Application of Next-Generation Sequencing for Abiotic Stress Tolerance

OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences

Volumn , Issue , 2013, Pages 347-365

  Mondal, Tapan Kumar ^a   Sutoh, Keita ^b  

^a NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

^b Life Science Institute   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84949551126     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b14289-19     Document Type: Chapter

References (110)

1. Schadt, E.E., S., Turner, and A. Kasarskis. 2010. A window into third-generation sequencing. Human Molecular Genetics 19:227-240.
2. Zalapa, J.E., H. Cuevas, H. Zhu, S. Steffan, D. Senalik, E. Zeldin et al. 2012. Using next-generation sequencing approaches for the isolation of simple sequence repeat (SSR) loci in the plant sciences. American Journal of Botany 99:193-208.
3. Bentley, D.R. 2006. Whole-genome re-sequencing. Current Opinion in Genetics and Development 16:545-552.
4. Ashelford, K., M.E. Eriksson, C.M. Allen, R.D. Amore, M. Johansson, P. Gould et al. 2011. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biology 12:28-40.
5. Shulaev, V., D.J. Sargent, R.N. Crowhurst, T.C. Mockler, O. Folkerts, A.L.D. Elcher et al. 2011. The genome of woodland strawberry (Fragaria vesca). Nature Genetics 43:109-116.
6. Rothberg, J.M., W. Hinz, T.W. Rearick, J. Schultz, W. Mileski, M. Davey et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348-352.
7. Levene, M.J., J. Korlach, S.W. Turner, M. Foquet, H.G. Craighead, and W.W. Webb. 2003. Zero-mode waveguides for single-molecule analysis at high concentration. Science 299:682-686.
8. Hardin, S.H. 2008. Real-time DNA sequencing. In Next Generation Genome Sequencing: Towards Personalized Medicine, edited by Janitz, M., 97-102, Weinheim, Germany: Wiley-VCH Verlag GmbH and Co. KGaA.
9. Lieberman, K.R., G.M. Cherf, M.J. Doody, F. Olasagasti, Y. Kolodji, and M. Akeson. 2010. Possessive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. Journal of the American Chemical Society 132:17961-17972.
10. Krishnan, N.M., S. Pattnaik, S.A. Deepak, A.K. Hariharan, P. Gaur, R. Chaudhary et al. 2011. De novo sequencing and assembly of Azadirachta indica fruit transcriptome. Current Science 10:1533-1561.
11. Singh, N.K., D.K. Gupta, P.K. Jayaswal, M.K. Mahato, S. Dutta, S. Singh et al. 2012. The first draft of the pigeon pea genome sequence. Journal of Plant Biochemistry Biotechnology 1:98-112.
12. Gahlan, P., H.R. Singh, R. Shankar, N. Sharma, A. Kumari, V. Chawla et al. 2012. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics 13:126-138.
13. Novaes, E., D.R. Drost, W.G. Farmerie, J.P. Pappas, D. Grattapaglia, R.R. Sederoff et al. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312-319.
14. Collins, L.J., P.J. Biggs, C. Voelckel, and S. Joly. 2008. An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Informatics 21:3-14.
15. Wall, P.K., J. Leebens-Mack, A.S. Chanderbali, A. Barakat, E. Wolcott, H. Liang et al. 2009. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10:347-366.
16. Bundock, P.C., F.G. Eliott, G. Ablett, A.D. Benson, R.E. Casu, K.S. Aitken et al. 2009. Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnology 7:347-354.
17. Dassanayake, M., J.S. Haas, H.J. Bohnert, and J.M. Cheeseman. 2009. Shedding light on an extremophile lifestyle through transcriptomics. New Phytologist 183:764-775.
18. Lee, R.M., J. Thimmapuram, A. Kate, T.G. Gong, A.G. Hernandez, C.L. Wright et al. 2009. Sampling the waterhemp (Amaranthus tuberculatus) genome using pyrosequencing technology. Weed Science 57:463-469.
19. Wang, W.Y., Q. Wang, Q. Zhang, and D. Guo. 2009. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 10:465-475.
20. Barakat, A., D.S. Diloreto, Y. Zhang, C. Smith, K. Baier, W.A. Powell et al. 2009. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology 9:51-62.
