Genome sequencing initiative

Genetics, Genomics and Breeding of Stone Fruits

Volumn , Issue , 2012, Pages 244-269

  Verde, Ignazio ^a   Vendramin, Elisa ^a   Dettori, Maria Teresa ^a   Micali, Sabrina ^a   Sosinski, Bryon ^b  

^a CRA Fruit Tree Research Center   (Italy)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

IPGI; NGS; Sanger WGS; SNP chip; Variant discovery

Indexed keywords

EID: 84989220041     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b13104     Document Type: Chapter

References (95)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-81.
2. Aranzana MJ, Garcia-Mas J, Carbò J, Arús P (2002) Development and variability analysis of microsatellite markers in peach. Plant Breed 121: 87-92.
3. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arús P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106: 819-825.
4. Aranzana MJ, Abbassi el-K, Howad W, Arús P (2010) Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genetics 11: 69.
5. Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218.
6. Baird WV, Estager AS, Wells J (1994) Estimating nuclear DNA content in peach and related diploid species using laser flow cytometry and DNA hybridization. J Am Soc Hort Sci 119: 1312-1316.
7. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918.
8. Bassil NV, Gilmore B, Main D, Peace C, Mockler T, Wilhelm L, van de Weg E, Davis T, Chagne D, Gardiner S, Crowhurst R, Verde I, Sosinski B, Morgante M, Arus P, Velasco R, Troggio T, Cestaro A, Fazio G, Norelli J, Rees J, Iezzoni A (2011) New age Of DNA marker discovery in the Rosaceae. In: Plant Anim Genomes XIX Conf, Jan 15-19, San Diego, CA, Abstr W 252.
9. Bennetezen JL, San Miguel P, Chen M, Tikhonov A, Francki M, Avramova Z (1998) Grass genomes. Proc Natl Acad Sci USA 95: 1975-1978.
10. Boudehri K, Bendahmane A, Cardinet G, Troadec C, Moing A, Dirlewanger E (2009) Phenotypic and fine genetic characterization of the D locus controlling fruit acidity in peach. BMC Plant Biol 9: 59.
11. Bozdag S, Close TJ, Lonardi S (2008) Computing the minimal tiling path from a physical map by integer linear programming. ALG IN BIOINF, Volume 5251/2008, 148-161, DOI: 10.1007/978-3-540-87361-7.
12. Byrne DH (1990) Isozyme variability in four diploid stone fruits compared with other woody perennial plants. J Hered 81: 68-71.
13. Cabrera A, Kozik A, Howad W, Arús P, Iezzoni A, van der Knaap E (2009) Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genomics 10: 562.
14. Cantini C, Iezzoni AF, Lamboy WF, Bortizki M, Struss D (2001) DNA fingerprinting of tetraploid cherry germplasm using simple sequence repeats. J Am Soc Hort Sci 126: 205-209.
15. Chaparro JX, Werner DJ, O’Malley D, Sederoff RR (1994) Targeted mapping and linkage analysis of morphological isozyme, and RAPD markers in peach. Theor Appl Genet 87: 805-815.
16. Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L.) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theor Appl Genet 99: 65-72.
17. Chain PSG, Grafham DV, Fulton RS, Fitz Gerald MG, et al. (2009) Genome project standards in a new era of sequencing. Science 326: 236-237.
18. Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicagotruncatula expressed sequenced tags using 454 life sciences technology. BMC Genom 7: 272-282.
19. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
20. Dettori MT, Quarta R, Verde I (2001) A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 44: 783-790.
21. Dirlewanger E, Moing A, Rothan C, Svanella L Pronier V, Guye A, Plomion C, Monet R (1999) Mapping QTL controlling fruit quality in peach (Prunus persica (L.) Batsch). Theor Appl Genet 98: 18-31.
