Development and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Chawade, Aakash ^a   Sikora, Per ^a   Bräutigam, Marcus ^a,b   Larsson, Mikael ^c   Vivekanand, Vivekanand ^a   Nakash, Montedar A ^b   Chen, Tingsu ^a,d   Olsson, Olof ^a,b  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b Erik Dahlbergsgatan 11A   (Sweden)

^c CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^d NATIONAL ENGINEERING RESEARCH CENTER FOR NON FOOD BIOREFINERY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; AVENA SATIVA;

BETA GLUCAN; LIGNIN; MESYLIC ACID ETHYL ESTER; PHLOROGLUCINOL;

ARTICLE; BIOSYNTHESIS; CHROMOSOME SEGREGATION; DNA SEQUENCE; DRUG EFFECT; GENETIC SCREENING; GENETICS; MASS SPECTROMETRY; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; MUTAGENESIS; MUTATION; NUCLEOTIDE SEQUENCE; OAT; PHENOTYPE; PLANT GENE; POLYMERASE CHAIN REACTION; POPULATION GENETICS; RANDOM AMPLIFIED POLYMORPHIC DNA; REPRODUCIBILITY;

AVENA SATIVA; BASE SEQUENCE; BETA-GLUCANS; CHROMOSOME SEGREGATION; CLONING, MOLECULAR; ETHYL METHANESULFONATE; GENES, PLANT; GENETIC TESTING; GENETICS, POPULATION; LIGNIN; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTATION; PHENOTYPE; PHLOROGLUCINOL; POLYMERASE CHAIN REACTION; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 77954569490     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-86     Document Type: Article

References (60)

