Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Peace, Cameron ^a   Bassil, Nahla ^b   Main, Dorrie ^a   Ficklin, Stephen ^a   Rosyara, Umesh R ^c   Stegmeir, Travis ^c   Sebolt, Audrey ^c   Gilmore, Barbara ^b   Lawley, Cindy ^d   Mockler, Todd C ^e   Bryant, Douglas W ^e,f   Wilhelm, Larry ^g   Iezzoni, Amy ^c  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b USDA ARS National Clonal Germplasm Repository   (United States)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d ILLUMINA INC   (United States)

^e DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^f Intuitive Genomics Inc   (United States)

^g OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BASE PAIRING; CONTROLLED STUDY; CROP; DIPLOIDY; DNA MICROARRAY; DNA SEQUENCE; FRUIT BREEDING; GENE DOSAGE; GENE FREQUENCY; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GERMPLASM; NONHUMAN; PLANT GENOME; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SOUR CHERRY; SWEET CHERRY; TETRAPLOIDY;

BREEDING; DATABASES, GENETIC; DIPLOIDY; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; PRUNUS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

PRUNUS AVIUM; PRUNUS CERASUS; PRUNUS PERSICA;

EID: 84871449264     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048305     Document Type: Article

References (35)

1. Olden EJ, Nybom N, (1968) On the origin of Prunus cerasus L. Hereditas 59: 327-345.
2. Tavaud M, Zanetto A, David JL, Laigret F, Dirlewanger E, (2004) Genetic relationships between diploid and allotetraploid cherry species (Prunus avium, Prunus × gondouinii and Prunus cerasus). Heredity 93: 631-638.
3. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, et al. (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci 101: 9891-9896.
4. Olmstead JW, Sebolt AM, Cabrera A, Sooriyapathirana SS, Hammar S, et al. (2008) Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genet Genomes 4: 897-910.
5. Clarke J, Sargent D, Bošković R, Belaj A, Tobutt K, (2009) A cherry map from the inter-specific cross Prunus avium 'Napoleon' × P. nipponica based on microsatellite, gene-specific and isoenzyme markers. Tree Genet Genomes 5: 41-51.
6. Cabrera A, Rosyara UR, de Franceschi P, Sebolt A, Sooriyapathirana SS, et al. (2012) Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map. Tree Genet Genomes 8: 237-247.
7. Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, et al. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7 (2):: e31745.
8. Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, et al. (2011) A large maize (Zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6 (12):: e28334.
9. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, et al. (2009) Genome wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106: 12273-12278.
10. 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.
11. Felcher K, Coombs J, Massa AN, Hansey C, Hamilton JP, et al. (2012) Integration of two diploid potato linkage maps with the potato physical map. PLoS ONE in press.
12. Akhunov E, Nicolet C, Dvorak J, (2009) Single nucleotide polymorphism genotyping in polyploidy wheat with the Illumina GoldenGate assay. Theor Appl Genet 119: 507-517.
13. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS ONE 7 (4):: e35668.
14. International Peach Genome Initiative, Peach Genome, Genome Database for Rosaceae website. Available: www.rosaceae.org/peach/genome. Accessed 2012 Jul 3.
15. Dirlewanger E, Claverie J, Wünsch A, Iezzoni AF (2007) Cherry. In: Kole, C, editor. Genome Mapping and Molecular Breeding in Plants. Fruits and Nuts. Springer-Verlag Berlin Heidelberg. pp. 103-118.
16. Iezzoni A, Weebadde C, Luby J, Yue CY, Peace CP, et al. (2010) RosBREED: Enabling marker-assisted breeding in Rosaceae. Acta Hortic 859: 389-394.
17. Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
18. Zhang G, Sebolt AM, Sooriyapathirana SS, Wang D, Bink MCAM, et al. (2010) Fruit size QTL analysis in an F1 population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry. Tree Genet Genomes 6: 25-36.
19. Illumina Inc. (2010a) GenomeStudio Genotyping module v1.0, User Guide. Illumina Inc., Towne Centre Drive, San Diego, CA, USA.
20. Illumina Inc. (2010b) Infinium® Genotyping Data Analysis: A guide for analyzing Infinium® genotyping data using the Illumina® GenomeStudio Genotyping Module. Illumina Inc., Towne Centre Drive, San Diego, CA, USA.
21. Illumina Inc. (2010c) Improved cluster generation with Gentrain2, Tech Note. Illumina Inc., Towne Centre Drive, San Diego, CA, USA.
22. Illumina Inc. (2006) "TOP/BOT" strand and "A/B" allele, Tech Note. Illumina Inc., 5200 Research Way, San Diego, CA, USA.
23. Illumina Inc. (2011) Calling polyploid genotypes with GenomeStudio software v2010.3/v1.8. Tech Note. Illumina Inc., Towne Centre Drive, San Diego, CA, USA.
24. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucl Acids Res 29: 308-311.
25. Jung S, Staton M, Lee T, Blenda A, Svancara R, et al. (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-1040.
26. Beaver JA, Iezzoni AF, Ramm CW, (1995) Isozyme diversity in sour, sweet, and ground cherry. Theor Appl Genet 90: 847-852.
27. Olmstead JW, Lang GA, Grove GG, (2001) Inheritance of powdery mildew resistance in sweet cherry. HortScience 36: 337-340.
28. Wharton PS, Iezzoni AF, Jones AL, (2003) Screening cherry germplasm for resistance to cherry leaf spot. Plant Disease 87: 471-477.
29. Klagges C, Campoy JA, Quero-García J, Guzmán A, Mansur L, et al. (2012) Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars. PLoS ONE (submitted).
30. Wen J, Berggren ST, Lee CH, Ickert-Bond S, Yi TS, et al. (2008) Phylogenetic inferences in Prunus (Rosaceae) using chloroplast ndhF and nuclear ribosomal ITS sequences. J Syst Evol 46: 322-332.
31. Bošković R, Tobutt KR, (2001) Genotyping cherry cultivars assigned to incompatibility groups by analysing stylar ribonucleases. Theor Appl Genet 103: 475-485.
32. Hauck NR, Ikeda K, Tao R, Iezzoni AF, (2006) The mutated S1-haplotype in sour cherry has an altered S-haplotype-specific F-Box protein gene. J Heredity 97: 514-520.
33. Tsukamoto T, Hauck NR, Tao R, Jiang N, Iezzoni AF, (2006) Molecular characterization of three non-functional S-haplotypes in sour cherry (Prunus cerasus). Plant Mol Biol 62: 371-383.
34. Tsukamoto T, Hauck NR, Tao R, Jiang J, Iezzoni AF, (2010) Molecular and genetic analysis of four non-functional S haplotype variants derived from a common ancestral S haplotype identified n sour cherry (Prunus cerasus L.). Genetics 184: 411-427.
35. Beaver J, Iezzoni AF, (1993) Allozyme inheritance in tetraploid sour cherry (Prunus cerasus L.). J Amer Soc Hort Sci 118: 873-877.