22. Dirlewanger E, Cosson P, Tavaud M, Aranzana J, Poizat C, Zanetto A, Arus P, Laigret F (2002) Development of microsatellite markers in peach [ Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunusavium L.). Theor Appl Genet 105: 127-138.
23. Dirlewanger E, Graziano E, Joobeur T, Garriga-Calderé F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101: 9891-9896.
24. Eduardo I, Pacheco I, Chietera G, Bassi D, Pozzi C, Vecchietti A, Rossini L. (2011) QTL analysis of fruit quality traits in two peach intraspecific populations and importance of maturity date pleiotropic effect. Tree Genet Genomes 7: 323-335.
25. Emberton J, Ma J, Yuan Y, San Miguel P, Bennete JL (2005) Gene enrichment in maize with hypomethilated partial restriction (HMPR) libraries. Genome Res 15: 1441-1446.
26. Esmenjaud D, Voisin R, Van Ghelder C, Bosselut N, Lafargue B, Di Vito M, Dirlewanger E, Poëssel JL, Kleinhentz M (2009) Genetic dissection of resistance to root-knot nematodes Meloidogyne spp. in plum, peach, almond, and apricot from various segregating interspecific Prunus progenies. Tree Genet Genomes 5: 279-289.
27. Etienne C, Rothan C, Moing A, Plomion C, Bodenes C, Dumas LS, Cosson P, Pronier V, Monet R, Dirlewanger E (2002) Candidate genes and QTL for sugar and organic acid content in peach (Prunus persica (L.) Batsch). Theor Appl Genet 105: 145-159.
28. Eveland AL, McCarty DR and Koch KE (2008) Transcript profiling by 3'-untranslated region sequencing resolves expression of gene families. Plant Physiol 146: 32-44.
29. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
30. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8: 175-185.
31. Fan S, Bielenberg DG, Zhebentyayeva TN, Reighard GL, Okie WR, Holland D, Abbott AG (2010) Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica). New Phytol 185: 917-930.
32. Farrar K, Donnison IS (2007) Construction and screening of BAC libraries made from Brachypodium genomic DNA. Nat Protoc 2: 1661-1674.
33. Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16: 77-88.
34. Foulongne M, Pascal T, Arus P, Kervella J (2003) The potential of Prunusdavidiana for introgression into peach [Prunus persica (L.) Batsch] assessed by comparative mapping. Theor Appl Genet 107: 227-238.
35. Gunderson KL (2009) Whole-genome genotyping on bead arrays. Meth Mol Biol 529: 197-213.
36. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171: 1305-1309.
37. Hutchison CA (2007) DNA sequencing: bench to bedside and beyond. Nucl Acids Res 35: 6227-6237.
38. Illa E, Eduardo I, Audergon JM, Barale F, Dirlewanger E, Li X, Moing A, Lambert P, Le Dantec L, Gao Z, Poessel JL, Pozzi C, Rossini L, Vecchietti A, Arus P, Howad W (2011) Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality. Mol Breed DOI: 10.1007/s11032-010-9518-x.
39. International Human Genome Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
40. International Peach Genome Initiative (2010) www.rosoceae.org/peach/genome.
41. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
42. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13: 91-96.
43. Jones-Rhoades MW, Bartel DP, Bonnie Bartel (2006) Micro RNAs and their regulatory roles in plants.Annu Rev Plant Biol 57: 19-53.
44. 2 progeny. Theor Appl Genet 97: 1034-1041.
45. Jakne J, Meyer JDF, Suzuki G, McCallum J, Cheung F, Town CD, Havey MJ (2008) Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration. Mol Genet Genom 280: 287-292.
46. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott AG, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucl Acids Res 36: D1034-D1040.
47. Kims S, Tang H (2007) Genome Sequencing Technology and Algorithms. 1st Artech House, Norwood, MA, USA © ISBN:1596930942 9781596930940.
