Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice

Molecular Breeding

Volumn 24, Issue 1, 2009, Pages 93-101

  Lee, Gi An ^a,b   Koh, Hee Jong ^b   Chung, Hun Ki ^a   Dixit, Anupam ^c   Chung, Jong Wook ^d   Ma, Kyung Ho ^a   Lee, Sok Young ^a   Lee, Jung Ro ^a   Lee, Gang Seob ^a   Gwag, Jae Gyun ^a   Kim, Tae San ^a   Park, Yong Jin ^e  

^a National Institute of Animal Science   (South Korea)

^b Seoul National University   (South Korea)

^c SARDAR VALLABHBHAI PATEL UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

^d Konkuk University   (South Korea)

^e Kongju National University   (South Korea)

Author keywords

DNA marker; Genotyping; Rice; SNP (single nucleotide polymorphism); Starch biosynthesis

Indexed keywords

BIOCHEMISTRY; BIOSYNTHESIS; CLUSTER ANALYSIS; GENES; NUCLEOTIDES; PLANTS (BOTANY);

CLEAVED AMPLIFIED POLYMORPHIC SEQUENCES; DNA MARKERS; GENOTYPING; HIGHLY STABLES; MEAN VALUES; PHENOTYPIC VARIATIONS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISMS; STARCH BIOSYNTHESIS;

STARCH;

EID: 70349980670     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-009-9278-7     Document Type: Article

References (34)

1. Bao JS, Sun M, Corke H (2002) Analysis of the genetic behavior of some starch properties in indica rice: thermal properties, gel texture, swelling volume (Oryza sativa L.). Theor Appl Genet 104:408-413. doi:10.1007/s001220100688
2. Bao JS, Corke H, Sun M (2006a) Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theor Appl Genet 113:1185-1196. doi:10.1007/s00122-006-0394-z
3. Bao JS, Corke H, Sun M (2006b) Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor Appl Genet 113:1171-1183. doi:10.1007/s00122-006-0355-6
4. Barany F (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA 88:189-193. doi:10.1073/pnas.88.1.189
5. Bhave MR, Lawrence S, Barton C, Hannah LC (1990) Identification and molecular characterization of shrunken-2 cDNA clones of maize. Plant Cell 2:581-588
6. Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) Aberrant splicing of intron 1 leads to the heterogeneous 50 UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 14:459-465. doi:10.1046/j.1365-313X.1998.00126.x
7. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19-21. doi:10.1007/BF02712670
8. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524-535
9. Hannah LC, Nelson OE (1976) Characterization of ADP-glucose pyrophosphorylase from shrunken-2 and brittle-2 mutants of maize. Biochem Genet 14:547-560. doi:10.1007/BF00485834
10. Hirano HY, Sano Y (1998) Enhancement of Wx gene expression and the accumulation of amylose in response to cool temperatures during seed development in rice. Plant Cell Physiol 39:807-812
11. Isaksson A, Landegren U, Syvaenen AC (2000) Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem. Eur J Hum Genet 8:154-156. doi:10.1038/sj.ejhg.5200424
12. Issiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 50 splice site of the first intron. Plant J 15:133-138. doi:10.1046/j.1365-313X.1998.00189.x
13. James MG, Denyer K, Myers AM (2003) Starch synthesis in the cereal endosperm. Curr Opin Plant Biol 6:215-222. doi:10.1016/S1369-5266(03)00042-6
14. Juliano BO (1971) A simplified assay for milled-rice amylose. Cereal Sci Today 16:334-340
15. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403-410. doi:10.1046/j.1365-313X.1993.04020403.x
16. Labrune P, Melle D, Rey F (1991) Single-strand conformation polymorphism for detection of mutations and base substitutions in phenylketonuria. Am J Hum Genet 48:1115
17. Landegren U, Nilsson M, Kwok PY (1998) Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res 8:769-776
18. Larkin PD, Park WD (2003) Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.). Mol Breed 12:335-339. doi:10.1023/B:MOLB.0000006797.51786.92
19. Larkin PD, McClung AM, Ayres NM, Park WD (2003) The effect of the waxy locus (Granule bound starch synthase) on pasting curve characteristics in specialty rice (Oryza sativa L.). Euphytica 131:243-253. doi:10.1023/A:1023962406605
20. Liu K, Muse SV (2005) Power marker: an integrated analysis environment for genetic marker analysis. Oxford University Press, USA, pp 2128-2129
21. Myers RM, Lumelsky N, Lerman LS, Maniatis T (1985) Detection of single base substitutions in total genomic DNA. Nature 313:495-498. doi:10.1038/313495a0
22. Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387-392. doi:10.1046/j.1365-313X.1998.00124.x
23. Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613-615. doi:10.1016/S0168-9525(02)02820-2
24. Newton CR, Graham A, Heptinstall LE (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17:2503-2516. doi:10.1093/nar/17.7.2503
25. Preiss J (1997) Modulation of starch synthesis. In: Foyer CH, Quick WP (eds) A molecular approach to primary metabolism in higher plants. Tailor & Francis Ltd, London, pp 81-104
26. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94-100. doi:10.1016/S1369-5266(02)00240-6
27. Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467-473. doi:10.1007/BF00254822
28. Sarkar G, Yoon HS, Sommer SS (1992) Dideoxy fingerprinting (ddE): a rapid and efficient screen for the presence of mutations. Genomics 13:441-443. doi:10.1016/0888-7543(92)90266-U
29. Schultz JA, Juvik JA (2004) Current models for starch synthesis and the sugary enhancer1 (se1) mutation in Zea mays. Plant Physiol Biochem 42:457-464. doi:10.1016/j.plaphy.2004.05.008
30. Shirasawa K, Monna L, Kishitani S, Nishio T (2004) Single nucleotide polymorphisms in randomly selected genes among japonica rice (Oryza sativa L.). Varieties identified by PCR-RF-SSCP. DNA Res 11:275-283. doi:10.1093/dnares/11.4.275
31. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-517. doi:10.1016/S0022-2836(75)80083-0
32. Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A (2003) Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Sci Limerick 165:1193-1199. doi:10.1016/S0168-9452(03)00326-1
33. Wang ZY, Zheng FQ, Shen GZ, Gao JP, Snustad DP, Li MG, Zhang JL, Hong MM (1995) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613-622. doi:10.1046/j.1365-313X.1995.7040613.x
34. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92. doi:10.1126/science.1068037