21. Alagna, F., N.D. Agostino, L. Torchia, M. Servili, R. Rao, M. Pietrella et al. 2009. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 10:399-414.
22. Riggins, C.W., Y. Peng, J.R.C.N. Stewart, and P.J. Tranel. 2010. Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Management Science 66:1042-1052.
23. Guo, S., Y. Zheng, J. Joung, S. Liu, Z. Zhang, O.R. Crasta et al. 2010. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11:384-395.
24. Mizrachi, E., C.A. Hefer, M. Ranik, F. Joubert, and A.A. Myburg. 2010. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 11:681-687.
25. Swarbreck, S.M., E.A. Lindquist, D.D. Ackerly, and G.L. Andersen. 2011. Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. Plant and Cell Physiology 52:317-332.
26. Franssen, S.U., R.P. Shrestha, A. Bräutigam, E. Bornberg-Bauer, and A.P. Weber. 2011. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 12:227-245.
27. Der, J.P., M.S. Barker, N.J. Wickett, C.W. Depamphilis, and P.G. Wolf. 2011. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 12:99-113.
28. Angeloni, F., C.A.M. Wagemaker, M.S.M. Jetten, H.J.M. Opden, I. Camp, E.M. Janssen-Megens et al. 2011. De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next generation sequencing techniques. Molecular Ecology Research 11:662-674.
29. Wenping, H., Z. Yuan, S. Jie, Z. Lijun, and W. Zhezhi. 2011. De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients. Genomics 98:272-279.
30. Moragues, M., J. Comadran, R. Waugh, I. Milne, A.J. Flavell, and J.R. Russell. 2010. Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theoretical and Applied Genetics 120:1525-1534.
31. Cosart, T., A. Beja-Pereira, S. Chen, S.B. Ng, J. Shendure, and G. Luikart. 2011. Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics 12:347-355.
32. Cao, J., K. Schneeberger, S. Ossowski, T. Günther, S. Bender, J. Fitz et al. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43:956-963.
33. Lister, R., and J.R. Ecker. 2009. Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research 19:959-966.
34. Lai, J., R. Li, X. Xu, W. Jin, M. Xu, H. Zhao et al. 2010. Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics 42:1027-1030.
35. Xu, Z., S. Zhong, X. Li, W. Li, S.J. Rothstein, S. Zhang et al. 2011. Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots. PLoS One 6:28009-28018.
36. Xu, X., X. Liu, S. Ge, J.D. Jensen, F. Hu, X. Li et al. 2011. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30:105-111.
37. Branca, A., T.D. Paape, P. Zhou, R. Briskine, A.D. Farmer, J. Mudge et al. 2011. Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences of the United States of America 108:864-870.
38. Lam, H.M., X. Xu, X. Liu, W. Chen, G. Yang, F.L. Wong et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42:1053-1059.
39. Nobuta, K., K. Vemaraju, and B.C. Meyers. 2007. Methods for analysis of gene expression in plants using MPSS. Methods in Molecular Biology 406:387-408.
40. Mutasa-Göttgens, E.S., A. Joshi, H.F. Holmes, P. Hedden, and B. Göttgens. 2012. A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome scale analysis of vernalization and gibberellins responses. BMC Genomics 13:99-117.
41. Rowland, L.J., N. Alkharouf, O. Darwish, E.L. Ogden, J.J. Polashock, N.V. Bassil et al. 2012. Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biology 12:46-61.
42. Molina, C., M. Zaman-Allah, F. Khan, N. Fatnassi, R. Horres, B. Rotter et al. 2011. The salt-responsive transcriptome of chickpea roots and nodules via deep SuperSAGE. BMC Plant Biology 11:31-57.
43. Ranjan, A., D. Nigam, M.H. Asif, R. Singh, S. Ranjan, S. Mantri et al. 2012. Genome wide expression profiling of two accession of G. herbaceum L. in response to drought. BMC Genomics 13:94-112.
44. Dugas, D.V., M.K. Monaco, A. Olsen, R.R. Klein, S. Kumari, D. Ware et al. 2011. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics 12:514-535.
45. Sunkar, R., X. Zhou, Y. Zheng, W. Zhang, and J.K. Zhu. 2008. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology 8:25-42.