48. Lambert P, Pascal T (2011) Mapping Rm2 gene conferring resistance to the green peach aphid (Myzuspersicae Sulzer) in the peach cultivar “Rubira®". Tree Genet Genomes 7: 1057-1068.
49. Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticumaestivum L.). Genome 48: 1120-1126.
50. Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C (2008) Version VI of the ESTreedb: an improved tool for peach transcriptome analysis. BMC Bioinformatics 9 (Suppl 2): S9.
51. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
52. Luckey JA, Drossman H, Kostichka AJ, Mead DA, D’Cunha J, Norris TB, Smith LM (1990) High speed DNA sequencing by capillary electrophoresis. Nucl Acids Res 18: 4417-4421.
53. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci USA 74: 560-564.
54. Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46.
55. Messina R, Lain O, Marrazzo MT, Cipriani G, Testolin R (2004) New set of micro satellite loci isolated in apricot. Mol Ecol Notes 4: 432-434.
56. Mnejja M, Garcia-Mas J, Howad W, Badenes ML, Arús P (2004) Simple-sequence repeat (SSR) markers of Japanese plum (Prunussalicina Lindl.) are highly polymorphic and transferable to peach and almond. Mol Ecol Notes 4: 163-166.
57. Mnejja M, Garcia-Mas J, Audergon JM, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet Genomes 6: 689-700.
58. Monet R (1989) Peach genetics: past, present and future. Acta Hort 254: 49-53.
59. Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 312.
60. Olukolu B, Trainin T, Fan S, Kole C, Bielenberg D, Reighard G, Abbott A, Holland D (2009) Genetic linkage mapping for molecular dissection of chilling requirement and budbreak in apricot (Prunusarmeniaca L.). Genome 52: 819-828.
61. Peace CP, Crisosto CH, Gradziel TM (2005) Endopolygalacturonase: a candidate gene for free stone and melting in peach. Mol Breed 16: 21-31.
62. Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, Zagursky RJ, Cocuzza AJ, Jensen A, Baumeister K (1987) A system for rapid DNA sequencing with fluorescent chainterminating dideoxynucleotides. Science 238: 336-341.
63. Quilot B, Wu BH, Kervella J, Génard M, Foulongne M, Moreau K (2004) QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. Theor Appl Genet 109: 884-897.
64. Rabinowicz PD (2007)Plant genomic sequencing using gene-enriched libraries. Chem Rev 107: 3377-3390.
65. Rajapakse S, Bethoff LE, He G, Estager AE, Scorza R, Verde I, Ballard RE, Baird WV, Callahan A, Monet R, Abbott AG (1995) Genetic Linkage mapping in peach using morphological, RFLP and RAPD markers. Theor Appl Genet 90: 503-510.
66. Roach JC, Boysen C, Wang K, Hood L (1995) Pairwise end aequencing: A unified approach to genome mapping and sequencing. Genomics 26: 345-353.
67. Sanger F, Nichklen S Coulson AR (1977a) DNA sequencing with chain-terminating inhibitor. Proc Natl Acad Sci USA 74: 5463-5467.
68. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes JC, Hutchinson CA III, Slocombe PM, Smith M (1977b) Nucleotide sequence of bacteriophage φ X 174 DNA. Nature 265: 687-695.
69. Sanger F, Coulson AR, Friedmann T, Air GM, Barrell BG, Brown NL, Fiddes JC, Hutchinson CA III, Slocombe P, Smith M (1978) Nucleotide sequence of bacteriophage φX174 DNA. J Mol Biol125: 225-246.
70. Scalabrin S, Policriti A, Nadalin F, Pinosio S, Cattonaro F, Vendramin E, Aramini V, Verde I, Bassi D, Pirona R, Rossini L, Testolin R, Morgante M (2011) A catalog of molecular diversity of Prunusgermplasm gathered from aligning NGS reads to the peach reference sequence: bioinformatic approaches and challenges. Acta Hort (in press).
71. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S et al (2009) The B73 maize genome: complexity, diversity and dynamics. Science 326: 1112-1115.
72. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