1. Grass phylogeny working group. , http://www.umsl.edu/services/kellogg/gpwg/default.htm
2. FAO Food and Agriculture Organization. ProdSTAT; FAOSTAT 2008, FAO.
3. World Agricultural Production. , http://www.fas.usda.gov/wap_arc.asp
4. Suttie JM, Reynolds SG. Fodder oats: a world overview. FAO Plant Production and Protection Series 2004, 266. FAO.
5. Aman P, Graham H. Analysis of total and insoluble mixed-linked (1,3;1,4) beta.-D-glucans in barley and oats. Journal of Agricultural Food Chemistry 1987, 35(5):704-709.
6. Brown L, Rosner B, Willett WW, Sacks FM. Cholesterol-lowering effects of dietary fiber: a meta-analysis. Am J Clin Nutr 1999, 69(1):30-42.
7. Davidson MH, Dgan LD, Burns JH, Bova J, Story K, Drennan KB. The hypocholesterolemic effects of beta-glucan in oatmeal and oat bran. A dose-controlled study. JAMA 1991, 265(14):1833-1839. 10.1001/jama.265.14.1833, 2005733.
8. Ripsin CM, Keenan JM, Jacobs DR, Elmer PJ, Welch RR, Van Horn L, Liu K, Turnbull WH, Thye FW, Kestin M, et al. Oat products and lipid lowering. A meta-analysis. JAMA 1992, 267(24):3317-3325. 10.1001/jama.267.24.3317, 1317928.
9. Shewry PR, Piironen V, Lampi AM, Nystrom L, Li L, Rakszegi M, Fras A, Boros D, Gebruers K, Courtin CM, et al. Phytochemical and fiber components in oat varieties in the HEALTHGRAIN Diversity Screen. J Agric Food Chem 2008, 56(21):9777-9784. 10.1021/jf801880d, 18921980.
10. Leeds AR. Oats reassessed. Nutrition Bulletin 2007, 13:153-160.
11. Stoskopf NC, Nathaniel RK, Reinbergs E. Comparison of Spring Wheat and Barley with Winter Wheat: Yield Components in Ontario1. Agron J 1974, 66:748-750.
12. Watson DJ, Thorne GN, French SAW. Analysis of Growth and Yield of Winter and Spring Wheats. Annals of Botany 1963, 27.
13. Casler MD, Jung HJ. Relationships of fibre, lignin, and phenolics to in vitro fibre digestibility in three perennial grasses. Animal feed science and technology 2006, 125(1-2):151-161.
14. Jung HJ. Forage lignins and their effect on fiber digestibility. J Agron 1989, 81:33-38.
15. van Egmond HP, Schothorst RC, Jonker MA. Regulations relating to mycotoxins in food: perspectives in a global and European context. Anal Bioanal Chem 2007, 389(1):147-157. 10.1007/s00216-007-1317-9, 17508207.
16. Rines HW, Molnar SJ, Tinker NA, Phillips RL. Oat. In Genome Mapping and Molecular Breeding in Plants, Cereals and Millets 2006, 1:211-242. Berlin: Springer-Verlag, Kole C.
17. Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzl P, Rines HW, Bjornstad A, Howarth CJ, Jannink JL, Anderson JM, et al. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics 2009, 10:39. 10.1186/1471-2164-10-39, 2661094, 19159465.
18. Bennett MD, Smith JB. Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 1976, 274(933):227-274. 10.1098/rstb.1976.0044, 6977.
19. Leggett JM. Classification and Speciation of Avena. Oat Science and Technology, Agronomy Monograph 33 1992, 29-52. Madison WI: American Society of Agronomy and Crop Science, Sorrells ME, Marshall HG.
20. Brautigam M, Lindlof A, Zakhrabekova S, Gharti-Chhetri G, Olsson B, Olsson O. Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biol 2005, 5:18. 10.1186/1471-2229-5-18, 1236939, 16137325.
21. Hoffmann GR. Genetic effects of dimethyl sulfate, diethyl sulfate, and related compounds. Mutat Res 1980, 75(1):63-129.
22. McCallum CM, Comai L, Greene EA, Henikoff S. Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 2000, 123(2):439-442. 10.1104/pp.123.2.439, 1539256, 10859174.
23. Bentley A, MacLennan B, Calvo J, Dearolf C. Targeted recovery of mutations in Drosophila. Genetics 2000, 156(3):1169-1173. 1461331, 11063692.
24. Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson JE, Odden AR, et al. Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 2003, 164(2):731-740. 1462604, 12807792.
25. Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R. A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 2004, 40(1):143-150. 10.1111/j.1365-313X.2004.02190.x, 15361148.
26. Talame V, Bovina R, Sanguineti MC, Tuberosa R, Lundqvist U, Salvi S. TILLMore, a resource for the discovery of chemically induced mutants in barley. Plant Biotechnol J 2008, 6(5):477-485. 10.1111/j.1467-7652.2008.00341.x, 18422888.
27. Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M, Wang TL. TILLING mutants of Lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. Plant Physiol 2007, 144(2):806-820. 10.1104/pp.107.097063, 1914161, 17468221.
28. Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M. A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 2003, 131(3):866-871. 10.1104/pp.102.017384, 1540285, 12644638.
29. Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D. A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 2005, 23(1):75-81. 10.1038/nbt1043, 15580263.
30. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, et al. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 2004, 4:12. 10.1186/1471-2229-4-12, 512284, 15282033.
31. Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N. MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 2008, 279(3):213-223. 10.1007/s00438-007-0293-2, 17952471.
32. Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S, Comai L. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 2007, 7:19. 10.1186/1471-2229-7-19, 1858691, 17428339.
33. Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Clepet C, Aubourg S, Rameau C, Caboche M, Bendahmane A. Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 2007, 51(6):1116-1125. 10.1111/j.1365-313X.2007.03201.x, 17651368.
34. Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, et al. TILLING to detect induced mutations in soybean. BMC Plant Biol 2008, 8:9. 10.1186/1471-2229-8-9, 2266751, 18218134.
35. Jalani BS, Frey KJ, Bailey TB. Contribution of growth rate and harvest index to grain yield of oats (Avena sativa L.) following selfing and outcrossing of M1 plants. Euphytica 1979, 28(2):219-225.
36. Boom D, Ehrich M. Discovery and identification of sequence polymorphisms and mutations with MALDI-TOF MS. Methods Mol Biol 2007, 366:287-306. full_text, 17568131.
37. Guo D, Chen F, Inoue K, Blount JW, Dixon RA. Downregulation of caffeic acid 3-O-methyltransferase and caffeoyl CoA 3-O-methyltransferase in transgenic alfalfa. impacts on lignin structure and implications for the biosynthesis of G and S lignin. Plant Cell 2001, 13(1):73-88. 10.1105/tpc.13.1.73, 102215, 11158530.
38. Rowe JB, Crosbie GB. The digestibility of grain of two cultivars of oats differing in lignin content. Australian Journal of Agricultural Research 1988, 39(4):639-644.
39. Nilsson U, Johansson M, Nilsson A, Bjorck I, Nyman M. Dietary supplementation with beta-glucan enriched oat bran increases faecal concentration of carboxylic acids in healthy subjects. Eur J Clin Nutr 2008, 62(8):978-984. 10.1038/sj.ejcn.1602816, 17522598.
40. Doyle JJ, Doyle JL, Bailey-Hortorium LH. Isolation of plant DNA from fresh tissue. Focus 1990, 12:13-15.
41. Speer EO. A method of retaining phloroglucinol proof of lignin. Stain Technol 1987, 62(4):279-280.
42. Dence CW. The determination of lignin. Methods in lignin chemistry 1992, 33-61. heidelberg: Springer Verlag, Lin SY, Dence CW.
43. Thompson RK, Mustafa AF, McKinnon JJ, Maenz D, Rossnagel B. Genotypic differences in chemical composition and ruminal degradability of oat hulls. Can J Anim Sci 2000, 80:377-379.
44. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4(7):1073-1081. 10.1038/nprot.2009.86, 19561590.
45. PSSM viewer. , http://www.ncbi.nlm.nih.gov/Class/Structure/pssm/pssm_viewer.cgi
46. Henikoff S, Comai L. Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 2003, 54:375-401. 10.1146/annurev.arplant.54.031902.135009, 14502996.
47. Rajhathy T, Hugh T. Cytogenetics of oats (avena L.). 1974, Q = Ottawa: la Societe de Genetique du Canada.
48. Nomura T, Ishihara A, Yanagita RC, Endo TR, Iwamura H. Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat. Proc Natl Acad Sci USA 2005, 102(45):16490-16495. 10.1073/pnas.0505156102, 1283429, 16260753.
49. Monties B. Plant Phenolics. Methods in Plant Biochemistry 1989, 1:113-157. New York: Academic Press, Dey PM, Harborne JB.
50. Hatfield R, Fukshima RS. Can lignin be accuretely measured?. Crop science 2005, 45(3):832-839.
51. Neish WJ, Key L. Polyamines and glutathione in tissues of lactating rats (Rattus rattus) and in the Rd-3 adcites tumour. Comp Biochem Physiol 1968, 27(3):709-714. 10.1016/0010-406X(68)90611-7, 5751557.
52. Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A, Fincher GB. Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1,3;1,4)-beta-D-glucans. Science 2006, 311(5769):1940-1942. 10.1126/science.1122975, 16574868.
53. Doblin MS, Pettolino FA, Wilson SM, Campbell R, Burton RA, Fincher GB, Newbigin E, Bacic A. A barley cellulose synthase-like CSLH gene mediates (1,3;1,4)-beta-D-glucan synthesis in transgenic Arabidopsis. Proc Natl Acad Sci USA 2009, 106(14):5996-6001. 10.1073/pnas.0902019106, 2667043, 19321749.
54. Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, et al. Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 2003, 13(3):524-530. 10.1101/gr.977903, 430291, 12618384.
55. Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S. High-throughput screening for induced point mutations. Plant Physiol 2001, 126(2):480-484. 10.1104/pp.126.2.480, 1540114, 11402178.
56. Stanssens P, Zabeau M, Meersseman G, Remes G, Gansemans Y, Storm N, Hartmer R, Honisch C, Rodi CP, Bocker S, et al. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res 2004, 14(1):126-133. 10.1101/gr.1692304, 314289, 14707174.
57. Tost J, Gut IG. Genotyping single nucleotide polymorphisms by MALDI mass spectrometry in clinical applications. Clin Biochem 2005, 38(4):335-350. 10.1016/j.clinbiochem.2004.12.005, 15766735.
58. Zhong R, Iii WH, Negrel J, Ye ZH. Dual methylation pathways in lignin biosynthesis. Plant Cell 1998, 10(12):2033-2046. 10.1105/tpc.10.12.2033, 143971, 9836743.
59. Iiyama K, Wallis AFA. An improved acetyl bromide procedure for determining lignin in woods and wood pulps. Wood Science and Technology 1988, 22(3):271-280.
60. Morrison IM. A semi-micro method for the determination of lignin and its use in predicting the digestibility of forage crops. J Sci Food Agric 1972, 23(6):455-463. 10.1002/jsfa.2740230405, 5029974.