De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Mousavi, Mohaddeseh ^a   Tong, Chunfa ^a   Liu, Fenxiang ^a   Tao, Shentong ^a   Wu, Jiyan ^a   Li, Huogen ^a   Shi, Jisen ^a  

^a NANJING FORESTRY UNIVERSITY   (China)

Author keywords

Genetic linkage map; Populus; Restriction site associated DNA; Single nucleotide polymorphism; Whole genome sequencing

Indexed keywords

BREEDING; DNA SEQUENCE; FOREST; GENE MAPPING; GENE MUTATION; GENETIC LINKAGE; GENETIC MARKER; GENETIC RESOURCE; GENOMICS; KARYOTYPE; POPULUS; PROGENY; QUANTITATIVE TRAIT LOCUS; RESTRICTION SITE; SINGLE NUCLEOTIDE POLYMORPHISM; CHIMERA; CHROMOSOMAL MAPPING; GENETICS; PLANT CHROMOSOME; PLANT GENOME; PROCEDURES; RESTRICTION MAPPING;

CHIMERA; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENETIC LINKAGE; GENOME, PLANT; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULUS; QUANTITATIVE TRAIT LOCI; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA;

EID: 84982223871     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3003-9     Document Type: Article

References (50)

1. White TL, Adams WT, Neale DB. Forest genetics. 1st ed. Cambridge, MA: CABI Publishing; 2007.
2. Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, et al. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J. 2007;50(6):1063-78.
3. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, et al. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Gen. 1999;22(3):271-5.
4. Schein J, Kucaba T, Sekhon M, Smailus D, Waterston R, Marra M. High-throughput BAC fingerprinting. In: Zhao S, Stodolsky M, editors. Bacterial artificial chromosomes. Vol. 1: Library Construction, Physical Mapping, and Sequencing. Totawa, NJ: Humana Press; 2004. p. 143-56.
5. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313:1596-604.
6. Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, et al. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2014; doi: 10.1038/ncomms3797.
7. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497(7451):579-84.
8. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics. 2013;29(12):1492-7.
9. Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marcais G, et al. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 2014;196(3):875-90.
10. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, et al. The genome of Eucalyptus grandis. Nature. 2014;510(7505):356-62.
11. Bartholome J, Mandrou E, Mabiala A, Jenkins J, Nabihoudine I, Klopp C, et al. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol. 2015;206(4):1283-96.
12. Fierst JL. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools. Front Genet. 2015; doi: 10.3389/fgene.2015.00220.
13. Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, et al. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 2015; doi: 10.1186/s13059-014-0573-1.
14. Neale DB, Kremer A. Forest tree genomics: growing resources and applications. Nat Rev Genet. 2011;12(2):111-22.
15. Hudson CJ, Freeman JS, Kullan AR, Petroli CD, Sansaloni CP, Kilian A, et al. A reference linkage map for Eucalyptus. BMC Genomics. 2012; doi: 10.1186/1471-2164-13-240.
16. Muchero W, Guo J, DiFazio SP, Chen JG, Ranjan P, Slavov GT, et al. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. BMC Genomics. 2015; doi: 10.1186/s12864-015-1215-z.
17. Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, et al. Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3: Genes Genomes. Genetics. 2014;4(9):1681-7.
18. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS One. 2008; doi: 10.1371/journal.pone.0003376.
19. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS One. 2011; doi: 10.1371/journal.pone.0019379.
20. Sun XW, Liu DY, Zhang XF, Li WB, Liu H, Hong WG, et al. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PloS One. 2013; doi: 10.1371/journal.pone.0058700.
21. Eaton DA. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics. 2014;30(13):1844-9.
22. Chutimanitsakun Y, Nipper RW, Guesta-Marcos A, Cistue L, Corey A, Filichkina T, et al. Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics. 2011;12:4.
23. Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet. 2011;122:1467-80.
24. Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, et al. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PloS One. 2011; doi: 10.1371/journal.pone.0019315.
25. Wang N, Fang L, Xin H, Wang L, Li S. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC Plant Biol. 2012;12:148.
26. Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics. 2013;14:32.
27. Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H, et al. Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton. PloS One. 2015; doi: 10.1371/journal.pone.0124781.
28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
29. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
31. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genetics. 2011;43(5):491-8.
32. Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes Genomes. Genetics. 2011;1:171-82.
33. Willing EM, Hoffmann M, Klein JD, Weigel D, Dreyer C. Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics. 2011;27(16):2187-93.
34. Chong Z, Ruan J, Wu CI. Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics. 2012;28(21):2732-7.
35. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. Special features of RAD Sequencing data: implications for genotyping. Mol Ecol. 2013;22(11):3151-64.
36. Tong CF, Li HG, Wang Y, Li XR, Ou JJ, Wang DY, et al. Construction of high-density linkage maps of Populus deltoides × P. simonii using restriction-site associated DNA sequencing. PloS One. 2016; doi: 10.1371/journal.pone.0150692.
37. Doyle JJ, Doyle JL. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytologist Bulletin. 1987;19:11-5.
38. Patel RK, Jain M. NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PloS One. 2012; doi: 10.1371/journal.pone.0030619.
39. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, et al. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 2008;18(5):810-20.
40. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20(2):265-72.
41. Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics. 1994;137:1121-37.
42. Van Ooijen JW. JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Wageningen: Kyazma B. V; 2006.
43. Tong CF, Zhang B, Shi JS. A hidden Markov model approach to multilocus linkage analysis in a full-sib family. Tree Genet Genomes. 2010;6(5):651-62.
44. Falk CT. A simple scheme for preliminary ordering of multiple loci: application to 45 CF families. In: Elston RC, Spence MA, Hodge SE, MacCluer JW, editors. Multipoint mapping and linkage based upon affected pedigree members, Genetic Workshop 6. New York: Liss; 1989. p. 17-22.
45. Yin T, DiFazio S, Gunter LE, Zhang X, Sewell MM, Woolbright SA, et al. Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res. 2008;18:422-30.
46. Zhang B, Tong CF, Yin T, Zhang X, Zhuge Q, Huang M, et al. Detection of quantitative trait loci influencing growth trajectories of adventitious roots in Populus using functional mapping. Tree Genet Genomes. 2009;5:539-52.
47. Berlin S, Lagercrantz U, von Arnold S, Ost T, Ronnberg-Wastljung AC. High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus. BMC Genomics. 2010;11:129.
48. Maliepaard C, Jansen J, Van Ooijen JW. Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Gen Res. 1997;70:237-50.
49. Weir BS. Genetic data analysis II: methods for discrete population genetic data. 2nd ed. Sunderland, MA, USA: Sinauer Associates Inc; 1996.
50. Wu RL, Ma CX, Casella G. Statistical genetics of quantitative traits: linkage, maps and QTL. New York: Springer; 2007.