73. Shendure J (2008) The beginning of the end for microarrays? Nat Meth 5: 585-587.
74. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89: 8794-8797.
75. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SB, Hood LE (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321: 674-679.
76. Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 101: 421-428.
77. Sosinski B, Verde I, Morgante M, Rokhsar D, and The International Peach Genome Initiative (IPGI) (2010) A first draft of the peach genome sequence and its use for genetic diversity analysis in peach. 5th Intl Rosaceae Genome Conf, Stellenbosch, South Afroca, Nov 14-17.
78. Swerdlow H, Gesteland R (1990) Capillary gel electrophoresis for rapid, high resolution DNA sequencing. Nucl Acids Res 18: 1415-1419.
79. Testolin R, Marrazzo T, Cipriani G, Quarta R, Verde I, Dettori MT, Pancaldi M, Sansavini S (2000) Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43: 512-520.
80. Testolin R, Messina R, Lain O, Marrazzo MT, Huang WG, Cipriani G (2004) Microsatellites isolated in almond from an AC-repeat enriched library. Mol Ecol Notes 4: 459-461.
81. Vendramin E, Dettori MT, Giovinazzi J, Micali S, Quarta R, Verde I (2007) A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species. Mol Ecol Notes 7: 307-310.
82. Vendramin E, Scalabrin S, Felice N, Del Fabbro C, Aramini V, Dettori MT, Quarta R, Cattonaro F, Morgante M, Verde I (2010) Whole-genome trascriptional landscape definition and gene annotation improvement in peach by RNA-seq on Illumina platform.Proc XLVIII Ital Soc of Agri Genet-SIFV-SIGA Joint Meeting Matera, Italy, 27/30 Sept.
83. Verde I, Quarta R, Cerdrola C, Dettori MT (2002) QTL analysis of agronomic traits in a BC1 peach population. Acta Hort 592: 291-297.
84. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG, Motto M, Quarta R (2005) Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)]. x P.ferganensis BC1 linkage map: saturation and coverage improvement. Theor Appl Genet 111: 1013-1021.
85. Verde I, Cattonaro F, Scalabrin S, Vendramin E, Policriti A, Del Fabbro C, Quarta R, Aramini V, Dettori MT, Rokhsar DS, Sosinski B, Morgante M (2011) Whole genome resequencing reveals a reduced nucleotide variability in peach. In: Plant Anim Genomes XIX Conf, Jan 15-19, San Diego, CA, Abstr W 249.
86. Viruel MA, Messeguer R, de Vicente MC, Garcia-Mas J, Puigdomènech P, Vargas F, Arùs P (1995) A linkage map with RFLP and isozyme markers for almond. Theor Appl Genet 91: 964-971.
87. Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155: 407-420.
88. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32-42.
89. Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA (1994) Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucl Acids Res 22: 4922-4931.
90. Zhang HB, Wu C (2001) BAC as tools for genome sequencing. Plant Physiol Biochem 39: 195-209.
91. Zhebentyayeva TN, Swire-Clark G, Georgi LL, Garay L, Jung S, Forrest S, Blenda AV, Blackmon B, Mook J, Horn R, Howad W, Arús P, Main D, Tomkins JP, Sosinski B, Baird WV, Reighard GL, Abbott AG (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genomes 4: 745-756.
92. Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W (2008) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res 19: 70-78.
93. Zhu JK (2008) Epigenome sequencing comes of age. Cell 133: 395-397.
94. Yamamoto T, Mochida K, Imai T, Shi YZ, Ogiwara I, Hayashi T (2002) Microsatellite markers in peach [Prunus persica (L.) Batsch] derived from an enriched genomic and cDNA libraries. Mol Ecol Notes 2: 298-301.
95. Yamamoto T, Yamaguchi M, Hayashi T (2005) An integrated genetic linkage map of peach by SSR, STS, AFLP and RAPD J Jpn Soc Hort Sci 74: 204-213.