High-throughput genotyping of unknown genomic terrain in complex plant genomes: Lessons from a case study

Molecular Breeding

Volumn 26, Issue 4, 2010, Pages 711-718

  Sandve, Simen Rød ^a   Rudi, Heidi ^a   Dørum, Guro ^a   Berg, Paul Ragnar ^a   Rognli, Odd Arne ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

Genotyping error; MassARRAY; Paralogs; Plant

Indexed keywords

GENOME; INDIUM COMPOUNDS; MOLECULAR BIOLOGY; PLANTS (BOTANY); TEMPERATURE; THROUGHPUT;

CASE-STUDIES; COMPLEX PLANTS; GENOMICS; GENOTYPING; GENOTYPING ERRORS; HIGH THROUGHPUT GENOTYPING; MASSARRAY; PARALOGS; PLANT; PLANT GENOMES;

GENES;

EID: 78049300889     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-010-9479-0     Document Type: Article

References (18)

1. Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119: 507-517.
2. Bérard A, Le Paslier MC, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C (2009) High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.). Plant Biotechnol J 7: 364-374.
3. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
4. Bray MS, Boerwinkle E, Doris PA (2001) High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: practice, problems and promise. Hum Mutat 17: 296-304.
5. Butler H, Ragoussis J (2008) BeadArray-based genotyping. In: Starkey J, Elaswarapu R (eds) Methods in molecular biology, vol 439: Genomics protocols, 2nd edn. Humana Press Inc., Totowa, NJ, pp 53-74.
6. Choi I-Y, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon M-S, Hwang E-Y, Yi S-I, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176: 685-696.
7. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93: 10274-10279.
8. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99: 8133-8138.
9. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
10. Hyten D, Song Q, Choi I-Y, Yoon M-S, Specht J, Matukumalli L, Nelson R, Shoemaker R, Young N, Cregan P (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116: 945-952.
11. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
12. Lam K-WG, Jeffreys AJ (2006) Processes of copy-number change in human DNA: the dynamics of α-globin gene deletion. Proc Natl Acad Sci USA 103: 8921-8927.
13. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S-I, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu S-H, Stueber K, Theodoulou FL, Tu H, van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
14. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
15. Sandve SR, Rudi H, Asp T, Rognli OA (2008) Tracking the evolution of a cold stress associated gene family in cold tolerant grasses. BMC Evol Biol 8: 245.
16. Storz JF, Baze M, Waite JL, Hoffmann FG, Opazo JC, Hayes JP (2007) Complex signatures of selection and gene conversion in the duplicated globin genes of house mice. Genetics 177: 481-500.
17. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
18. Yang Z, Nielsen R, Goldman N, Pedersen A-MK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.