Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

BMC Biology

Volumn 8, Issue , 2010, Pages

  Celton, Jean Marc ^a   Christoffels, Alan ^a   Sargent, Daniel J ^b   Xu, Xiangming ^b   Rees, D Jasper G ^a,c  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b EAST MALLING RESEARCH   (United Kingdom)

^c AGRICULTURAL RESEARCH COUNCIL   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

FRAGARIA VESCA; FRAGARIA X ANANASSA; MALUS X DOMESTICA; VENTURIA INAEQUALIS;

ALGORITHM; ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; FUNGAL GENOME; FUNGUS; GENE LIBRARY; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PLANT GENOME; SINGLE NUCLEOTIDE POLYMORPHISM; STRAWBERRY; VALIDATION STUDY;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; FRAGARIA; FUNGI; GENETIC LINKAGE; GENOME, FUNGAL; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOMIC LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 78650618921     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-8-155     Document Type: Article

References (20)

1. The Bovine Genome Sequencing and Analysis Consortium The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324(5926):522-528. 10.1126/science.1169588, 2943200, 19390049, The Bovine Genome Sequencing and Analysis Consortium.
2. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 2008, 452:991-997. 10.1038/nature06856, 2836516, 18432245.
3. Huang S, Li R, Zhang Z, Li L, Gu X, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet 2009, 41:1275-1281. 10.1038/ng.475, 19881527.
4. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, RA H, Hirst M, et al. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 2009, 10:R94. 10.1186/gb-2009-10-9-r94, 2768983, 19747388.
5. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Gen Re 2008, 18:810-820.
6. Hernandez D, Francois P, Farinelli L, Schrenzel L. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Gen Res 2008, 15:802-809.
7. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Gen Res 2008, 18:821-829.
8. Sobrino B, Brion M, Carracedó A. SNPs in forensic genetics: a review on SNP typing methodologies. For Sci Int 2005, 154:181-194.
9. Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD. Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 2000, 155:407-420. 1461083, 10790413.
10. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P. Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 2005, 171:1305-1309. 10.1534/genetics.105.043661, 1456826, 16118196.
11. Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arús P, Simpson DW, Tobutt KR, Monfort A. The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 2008, 51:120-127. 10.1139/G07-107, 18356946.
12. MacHardy WE. Apple Scab: Biology, Epidemiology and Management 1996, Minnesota: American Phytopathological Society.
13. Broggini GAL, Le Cam B, Parisi L, Wu C, Zhang H-B, Gessler C, Patocchi A. Construction of BAC clones spanning the region of the apple scab avirulence gene. AvrVg Fung Gen Bio 2007, 44:44-41.
14. Folta KM, Davis TM. Strawberry genes and genomics. Crit Rev Plant Sci 2006, 25:399-415.
15. Shulaev V, Sargent DJ, Crowhurst RN, Mockler T, Veilleux RE, Folkerts O, Delcher AL, Jaiswal P, Liston A, Mane SP, et al. Whole genome sequencing and analysis of diploid strawberry, Fragaria vesca, a compact and versatile perennial Rosaceous fruit. Nat Genet 2010,
16. Sargent DJ, Davis TM, Tobutt KR, Wilkinson MJ, Battey NH, Simpson DW. A genetic linkage map of microsatellite, gene specific and morphological markers in diploid Fragaria. Theor Appl Genet 2004, 109:1385-1391. 10.1007/s00122-004-1767-9, 15290052.
17. Xu X, Roberts T, Barbara D, Harvey NG, Gao L, Sargent DJ. A genetic linkage map of Venturia inaequalis, the causal agent of apple scab. BMC Res Notes 2009, 2:163. 10.1186/1756-0500-2-163, 2732633, 19689797.
18. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Gen Res 2008, 18:1851-1858.
19. Doyle JJ, Doyle JL. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bull 1987, 19:11-15.
20. De La Rosa R, James CM, Tobutt KR. Isolation and characterisation of polymorphic microsatellites in olive (Olea europaea L.) and their transferability to other genera in the Oleaceae. Mol Ecol Notes 2002, 2:265-267.