46. Meng, Y., and C. Shao. 2012. Large-scale identification of mirtrons in Arabidopsis and rice. PLoS One 7:31163-31170.
47. Li, B., Y. Qin, H. Duan, W. Yin, and X. Xia. 2011. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. Journal of Experimental Botany 62:3765-3779.
48. Wang, T., L. Chen, M. Zhao, Q. Tian, and W.-H. Zhang. 2011. Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12:367-378.
49. Kulcheski, F.R., L.F.V. Oliveira, L.G. Molina, M.P. Almerão, F.A. Rodrigues, J. Marcolino et al. 2011. Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics 12:307-324.
50. Lv, S., X. Nie, L. Wang, X. Du, S.S. Biradar, X. Jia et al. 2012. Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing. International Journal of Molecular Science 13:2973-2984.
51. Blanca, E.B.-F., L. Gao, N.N. Diop, Z. Wu, J.D. Ehlers, P.A. Roberts et al. 2011. Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biology 11:127-138.
52. Li, H., Y. Dong, H. Yin, N. Wang, J. Yang, X. Liu et al. 2011. Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biology 11:170-182.
53. Ren, Y., L. Chen, Y. Zhang, X. Kang, Z. Zhang, and Y. Wang. 2012. Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress. Functional and Integrative Genomics 10.1007/s10142-012-0271-6.
54. Tang, Z., L. Zhang, C. Xu, S. Yuan, F. Zhang, Y. Zheng et al. 2012. Uncovering small RNA-mediated responses to cold stress in a wheat thermo-sensitive genic male sterile line by deep sequencing. Plant Physiology 159(2):721-738.
55. Zhang, J., Y. Xu, Q. Huan, and K. Chong. 2009. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10:449-465.
56. An, F.-M., S.-R. Hsiao, and M.-T. Chan. 2011. Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in Phalaenopsis orchid. PLoS One 6:18937-18948.
57. Chen, L., Y. Zhang, Y. Ren, J. Xu, Z. Zhang, and Y. Wang. 2012. Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing. Biochemistry Biophysics Research Communication 417:892-896.
58. Zhao, M., H. Tai, S. Sun, F. Zhang, Y. Xu, and W.-X. Li. 2012. Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency. PLoS One 7:29669-29680.
59. Hsieh, L.-C., S.-I. Lin, A.C. Shih, J.-W. Chen, W.-Y. Lin, C.-Y. Tseng et al. 2009. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology 151:2120-2132.
60. Chen, L., T. Wang, M. Zhao, Q. Tian, and W.-H. Zhang. 2012. Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. Planta 235:375-386.
61. Moldovan, D., A. Spriggs, J. Yang, J.B. Pogson, E.S. Dennis, W. Iain et al. 2010. Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. Journal of Experimental Botany 61:165-177.
62. Li, T., H. Li, Y.-X. Zhang, and J.-Y. Liu. 2011. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acid Research 39:2821-2833.
63. Guo, H., Y. Kan, and W. Liu. 2011. Differential expression of miRNAs in response to topping in flue-cured tobacco (Nicotiana tabacum) roots. PLoS One 6:28565-28580.
64. Yu, X., H. Wang, Y. Lu, M.D. Ruiter, M. Cariaso, M. Prins et al. 2012. Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. Journal of Experimental Botany 63:1025-1038.
65. Chen, L., T. Wang, M. Zhao, and W. Zhang. 2012. Ethylene-responsive miRNAs in roots of Medicago truncatula identified by high-throughput sequencing at whole genome level. Plant Science 184:14-19.
66. Glaszmann, J.C., B. Kilian, H.D. Upadhyaya, and R.K. Varshney. 2010. Accessing genetic diversity for crop improvement. Current Opinion of Plant Biology 13:167-173.
67. Hawkins, R.D., G.C. Hon, and B. Ren. 2010. Next-generation genomics: An integrative approach. Nature Review Genetics 11:476-486.
68. Bansal, V., O. Harismendy, R. Tewhey, S.S. Murray, N.J. Schork, E.J. Topol et al. 2010. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Research 20:537-545.
