Erratum to: Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations(Theor Appl Genet, (2013), 126, (2699-2716), Doi:10.1007/s00122-013-2166-x;Bridging the genotyping gap: Using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

Theoretical and Applied Genetics

Volumn 126, Issue 11, 2013, Pages 2699-2716

  Spindel, Jennifer ^a   Wright, Mark ^a   Chen, Charles ^a   Cobb, Joshua ^a   Gage, Joseph ^a   Harrington, Sandra ^a   Lorieux, Mathias ^c,d   Ahmadi, Nourollah ^b   McCouch, Susan ^a  

^a Department of Obstetrics Gynecology   (United States)

^b CIRAD   (France)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^d INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ALUMINUM; ERROR CORRECTION; GENES; MAPPING; PLANTS (BOTANY);

BIOINFORMATICS ANALYSIS; BREEDING POPULATIONS; HIGH DEGREE OF ACCURACY; MAPPING POPULATIONS; NEXT-GENERATION SEQUENCING; RECOMBINANT INBRED LINES; RICE (ORYZA SATIVA); SEGREGATION DISTORTION;

POPULATION STATISTICS;

JAPONICA; ORYZA SATIVA;

ALUMINUM;

ADAPTATION; ARTICLE; BREEDING; CHROMOSOME BREAKAGE; CHROMOSOME MAP; CHROMOSOME SEGREGATION; DNA SEQUENCE; DRUG EFFECT; GENETIC MARKER; GENETIC RECOMBINATION; GENETICS; GENOTYPING TECHNIQUE; HISTOLOGY; METHODOLOGY; PLANT LEAF; QUANTITATIVE TRAIT LOCUS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM;

ADAPTATION, PHYSIOLOGICAL; ALUMINUM; BREEDING; CHROMOSOME BREAKAGE; CHROMOSOME MAPPING; CHROMOSOME SEGREGATION; GENETIC MARKERS; GENOTYPING TECHNIQUES; ORYZA SATIVA; PLANT LEAVES; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84887613153     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-015-2618-6     Document Type: Erratum

References (49)

