Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Bianco, Luca ^a   Cestaro, Alessandro ^a   Sargent, Daniel James ^a   Banchi, Elisa ^a   Derdak, Sophia ^b   Di Guardo, Mario ^a,c   Salvi, Silvio ^d   Jansen, Johannes ^c   Viola, Roberto ^a   Gut, Ivo ^b   Laurens, Francois ^e   Chagné, David ^f   Velasco, Riccardo ^a   Van De Weg, Eric ^c   Troggio, Michela ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b Parc Cientific de Barcelona   (Spain)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d UNIVERSITY OF BOLOGNA   (Italy)

^e Universite d'Angers   (France)

^f THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANALYZER; ARTICLE; BREEDING METHOD; CONSENSUS; CONTROLLED STUDY; CULTIVAR; GENE MAPPING; GENE SEQUENCE; GENETIC MARKER; GENETIC PROCEDURES; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; MALUS; MALUS DOMESTICA; MALUS MICROMALUS; NONHUMAN; PARALOGY; PEDIGREE; PHYSICAL CHEMISTRY; PLANT CHROMOSOME; PLANT GENOME; PREDICTION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY; BIOLOGY; GENETIC ASSOCIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; REPRODUCIBILITY;

MALUS X DOMESTICA;

GENETIC MARKER;

COMPUTATIONAL BIOLOGY; GENETIC MARKERS; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALUS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 84907815005     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0110377     Document Type: Article

References (47)

1. Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, et al. (2008) Multiple models for Rosaceae genomics. Plant Physiol 47(3): 985-1003.
2. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, et al. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42(10): 833-839.
3. Chagne 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.
4. Montanari S, Saeed M, Knaebel M, Kim Y, Troggio M, et al (2013) Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids. PLoS One 8(10): e77022.
5. Antanaviciute L, Fernandez-Fernandez F, Jansen J, Banchi E, Evans KM, et al. (2012): Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genomics 13: 203.
6. Troggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, et al. (2013) Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin. PLoS One 8(6): e67407.
7. Clark MD, Schmitz CA, Rosyara UR, Luby JJ, Bradeen JM (2014) A consensus'Honeycrisp' apple (Malus 6 domestica) genetic linkage map from three full-sib progeny populations. Tree Genet Genomes DOI 10.1007/s11295-014-0709-1.
8. Kumar S, Garrick DJ, Bink MCAM, Whitworth C, Chagne D, Volz RK (2013) Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14: 393.
9. Kumar S, Chagne D, Bink MCAM, Volz RK, Whitworth C, et al. (2012) Genomic Selection for Fruit Quality Traits in Apple (Malus x domestica Borkh.). PLoS One 7(5): e36674.
10. Pikunova A, Madduri M, Sedov E, Noordijk Y, Peil A, et al. (2014) 'Schmidt's Antonovka' is identical to 'Common Antonovka', an apple cultivar widely used in Russia in the breeding for biotic and abiotic stresses. Tree Genet Genomes 10: 261-271.
11. Bink M, J J, Madduri M, Voorrips R, Durel C, Kouassi A, et al. (2014) Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 127: 1073-1090.
12. Khan MA, Korban SS (2012) Association mapping in forest trees and fruit crops. J Exp Bot 63(11): 4045-4060.
13. Noiton DAM, Alspach PA (1996) Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Socr Hortic Sci 121(5): 773-782.
14. Durel CE, Laurens F, Fouillet A, Lespinasse Y (1998) Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple. Theor Appl Genet 96(8): 1077-1085.
15. Salvi S, Micheletti D, Magnago P, Fontanari M, Viola R, et al. (2014) One-step reconstruction of multigeneration pedigree networks in apple (Malus 6 domestica Borkh.) and the parentage of Golden Delicious. Mol Breed DOI 10.1007/s11032-014-0054-y.
16. Lespinasse Y, Bouvier L, Djulbic M, Chevreau E (1999) Haploidy in apple and pear. Acta Horticult 484: 49-54.
17. Evans KM, Patocchi A, Rezzonico F, Mathis F, Durel CE, et al. (2011) Genotyping of pedigreed apple breeding material with a genome-covering set of SSRs: trueness-to-type of cultivars and their parentages. Mol Breed 28(4): 535-547.
18. Marco-Sola S, Sammeth M, Guigo R, Ribeca P, (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Meth 9(12): 1185-1188.
19. Homer N, Merriman B, Nelson SF (2009) BFAST: An Alignment Tool for Large Scale Genome Resequencing. PLoS One 4(11): e7767.
20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) Genome Project Data P: The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16): 2078-2079.
21. Derrien T, Estelle J, Marco Sola S, Knowles DG, Raineri E, et al. (2012). Fast Computation and Applications of Genome Mappability. PLoS One 7(1): e30377.
22. 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.
23. Van de Weg W, Di Guardo M, Koehorst-Putten H, Longhi S, Noordijk Y, et al. (2014) A Pipeline for Robust Marker Calling from Infinium SNP Arrays for Diploid Crops. In: International Plant & Animal Genome XXII, San Diego, California, U.S.A.
24. Van Ooijen J (2006) JoinMapH 4, Software for the calculation of genetic linkage maps in experimental populations. In. Wageningen, Netherlands: Kyazma B.V.
25. Van Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93(5): 343-349.
26. Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, et al. (2012) Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry. PLoS One 7(12): e48305.
27. Myles S, Chia J-M, Hurwitz B, Simon C, Zhong GY, et al. (2010) Rapid Genomic Characterization of the Genus Vitis. PLoS One 5(1): e8219.
28. Ganal MW, Durstewitz G, Polley A, Berard 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.
29. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, et al. (2012) Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS One 7(4): e36347.
30. Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, et al. (2013) Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean. PLoS One 8(1): e54985.
31. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, et al. (2012) Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato. PLoS One 7(7): e40563.
32. Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ (2013) High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array. Plant Biotech J 11(9): 1112-1125.
33. Pavy N, Gagnon F, Rigault P, Blais S, Deschenes A, et al. (2013) Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Mol Ecol Resour 13(2): 324-336.
34. Li X, Han Y, Wei Y, Acharya A, Farmer AD, et al. (2014) Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium. PLoS One 9(1): e84329.
35. Chen H, Xie W, He H, Yu H, Chen W, et al. (2014) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7(3): 541-553.
36. Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, et al. (2010) Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res 20(4): 537-545.
37. Wang Z, Cai H, Bai X, Ji W, Li Y, et al. (2012) Isolation of GsGST19 from Glycine soja and analysis of saline-alkaline tolerance for transgenic Medicago sativa. Acta Agron Sin 38(6): 971-979.
38. Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, et al. (2011) Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet Genomes 7(4): 857-868.
39. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. (2008) Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS One 3(10): e3376.
40. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS One 6(5): e19379.
41. Pfender WF, Saha MC, Johnson EA, Slabaugh MB (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122(8): 1467-1480.
42. Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, et al. (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14: 2.
43. Liu H, Bayer M, Druka A, Russell JR, Hackett CA, et al. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics 15: 104.
44. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach. PLoS One 7(2): e32253.
45. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistue L, Corey A, et al. (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4.
46. Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G, et al. (2013) Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L. PLoS One 8(5): e64799.
47. Arnold B, Corbett-Detig RB, Hartl D, Bomblies K (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol Ecol 22(11): 3179-3190.