To facilitate genome-guided breeding in potato, we developed an 8303 Single Nucleotide Polymorphism (SNP) marker array using potato genome and transcriptome resources. To validate the Infinium 8303 Potato Array, we developed linkage maps from two diploid populations (DRH and D84) and compared these maps with the assembled potato genome sequence. Both populations used the doubled monoploid reference genotype DM1-3 516 R44 as the female parent but had different heterozygous diploid male parents (RH89-039-16 and 84SD22). Over 4,400 markers were mapped (1,960 in DRH and 2,454 in D84, 787 in common) resulting in map sizes of 965 (DRH) and 792 (D84) cM, covering 87% (DRH) and 88% (D84) of genome sequence length. Of the mapped markers, 33.5% were in candidate genes selected for the array, 4.5% were markers from existing genetic maps, and 61% were selected based on distribution across the genome. Markers with distorted segregation ratios occurred in blocks in both linkage maps, accounting for 4% (DRH) and 9% (D84) of mapped markers. Markers with distorted segregation ratios were unique to each population with blocks on chromosomes 9 and 12 in DRH and 3, 4, 6 and 8 in D84. Chromosome assignment of markers based on linkage mapping differed from sequence alignment with the Potato Genome Sequencing Consortium (PGSC) pseudomolecules for 1% of the mapped markers with some disconcordant markers attributable to paralogs. In total, 126 (DRH) and 226 (D84) mapped markers were not anchored to the pseudomolecules and provide new scaffold anchoring data to improve the potato genome assembly. The high degree of concordance between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the Infinium 8303 Potato Array. The broad genome coverage of the Infinium 8303 Potato Array compared to other marker sets will enable numerous downstream applications.
References
[1]
FAOSTAT (2007) Available: http://faostat.fao.org/site/339/default.？aspx via the Internet. Accessed 31 May 2010.
[2]
Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120: 1095–1103.
[3]
Gebhardt C, Ritter R, Barone A, Debener T, Walkemeier B, et al. (1991) RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor Appl Genet 83: 49–57.
[4]
Jacobs JME, Van Eck HJ, Arens P, Verkerk-Bakker B, te Lintel Hekkert B, et al. (1995) A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theor Appl Genet 91: 289–300.
[5]
Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, et al. (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genome-wide physical map. Genetics 173: 1075–1087.
[6]
Caromel B, Mugniéry D, Lefebvre V, Andrzejewski S, Ellissèche D, et al. (2003) Mapping QTLs for resistance against Globodera pallida (Stone) Pa2/3 in a diploid potato progeny originating from Solanum spegazzinii. Theor Appl Genet 106: 1517–1523.
[7]
Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, et al. (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259: 233–245.
[8]
Anithakumari AM, Tang J, van Eck HJ, Visser RGF, Leunissen JAM, et al. (2010) A pipeline for high throughput detection and mapping of SNPs from EST databases. Mol. Breeding 26: 65–75.
[9]
Ching A, Caldwell K, Jung M, Dolan M, Smith O, et al. (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19.
[10]
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, et al. (2003) Single-nucleotide polymorphisms in soybean. Genetics 163: 1123–1134.
[11]
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, et al. (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135: 1198–1205.
[12]
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793–800.
[13]
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–1115.
[14]
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183.
[15]
Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 186–195.
[16]
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, et al. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci 106: 12273–12278.
[17]
Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, et al. (2009) A first-generation haplotype map of maize. Science 326: 1115–1117.
[18]
Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, et al. (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12: 302.
[19]
Solanaceae Cooperative Agricultural Project (2011) Available: http://solcap.msu.edu/ via the Internet. Accessed 11 Nov 2011.
[20]
Paz MM, Veilleux RE (1999) Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breed 118: 53–57.
[21]
Douches DS, Quiros CF (1988) Genetic recombination in a diploid synaptic mutant and a Solanum tuberosum×S. chacoense diploid hybrid. Heredity 60: 183–191.
[22]
Rouppe vander Voort JNAM, van Zandvoort P, van Eck HJ, Folkertsma RT, Hutten RCB, et al. (1997) Use of allele specificity of co-migrating AFLP markers to align genetic maps from different potato genotypes. Mol Gen Genet 255: 428–447.
[23]
Veilleux RE, Miller AR (1998) Hybrid breakdown in the F1, between Solanum chacoense and S. phureja and gene transfer for leptine biosynthesis. J Amer Soc Hort Sci 123: 854–858.
[24]
Birhman RK, Laublin G, Cappadocia M (1994) Inheritance of a lethal yellow-cotyledon seedling mutant in Solanum chacoense Bitt. J Hered 85: 241–242.
[25]
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genet 43: 476–481.
[26]
JoinMap4 (2006) Available: http://www.kyazma.nl/index.php/mc.JoinMa？p via the Internet. Accessed 11 Nov 2011.
[27]
Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
[28]
Rezvoy CM, Charif D, Guéguen L, Marais GAB (2007) MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 23: 2188–2189.