1. Almeida GD, Makumbi D, Magorokosho C, Nair S, Borem A, Ribaut JM, Banziger M, Prasanna BM, Crossa J, Babu R (2013) QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance. Theor Appl Genet 126(3): 583-600. doi: 10. 1007/s00122-012-2003-7.
2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3(10): e3376. doi: 10. 1371/journal. pone. 0003376.
3. Bradbury PJ, Zhang Z, Dallas EK, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
4. Chen MS, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang FC, Kim H, Frisch D, Yu YS, Sun SH, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu JD, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo MZ, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14(3): 537-545. doi: 10. 1105/tpc. 010485.
5. Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV (2011) Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 156(2): 455-465. doi: 10. 1104/pp. 110. 169102.
6. Darvasi A, Weinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134(3): 943-951.
7. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12(7): 499-510.
8. Dupuis J, Siegmund D (1999) Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 151(1): 373-386.
9. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011a) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5): e19379. doi: 10. 1371/journal. pone. 0019379.
10. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011b) Powerpoint presentation: reduced representation sequencing for rapidly genotyping highly diverse species.
11. Famoso AN, Zhao K, Clark RT, Tung C-W, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7(8): e1002221. doi: 10. 1371/journal. pgen. 1002221.
12. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res 14(9): 1812-1819. doi: 10. 1101/gr. 2479404.
13. Garavito A, Guyot R, Lozano J, Gavory F, Samain S, Panaud O, Tohme J, Ghesquière A, Lorieux M (2010) A genetic model for the female sterility barrier between Asian and African cultivated rice species. Genetics 185(4): 1425-1440. doi: 10. 1534/genetics. 110. 116772.
14. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148(1): 479-494.
15. Harushima Y, Nakagahra M, Yano M, Sasaki T, Kurata N (2001) A genome-wide survey of reproductive barriers in an intraspecific hybrid. Genetics 159(2): 883-892.
16. Harushima Y, Nakagahra M, Yano M, Sasaki T, Kurata N (2002) Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160(1): 313-322.
17. Hemamalini GS, Shashidhar HE, Hittalmani S (2000) Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegetative stage in rice (Oryza sativa L.). Euphytica 112(1): 69-78. doi: 10. 1023/a: 1003854224905.
18. Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang JY, Zheng KL, Liu GF, Wang GC, Sidhu JS, Srivantaneeyakul S, Singh VP, Bagali PG, Prasanna HC, McLaren G, Khush GS (2003) Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107(4): 679-690. doi: 10. 1007/s00122-003-1269-1.
19. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19(6): 1068-1076. doi: 10. 1101/gr. 089516. 108.
20. Huang X, Kurata N, Wei X, Wang Z-X, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490(7421): 497-501. http://www. nature. com/nature/journal/v490/n7421/abs/nature11532. html (supplementary information).
21. Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ (2012) A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. Am J Bot 99(2): 383-396. doi: 10. 3732/ajb. 1100312.
22. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Meth 9(4): 357-359. http://www. nature. com/nmeth/journal/v9/n4/abs/nmeth. 1923. html (supplementary information).
23. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5): 589-595. doi: 10. 1093/bioinformatics/btp698.
24. Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CHM, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S, Khush GS (2003) QTL √ó environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108(1): 141-153. doi: 10. 1007/s00122-003-1401-2.
25. Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14(3): 604-610.
26. Maheswaran M, Subudhi PK, Nandi S, Xu JC, Parco A, Yang DC, Huang N (1997) Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theor Appl Genet 94(1): 39-45. doi: 10. 1007/s001220050379.
27. Mangin B, Goffinet B, Rebai A (1994) Constructing confidence intervals for QTL location. Genetics 138(4): 1301-1308.
28. Matsubara K, Ebana K, Mizubayashi T, Itoh S, Ando T, Nonoue Y, Ono N, Shibaya T, Ogiso E, Hori K, Fukuoka S, Yano M (2011) Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses. Mol Genet Genomics 286(5-6): 307-319. doi: 10. 1007/s00438-011-0648-6.
29. McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35(1-2): 89-99.
30. Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB, Paterson AH, Li ZK (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107(1): 89-101. doi: 10. 1007/s00122-003-1192-5.
31. Mei HW, Li ZK, Shu QY, Guo LB, Wang YP, Yu XQ, Ying CS, Luo LJ (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110(4): 649-659. doi: 10. 1007/s00122-004-1890-7.
32. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res 9(5): 163-171. doi: 10. 1093/dnares/9. 5. 163.
33. Prasad SR, Bagali PG, Hittalmani S, Shashidhar HE (2000) Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). Curr Sci 78(2): 162-164.
34. Rosyara UR, Gonzalez-Hernandez JL, Glover KD, Gedye KR, Stein JM (2009) Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration. Theor Appl Genet 118(8): 1617-1631. doi: 10. 1007/s00122-009-1010-9.
35. Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquiere A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106(5): 794-803. doi: 10. 1007/s00122-002-1088-9.
36. Stangoulis JR, Huynh B-L, Welch R, Choi E-Y, Graham R (2007) Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content. Euphytica 154(3): 289-294. doi: 10. 1007/s10681-006-9211-7.
37. This D, Comstock J, Courtois B, Xu YB, Ahmadi N, Vonhof WM, Fleet C, Setter T, McCouch S (2010) Genetic analysis of water use efficiency in rice (Oryza sativa L.) at the leaf level. Rice 3(1): 72-86. doi: 10. 1007/s12284-010-9036-9.
38. Thomson M, Zhao K, Wright M, McNally K, Rey J, Tung C-W, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail A, de Ocampo M, Mojica C, Reveche M, Dilla-Ermita C, Mauleon R, Leung H, Bustamante C, McCouch S (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29(4): 875-886. doi: 10. 1007/s11032-011-9663-x.
39. Virk PS, Ford-Lloyd BV, Newbury HJ (1998) Mapping AFLP markers associated with subspecific differentiation of Oryza sativa (rice) and an investigation of segregation distortion. Heredity 81: 613-620. doi: 10. 1046/j. 1365-2540. 1998. 00441. x.
40. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP-a new technique for DNA-fingerprinting. Nucleic Acids Res 23(21): 4407-4414. doi: 10. 1093/nar/23. 21. 4407.
41. Walsh MLaB (1998) Genetics and analysis of quantitative traits. Sinauer Associates Inc., Sunderland.
42. Wang L, Hao L, Li X, Hu S, Ge S, Yu J (2009) SNP deserts of Asian cultivated rice: genomic regions under domestication. J Evol Biol 22(4): 751-761. doi: 10. 1111/j. 1420-9101. 2009. 01698. x.
43. Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101(26): 9915-9920. doi: 10. 1073/pnas. 0401076101.
44. Wu JZ, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, Fujisawa M, Katagiri S, Saji S, Yoshiki S, Karasawa W, Yoshihara R, Hayashi A, Kobayashi H, Ito K, Hamada M, Okamoto M, Ikeno M, Ichikawa Y, Katayose Y, Yano M, Matsumoto T, Sasaki T (2003) Physical maps and recombination frequency of six rice chromosomes. Plant J 36(5): 720-730. doi: 10. 1046/j. 1365-313X. 2003. 01903. x.
45. Wu YP, Ko PY, Lee WC, Wei FJ, Kuo SC, Ho SW, Hour AL, Hsing YI, Lin YR (2010) Comparative analyses of linkage maps and segregation distortion of two F-2 populations derived from japonica crossed with indica rice. Hereditas 147(5): 225-236. doi: 10. 1111/j. 1601-5223. 2010. 02120. x.
46. Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F-2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253(5): 535-545.
47. Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30(1): 105-111. doi: 10. 1038/nbt. 2050.
48. Yan CJ, Liang GH, Chen F, Li X, Tang SZ, Yi CD, Tian S, Lu JF, Gu MH (2003) Mapping quantitative trait loci associated with rice grain shape based on an indica/japonica backcross population. Yi Chuan Xue Bao 30(8): 711-716.
49. Zhao Q, Zhang Y, Cheng ZK, Chen MS, Wang SY, Feng Q, Huang YC, Li Y, Tang YS, Zhou B, Chen ZH, Yu SL, Zhu JJ, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu YQ, Zhang LS, Liu YL, Yu Z, Fan DL, Weng QJ, Chen L, Lu TT, Liu XH, Jia PX, Sun TG, Wu YR, Zhang YJ, Lu Y, Li C, Wang R, Lei HY, Li T, Hu H, Wu M, Zhang RQ, Guan JP, Zhu J, Fu G, Gu MH, Hong GF, Xue YB, Wing R, Jiang JM, Han B (2002) A fine physical map of the rice chromosome 4. Genome Res 12(5): 817-823. doi: 10. 1101/gr. 48902.