3404.

[15] Aradhya MK, Zee F, Manshart RM . Isozyme variation in cultivated and wild pineapple. Euphytica 1994; 79: 87-99.

[16] Noyer JL, Lanaud C, Duval MF, Coppens G . RFLP study on rDNA variability in Ananas genus. Acta Hort 1997; 425: 153-160.

[17] Duval MF, Noyer JL, Perrier X, Coppens d’Eeckenbrugge G, Hamon P . Molecular diversity in pineapple assessed by RFLP markers. Theor Appl Genet 2001; 1: 83-90.

[18] Duval MF, Buso GSC, Ferreira FR et al. Relationships in Ananas and other related genera using chloroplast DNA restriction site variation. Genome 2003; 46: 990-1004.

[19] Popluechai S, Onto S, Eungwanichayapant PD . Relationships between some Thai cultivars of pineapple (Ananas comosus) revealed by RAPD analysis. Songklanakarin J Sci Technol 2007; 29: 1491-1497.

[20] Kato CY, Nagai C, Moore PH et al. Intra-specific DNA polymorphism in pineapple (Ananas comosus (L.) Merr.) assessed by AFLP markers. Genet Resour Crop Evol 2005; 51: 815-825.

[21] Wöhrmann T, Weising K . In silico mining for simple sequence repeat loci in a pineapple expressed sequence tag database and cross-species amplification of EST-SSR markers across Bromeliaceae. Theor Appl Genet 2011; 123: 635-647.

[22] Shoda M, Urasaki N, Sakiyama S et al. DNA profiling of pineapple cultivars in Japan discriminated by SSR markers. Breeding Sci 2012; 62: 352-359.

[23] Feng S, Tong H, Chen Y et al. Development of pineapple microsatellite markers and germplasm genetic diversity analysis. BioMed Res Int 2013; 2013: 11.

[24] Ji K, Zhang D, Motilal LA, Boccara M, Lachenaud P, Meinhardt LW . Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers. Genet Resour Crop Evol 2013; 60: 441-453.

[25] Cabezas JA, Ibáñez J, Lijavetzky D et al. A 48 SNP set for grapevine cultivar identification. BMC Plant Biol 2011; 11: 153.

[26] Wu GA, Prochnik S, Jenkins J et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnol 2014; 32: 656-662.

[27] Ge AJ, Han J, Li XD et al. Characterization of SNPs in strawberry cultivars in China. Genet Mol Res 2013; 12: 639-645.

[28] Koia JH, Moyle R, Botella JR . Microarray analysis of gene expression profiles in ripening pineapple fruits. BMC Plant Biol 2012; 12: 240.

[29] Moyle R, Fairbairn DJ, Ripi J et al. Developing pineapple fruit has a small transcriptome dominated by metallothionein. J Exp Bot 2005; 56: 101-112.

[30] Neuteboom LW, Kunimitsua WY, Webb D, Christopher DA . Characterization and tissue-regulated expression of genes involved in pineapple (Ananas comosus L.) root development. Plant Sci 2002; 5: 1021-1035.

[31] Ong WD, Voo L-YC, Kumar VS . De Novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing. PLoS One 2012; 7: e46937.

[32] Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA . QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 2006; 7: 438.

[33] Zhang HN, Wei YZ, Shen JY et al. Transcriptomic analysis of floral initiation in litchi (Litchi chinensis Sonn.) based on de novo RNA sequencing. Plant Cell Rep 2014; 33: 1723-1735.

[34] Platel RK, Jain M . NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 2012; 7: e30619.

[35] Wang J, Lin M, Crenshaw A et al. High-throughput single nucleotide polymorphism genotyping using nanofluidic dynamic arrays. BMC Genomics 2009; 10: 561.

[36] Fluidigm. Fluidigm SNP Genotyping User Guide Rev H1, PN 68000098. South San Francisco, CA: Fluidigm Corporation; 2011.

[37] Peakall R, Smouse PE . Genalex 6: Genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 2006; 6: 288-295.

[38] Peakall R. Smouse PE. GenAlEx 6.5: Genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics 2012; 8: 2537-2539.

[39] Dieringer D, Schlötterer C . Microsatellite analyser (MSA): A platform independent analysis tool for large microsatellite datasets. Mol Ecol Notes 2003; 3: 167-169.

[40] Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406-425.

[41] Felsenstein J. PHYLIP-phylogeny inference package (version 3.2). Cladistics 1989; 5: 164-166.

[42] Letunic I, Bork P . Interactive tree of life v2: Online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 2011; 39: W478- W478.

[43] Pritchard JK, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics 2000; 155: 945-959.

[44] Earl DA, vonHoldt BM . Structure Harvester: website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 2012; 4: 359-361.

[45] Marshall TC, Slate J, Kruuk LEB, Pemberton JM . Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 1998; 7: 639-655.

[46] Kalinowski ST, Taper ML, Marshall TC . Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 2007; 16: 1099-1106.

[47] Huang X, Madan A . CAP3: A DNA sequence assembly program. Genome Res 1999; 9: 868-877.

[48] Noyer JL . Preliminary study of genetic diversity of the genus Ananas by RFLP. Fruits (France) 1991; 46: 372-375.

[49] Irish BM, Cuevas HE, Simpson SA et al. Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS national plant germplasm system collection. Crop Sci 2014; 54: 2140-2151.

[50] Zerega N, Wiesner-Hanks T, Ragone D et al. Diversity in the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm. Tree Genet Genomes 2015; 11: 4.

[51] Gross BL, Volk GM, Richards C . Identification of “Duplicate” accessions within the USDA-ARS national plant germplasm system Malus collection. JASHS 2012; 5: 333-342.

[52] Marchant CJ . Chromosome evolution in the Bromeliaceae. Kew Bulletin 1967; 21: 161-168.

[53] Brown GK, Palací CA, Luther HE . Chromosome numbers in Bromeliaceae. Am J Bot 1997; 76: 85-88.

[54] Leal F, Soule J . Maipure, a new spineless group of pineapple cultivars. HortScience 1977; 12: 393-403.

[55] Wee YC, Thongtham MLC . Ananas comosus (L.) Merr. In: Verheij EWM, Coronel RE, editors. Plant Resources of South-East Asia No. 2 Edible Fruits and Nuts. Wageningen: The Netherlands, Pudoc; 1991. pp66- 71.

[56] Coppens d’Eeckenbrugge G, Leal F, Duval MF . Germplasm resources of pineapple. Hort Rev 1997; 21: 133-175.

[57] Clement CR, Cristo-Araújo MD, Coppens D’Eeckenbrugge G, Pereira AA, Picanço-Rodrigues D . Origin and domestication of native amazonian crops. Diversity 2010; 2: 72-106.