69. Davey, J.W., P.A. Hohenlohe, P.D. Etter, J.Q. Boone, J.M. Catchen, and M.L. Blaxter. 2011. Genome-wide genetic marker discovery and genotyping using next generation sequencing. Nature Review Genetics 12:499-510.
70. You, F.M., N. Huo, K.R. Deal, Y.Q. Gu, M.C. Luo, P.E. McGuire et al. 2011. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genome 12:59-78.
71. van Orsouw, N.J., R.C.J. Hogers, A. Janssen, F. Yalcin, S. Snoeijers, E. Verstege et al. 2007. Complexity reduction of polymorphic sequences (CRoPS™): A novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2:1172-1182.
72. Mammadov, J.A., W. Chen, R. Ren, R. Pai, W. Marchione, F. Yalçin et al. 2010. Development of highly polymorphic SNP markers from the complexity reduced portion of maize (Zea mays L.) genome for use in marker-assisted breeding. Theoretical and Applied Genetics 121:577-588.
73. Baxter, S.W., J.W. Davey, J.S. Johnston, A.M. Shelton, D.G. Heckel, C.D. Jiggins et al. 2011. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One 6:19315-19326.
74. Huang, X., Q. Feng, Q. Qian, Q. Zhao, L. Wang, A. Wang et al. 2009. High-throughput genotyping by whole-genome resequencing. Genome Research 19:1068-1076.
75. Andolfatto, P., D. Davison, D. Erezyilmaz, T.T. Hu, J. Mast, T. Sunayama-Morita et al. 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Research 21:610-617.
76. Elshire, R.J., J.C. Glaubitz, Q. Sun, J.A. Poland, K. Kawamoto, E.S. Buckler et al. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:19379-19389.
77. Ossowski, S., K. Schneeberger, J.I. Lucas-Lledó, N. Warthmann, R.M. Clark, R.G. Shaw et al. 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92-94.
78. Pool, J.E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010. Population genetic inference from genomic sequence variation. Genome Research 20:291-300.
79. Ganal, M.W., T. Altmann, and M.S. Röder. 2009. SNP identification in crop plants. Current Opinion of Plant Biology 12:211-217.
80. Barbazuk, W.B., and P.S. Schnable. 2011. SNP discovery by transcriptome pyrosequencing. Methods in Molecular Biology 729:225-246.
81. Ahmad, R., D.E. Parfitt, J. Fass, E. Ogundiwin, A. Dhingra, T.M. Gradziel et al. 2011. Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics 12:569-576.
82. Mondini, L., M. Nachit, E. Porceddu, and M.A. Pagnotta. 2012. Identification of SNP mutations in DREB1, HKT1, and WRKY1 genes involved in drought and salt stress tolerance in durum wheat (Triticum turgidum L. var durum). Omics: A Journal of Integrative Biology 16:178-187.
83. Li, Y., G. Haseneyer, C.-C. Schön, D. Ankerst, V. Korzun, P. Wilde et al. 2011. High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response. BMC Plant Biology 11:6-20.
84. Hao, Z., X. Li, C. Xie, J. Weng, M. Li, D. Zhang et al. 2011. Identification of functional genetic variations underlying drought tolerance in maize using SNP markers. Journal of Integrated Plant Biology 53:641-652.
85. Lu, Y., S. Zhang, T. Shah, C. Xie, Z. Hao, X. Li et al. 2010. Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proceedings of the National Academy of Sciences of the United States of America 107:19585-19590.
86. Hao, G.P., Z.Y. Wu, M.Q. Cao, G. Pelletier, D. Brunel, C.L. Huang et al. 2004. Nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana and its molecular evolution analyses. Yi Chuan Xue Bao 31:1415-1425.
87. Tao, Z., Y. Kou, H. Liu, X. Li, J. Xiao, and S. Wang. 2011. OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice. Journal of Experimental Botany 62:4863-4874.
88. Kumar, G.R., K. Sakthive, R.M. Sundaram, C.N. Neeraja, S.M. Balachandran, R.N. Shobha et al. 2010. Allele mining in crops: Prospects and potentials. Biotechnology Advances 28:451-461.
89. Homolka, A., T. Eder, D. Kopecky, M. Berenyi, K. Burg, and S. Fluch. 2012. Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing. BMC Research Notes 5:175-185.
