SNPs and an insertion sequence in five Wx-A1 alleles as factors for variant Wx-A1 protein in wheat

Euphytica

Volumn 192, Issue 3, 2013, Pages 325-338

  Yamamori, Makoto ^a   Guzmán, Carlos ^b  

^a NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^b UNIVERSITY OF CÓRDOBA   (Spain)

Author keywords

Insertion sequence; SNP; Starch; Triticum aestivum; Triticum dicoccoides; Wx gene

Indexed keywords

TRITICUM AESTIVUM; TRITICUM TURGIDUM SUBSP. DICOCCOIDES;

EID: 84880513589     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-012-0850-6     Document Type: Article

References (46)

1. Ainsworth C, Clark J, Balsdon J (1993) Expression, organization and structure of the genes encoding the waxy protein (granule-bound starch synthase) in wheat. Plant Mol Biol 22: 67-82.
2. Akagi H, Yokozeki Y, Inagaki A, Mori K, Fujimura T (2001) Micron, a microsatellite-targeting transposable element in the rice genome. Mol Genet Genomics 266: 471-480.
3. Clark JR, Robertson M, Ainsworth CC (1991) Nucleotide sequence of a wheat (Triticum aestivum L.) cDNA clone encoding the waxy protein. Plant Mol Biol 16: 1099-1101.
4. Cui X, Hsia AP, Liu F, Ashlock DA, Wise RP, Schnable PS (2003) Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics 163: 685-698.
5. Divashuk MG, Klimushina MV, Karlov GI (2011) Molecular genetic characteristics of the Wx-B1e allele from common wheat and applicability of the DNA markers for its identification. Russian J Genet 47: 1428-1432.
6. Fujita S, Kumagai T, Yanagimachi M, Sakuraba S, Sanpei R, Yamoto M, Tohara H (2012) Waxy wheat as a functional food for human consumption. J Cereal Sci 55: 361-365.
7. Guzman C, Caballero L, Alvarez JB (2011) Molecular characterization of the Wx-B1 allelic variants identified in cultivated emmer wheat and comparison with those of durum wheat. Mol Breed 28: 403-411.
8. Guzman C, Caballero L, Yamamori M, Alvarez JB (2012) Molecular characterization of a new waxy allele with partial expression in spelt wheat. Planta 235: 1331-1339.
9. Han XZ, Campanella OH, Guan H, Keeling PL, Hamaker BR (2002) Influence of maize starch granule-associated protein on the rheological properties of starch paste. Part I. Large deformation measurements of paste properties. Carbohydr Polym 49: 315-321.
10. Huang XQ, Brûlé-Babel A (2010) Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples. BMC Research Notes 3: 140.
11. Inukai T, Sako A, Hirano HY, Sano Y (2000) Analysis of intragenic recombination at wx in rice: correlation between the molecular and genetic maps within the locus. Genome 43: 589-596.
12. Jegasothy H, Wootton M, Fairclough RJ (2000) Agarose gel electrophoresis of wheat starch. J Cereal Sci 31: 75-78.
13. Jin Y, Bian T (2004) Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10: 1695-1697.
14. Kimura T, Saito A (2010) Heterogeneity of poly(A) sites in the granule-bound starch synthase I gene in sweet potato (Ipomoea batatas (L.) Lam.). Biosci Biotechnol Biochem 74: 667-669.
15. Kluth A, Sprunck S, Becker D, Lörz H, Lütticke S (2002) 5′ deletion of a gbss1 promoter region from wheat leads to changes in tissue and developmental specificities. Plant Mol Biol 49: 669-682.
16. Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
17. Leterrier M, Holappa LD, Broglie KE, Beckles DM (2008) Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications. BMC Plant Biol 8: 98.
18. Li Z, Chu X, Mouille G, Yan L, Kosar-Hashemi B, Hey S, Napier J, Shewry P, Clarke B, Appels R, Morell MK, Rahman S (1999) The localization and expression of the class II starch synthases of wheat. Plant Physiol 120: 1147-1155.
19. Li Z, Mulligan MK, Wang X, Miles MF, Lu L, Williams RW (2010) A transposon in Comt generates mRNA variants and causes widespread expression and behavioral differences among mice. PLoS ONE 5(8): e12181.
20. Li W, Gao Z, Xiao W, Wei YM, Liu YX, Chen GY, Pu ZE, Chen HP, Zheng YL (2012) Molecular diversity of restriction enzyme sites, Indels and upstream open reading frames (uORFs) of 50 untransalted regions (UTRs) of Waxy genes in Triticum L. and Aegilops L. species. Genet Resour Crop Evol. doi: 10. 1007/s10722-011-9787-1.
21. MacGregor EA (2002) Possible structure and active site residues of starch, glycogen and sucrose synthases. J Protein Chem 21: 297-306.
