Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth

Theoretical and Applied Genetics

Volumn 127, Issue 10, 2014, Pages 2159-2171

  Prashar, Ankush ^a   Hornyik, Csaba ^a   Young, Vanessa ^b   McLean, Karen ^a   Sharma, Sanjeev Kumar ^a   Dale, M Finlay B ^a,b   Bryan, Glenn J ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b Mylnefield Research Services   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PLANTS (BOTANY);

CENTROMERIC REGIONS; DIPLOID POTATOES; GENOME ASSEMBLY; GROWING SEASON; QUANTITATIVE TRAIT LOCUS; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS; TUBER EYE DEPTH; TUBER FORMATION;

CHROMOSOMES;

SOLANUM TUBEROSUM;

ANATOMY AND HISTOLOGY; CHROMOSOME MAP; DIPLOIDY; GENETIC LINKAGE; GENETICS; GENOTYPE; PLANT CHROMOSOME; PLANT GENOME; PLANT TUBER; POTATO; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DIPLOIDY; GENETIC LINKAGE; GENOME, PLANT; GENOTYPE; PLANT TUBERS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SOLANUM TUBEROSUM;

EID: 84919773613     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-014-2369-9     Document Type: Article

References (22)

1. 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
2. Bradshaw JE, Hackett CA, Lowe R, McLean K, Stewart HE, Tierney I, Vilaro MDR, Bryan GJ (2006) Detection of a quantitative trait locus for both foliage and tuber resistance to late blight Phytophthora infestans (Mont.) de Bary on chromosome 4 of a dihaploid potato clone (Solanum tuberosum subsp tuberosum). Theor Appl Genet 113:943–951
3. Bryan G, McLean K, Bradshaw J, De Jong W, Phillips M, Castelli L, Waugh R (2002) Mapping QTLs for resistance to the cyst nematode Globodera pallida derived from the wild potato species Solanum vernei. Theor Appl Genet 105:68–77
4. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7:e36347
5. Graham J, Hackett CA, Smith K, Woodhead M, MacKenzie K, Tierney I, Cooke D, Bayer M, Jennings N (2011) Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry. Theor Appl Genet 123:585–601
6. Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PloS One 8. doi:10.1371/journal.pone.0063939
7. Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genom 12:302
8. Kloosterman B, Abelenda JA, Carretero Gomez MdM, Oortwijn M, de Boer JM, Kowitwanich K, Horvath BM, van Eck HJ, Smaczniak C, Prat S, Visser RGF, Bachem CWB (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495:246–250
9. Li XQ, De Jong H, De Jong DM, De Jong WS (2005) Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes. Theor Appl Genet 110:1068–1073
10. Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2001) Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157:1369–1385
11. Maris B (1966) The modifiability of characters important in potato breeding. Euphytica 15:18–31
12. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197
13. Rezvoy C, Charif D, Gueguen L, Marais GAB (2007) MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 23:2188–2189
14. Sharma SK, Bolser D, de Boer J, Sonderkaer M, Amoros W, Carboni MF, D’Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejia N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RGF, Bachem CWB, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JME, Milbourne D, Martin DMA, Bryan GJ (2013) Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3-genes genomes. Genetics 3:2031–2047
15. Sliwka J, Wasilewicz-Flis I, Jakuczun H, Gebhardt C (2008) Tagging quantitative trait loci for dormancy, tuber shape, regularity of tuber shape, eye depth and flesh colour in diploid potato originated from six Solanum species. Plant Breeding 127:49–55
16. Uitdewilligen JGAML, Wolters A-MA, D’Hoop BB, Borm TJA, Visser RGF, van Eck HJ (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8(5):e62355
17. van Eck HJ (2007) Genetics of morphological and tuber traits. In: Vreugdenhil D (ed) Potato biology and biotechnology: advances and perspectives. Elsevier, Amsterdam, pp 91–115
18. van Eck HJ, Jacobs JME, Stam P, Ton J, Stiekema WJ, Jacobsen E (1994) Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs. Genetics 137:303
19. Van Ooijen JW (2006) JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands
20. Van Ooijen JW (2009) MapQTL 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, Wageningen, Netherlands
21. van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort J, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087
22. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468