90. Abdurakhmonov, I., and A. Abdukarimov. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics 5:1-18.
91. Zhao, K., C.W. Tung, G.C. Eizenga, M.H. Wright, M.L. Ali, A.H. Price et al. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communication 2:467-475.
92. Frary, A., T.C. Nesbitt, A. Frary, S. Grandillo, E. van der Knaap, B. Cong et al. 2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289:85-88.
93. Komatsuda, T., M. Pourkeirandish, C. He, P. Azhaguvel, H. Kanamori, D. Perovic et al. 2007. Six-rowed barley originated from a mutation in a homeodomainleucine zipper I-class homeobox gene. Proceedings of the National Academy of Sciences of the United States of America 104:1424-1429.
94. Schuenemann, V.J., K. Bos, S. DeWitte, S. Schmedes, J. Jamieson, A. Mittnik et al. 2011. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proceedings of the National Academy of Sciences of the United States of America 108:746-752.
95. Hall, D. 2010. Using association mapping to dissect the genetic basis of complex traits in plants. Brief Functional Genomics 9:157-165.
96. Yu, J., J.B. Holland, M.D. McMullen, and E.S. Buckler. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178:539-551.
97. Mackay, T.F.C., E.A. Stone, and J.F. Ayroles, 2009. The genetics of quantitative traits: Challenges and prospects. Nature Review Genetics 10:565-577.
98. Rafalski, J.A. 2010. Association genetics in crop improvement. Current Opinion of Plant Biology 13:174-180.
99. Setter, T.L., J. Yan, M. Warburton, J.M. Ribaut, Y. Xu, M. Sawkins et al. 2010. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. Journal of Experimental Botany 62:701-716.
100. Till, B.J., S.H. Reynolds, E.A. Greene, C.A. Codomo, L.C. Enns, J.E. Johnson et al. 2003. Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Research 13:524-530 (http://genome.cshlp.org/content/13/3/524.abstract-target-2).
101. Henikoff, S., and L. Comai. 2003. Single-nucleotide mutations for plant functional genomics. Annual Review of Plant Biology 54:375-401.
102. Henikoff, S., B.J. Till, and L. Comai. 2004. TILLING: Traditional mutagenesis meets functional genomics. Plant Physiology 135:630-636.
103. Comai, L., and S. Henikoff. 2006. TILLING: Practical single-nucleotide mutation discovery. The Plant Journal 45:684-694.
104. Cordeiro, G.M., F. Eliott, C.L. McIntyre, R.E. Casu, and R.J. Henry. 2006. Characterization of single nucleotide polymorphisms in sugarcane ESTs. Theoretical and Applied Genetics 113:331-343.
105. Cross, M., S.L. Lee, and R.J. Henry. 2007. A novel detection strategy for scanning multiple mutations using CEL I. Paper presented at the Plant and Animal Genomes Conference XV, Mutation Screening Workshop, San Diego, CA. January 13-17, 2007.
106. Negrão, S., C. Almadanim, I. Pires, K.L. McNally, and M.M. Oliveira. 2011. Use of EcoTILLING to identify natural allelic variants of rice candidate genes involved in salinity tolerance. Plant Genetic Resources 9:300-304.
107. Naredo, Ma. E.B., J. Cairns, H. Wang, G. Atienza, M.D. Sanciangco, R.J.A. Melgar et al. 2009. EcoTILLING as a SNP discovery tool for drought candidate genes in Oryza sativa germplasm. Philippine Journal of Crop Science 34:10-16.
108. Cseri, A., M. Cserháti, M. von Korff, B. Nagy, G.V. Horváth, A. Palágyi et al. 2011. Allele mining and haplotype discovery in barley candidate genes for drought tolerance. Euphytica 181:341-356.
109. Till, B.J., T. Zerr, L. Comai, and S. Henikoff. 2006. A protocol for TILLING and ecotilling in plants and animals. Nature Protocols 1:2465-2477.
110. Rigola, D., J.V. Oeveren, A. Janssen, A. Bonne, H. Schneiders, H.J.A. van der Poel et al. 2009. High-throughput detection of induced mutations and natural variation using KeyPoint™ technology. PLoS One 4:4761-4770.