22. Maningat CC, Seib PA, Bassi SD, Woo KS, Lasater GD (2009) Wheat starch: production properties, modification and uses. In: BeMiller J, Whistler R (eds) Starch: chemistry and technology, 3rd edn. Elsevier, New York, pp 441-510.
23. McIntosh RA, Dubcovsky J, Rogers WJ, Morris C, Appels R, Xia XC (2011) Catalogue of gene symbols for wheat. Komugi website, http://www. shigen. nig. ac. jp/wheat/komugi/genes/symbolClassList. jsp. accessed 30 June 2012.
24. Miura H, Araki E, Tarui S (1999) Amylose synthesis capacity of the three Wx genes of wheat cv. Chinese Spring. Euphytica 108: 91-95.
25. Monari AM, Simeone MC, Urbano M, Margiotta B, Lafiandra D (2005) Molecular characterization of new waxy mutants identified in bread and durum wheat. Theor Appl Genet 110: 1481-1489.
26. Morell M (2009) Wheat starch-structure, synthesis and functionality. In: Khan K, Shewry PR (eds) Wheat chemistry and technology, 4th edn. AACC International Inc, St Paul, pp 302-319.
27. Murai J, Taira T, Ohta D (1999) Isolation and characterization of the three Waxy genes encoding the granule-bound starch synthase in hexaploid wheat. Gene 234: 71-79.
28. Nakamura T, Vrinten P, Saito M, Konda M (2002) Rapid classification of partial waxy wheats using PCR-based markers. Genome 45: 1150-1156.
29. Nichols DJ, Keeling PL, Spalding M, Guan H (2000) Involvement of conserved aspartate and glutamate residues in the catalysis and substrate binding of maize starch synthase. Biochemistry 39: 7820-7825.
30. O'Brien L, Blakeney AB (1985) A census of methodology used in wheat variety development in Australia. Cereal Chem Division, R Aust Chem Institute, Melbourne (cited by Wrigley 2009).
31. Saito M, Nakamura T (2005) Two point mutations identified in emmer wheat generate null Wx-A1 alleles. Theor Appl Genet 110: 276-282.
32. Saito M, Konda M, Vrinten P, Nakamura K, Nakamura T (2004) Molecular comparison of waxy null alleles in common wheat and identification of a unique null allele. Theor Appl Genet 108: 1205-1211.
33. Shariflou MR, Sharp PJ (1999) A polymorphic microsatellite in the 3′ end of 'waxy' genes of wheat, Triticum aestivum. Plant Breed 118: 275-277.
34. Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ (2008) Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation. Nucleic Acids Res 36: 3150-3161.
35. Sim N-L, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40: Web Server issue W452-457. doi: 10. 1093/nar/gks539.
36. Soulaka AB, Morrison WR (1985) The amylose and lipid contents, dimensions, and gelatinisation characteristics of some wheat starches and their A- and B-granule fractions. J Sci Food Agric 36: 709-718.
37. Vanzetti LS, Pflüger L, Bainotti CT, Jensen C, Helguera M (2010) Identification of a null allele at the Wx-A1 locus in durum wheat (Triticum turgidum L. spp. durum Desf.). Plant Breed 129: 718-720.
38. Vrinten P, Nakamura T, Yamamori M (1999) Molecular characterization of waxy mutations in wheat. Mol Gen Genet 261: 463-471.
39. Wrigley CW (2009) Wheat: a unique grain for the world. In: Khan K, Shewry PR (eds) Wheat chemistry and technology, 4th edn. AACC International Inc, St Paul, pp 1-17.
40. Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ, Hunt AG (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci USA 108: 12533-12538.
41. Yamamori M (2009) Amylose content and starch properties generated by five variant Wx alleles for granule-bound starch synthase in common wheat (Triticum aestivum L.). Euphytica 165: 607-614.
42. Yamamori M, Yamamoto K (2011) Effects of two novel Wx-A1 alleles of common wheat (Triticum aestivum L.) on amylose and starch properties. J Cereal Sci 54: 229-235.
43. Yamamori M, Nakamura T, Endo TR, Nagamine T (1994) Waxy protein deficiency and chromosomal location of coding genes in common wheat. Theor Appl Genet 89: 179-184.
44. Yamamori M, Nakamura T, Nagamine T (1995) Polymorphism of two waxy proteins in the emmer group of tetraploid wheat, Triticum dicoccoides, T. dicoccum, and T. durum. Plant Breed 114: 215-218.
45. Yanagisawa T, Kiribuchi-Otobe C, Yoshida H (2001) An alanine to threonine change in the Wx-D1 protein reduces GBSSI activity in waxy mutant wheat. Euphytica 121: 209-214.
46. Yep A, Ballicora MA, Sivak MN, Preiss J (2004) Identification and characterization of a critical region in the glycogen synthase from Escherichia coli. J Biol Chem 279: 8359-8367.