Analysis of Starch Gene Diversity in the Wild Relatives of Oryza sativa

Tropical Plant Biology

Volumn 5, Issue 4, 2012, Pages 286-308

  Kasem, Shabana ^a   Waters, Daniel L E ^a   Henry, Robert J ^b  

^a SOUTHERN CROSS UNIVERSITY   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Genome; Oryza; Oryza sativa; Phylogeny; Rice; Starch; Wild rice

Indexed keywords

ORYZA; ORYZA SATIVA; POTAMOPHILA PARVIFLORA; ZIZANIA; ZIZANIA PALUSTRIS;

EID: 84871193725     PISSN: 19359756     EISSN: 19359764     Source Type: Journal    
DOI: 10.1007/s12042-012-9111-z     Document Type: Article

References (83)

1. Abbott RJ, Lowe AJ (2004) Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles. Biol J Linn Soc 82: 467-474.
2. Abedinia M, Henry RJ, Cripps-Clark S (1998) Distribution and phylogeny of Potamophila parviflora R. Br wild rice from eastern Australia. Genet Resour Crop Evol 45: 399-406.
3. Aggarwal RK, Brar DS, Nandi S et al (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98: 1320-1328.
4. Ammirajua JSS, Lub F, Sanyalc A et al (2008) Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20: 3191-3209.
5. Andersson L (2001) Studies on starch structure and the differential properties of starch branching enzymes. Swedish University, Uppsala, pp 1-36.
6. Ashikari M, Matsuoka M (2006) Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci 11: 344-350.
7. Bao J, Kong X, Xie J et al (2004) Analysis of genotypic and environmental effects on rice starch apparent amylose content, pasting viscosity, and gel texture. J Agric Food Chem 52: 6010-6016.
8. Bautista NS, Solis R, Kamijima O et al (2001) RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice. Genes Genet Syst 76: 71-79.
9. Bennetzen JL, Freeling M (1997) The unified grass genome: synergy in synteny. Genome Res 7: 301-346.
10. Brar D, Kush G (1997) Alien introgression in rice. Plant Mol Biol 35: 35-47.
11. Buso GSC, Rangel PHN, Ferreira ME (2001) Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid American wild rice species (Oryza spp.). Genome 44: 476-494.
12. Chen MH, Bergman CJ, Pinson SRM et al (2008a) Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection. J Cereal Sci 48: 781-788.
13. Chen M-H, Bergman C, Pinson S et al (2008b) Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection. J Cereal Sci 47: 536-545.
14. Cheng C, Tsuchimoto S, Ohtsubo H et al (2002) Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet Syst 77: 323-334.
15. Cranston KA, Hurwitz B, Ware D et al (2009) Species trees from highly incongruent gene trees in rice. Syst Biol 58: 489-500.
16. Dally AM, Second G (1990) Chloropast DNA diversity in wild and cultivated species of rice (genus Oryza, Section Oryza), cladistic mutation and genetic distance analysis. Theor Appl Genet 80: 209-222.
17. Doolittle WF (1999) Lateral genomics. Trends Genet 15: M5-M8.
18. Duan S, Lu B, Li Z et al (2007) Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences. Biochem Genet 45: 113-129.
19. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89: 3-10.
20. Freeling M (2001) Grasses as a single genetic system. Reassessment 2001. Plant Physiol 125: 1191-1197.
21. Gaut BS, Clegg MT (1993) Nucleotide polymorphism in the Adh1 locus of Pearl Millet (Pennisetum Glaucum) (Poaceae). Genetics 135: 1091-1097.
22. Ge S, Sang T, Lu B-R et al (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. PNAS 96: 14400-14405.
23. Guan HP, Keeling PL (1998) Starch biosynthesis: understanding the functions and interactions of multiple isozymes of starch synthase and branching enzyme. Trends Glycosci Glycotechnol 10: 307-319.
24. Guo Y-L, Ge S (2005) Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes. Am J Bot 92: 1548-1558.
25. Guo Y, Ma Y, Zhan Z et al (2006) Parameter optimization and field validation of the functional-structural model GREENLAB for maize. Ann Bot 97: 217-230.
26. Hall TA (1999) BioEdit: a user friendly biological sequence alignment editor and analysis program for windows 95/96 NT. Nucleic Acids Symp 41: 95-98.
27. Hirose T, Terao T (2004) A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta 220: 9-16.
28. Ishii T, Xu Y, McCouch SR (2001) Nuclear- and chloroplast-microsatellite variation in A-genome species of rice. Genome 44: 658-666.
29. Ishimaru T, Horigane AK, Ida M et al (2009) Formation of grain chalkiness and changes in water distribution in developing rice caryopses grown under high-temperature stress. J Cereal Sci 50: 166-174.
30. Joshi SP, Gupta VS, Aggarwal RK et al (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100: 1311-1320.
31. Kahn AB (1996) Aspects of the molecular phylogeny of three species of the wild rice genus, Zizania, based on nuclear rDNA sequences. Southwest Texas State University, Texas, pp 1-88.
32. Kaplinsky NJ, Braun DM, Penterman J et al (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci U S A 99: 6147-6151.
33. Keller I, Bensasson D, Nichols RA (2007) Transition-Transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS Genet 3: e22.
34. Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35: 25-34.
35. Kovarik A, Pires JC, Leitch AR et al (2005) Rapid concerted evolution of nuclear ribosomal DNA in two tragopogon allopolyploids of recent and recurrent origin. Genetics 169: 931-944.
36. Kumagai M, Wang L, Ueda S (2010) Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA. Gene 462: 44-51.
37. Larkin PD, McClung AM, Ayres NM et al (2003) The effect of the Waxy locus (Granule Bound Starch Synthase) on pasting curve characteristics in specialty rices (Oryza sativa L.). Euphytica 131: 243-253.
38. Lexer C, Lai Z, Rieseberg LH (2004) Candidate gene polymorphisms associated with salt tolerance in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species. New Phytol 161: 225-233.
39. Londo JP, Chiang YC, Hung KH et al (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. PNAS 103: 9578-9583.
40. Lu B-R, Naredo MEB, Juliano AB et al (1997) Hybridization of AA genome rice species from Asia and Australia II. Meiotic analysis of Oryza meridionalis and its hybrids. Genet Resour Crop Evol 44: 25-31.
41. Lu B-R, Zheng K, Qian H, Zhuang J (2002) Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor Appl Genet 106: 101-106.
42. Mason-Gamer RJ, Weil CF, Kellogg EA (1998) Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 15: 1658-1673.
43. McIntosh SR, Pacey-Miller T, Henry RJ (2005) A universal protocol for identification of cereals. J Cereal Sci 41: 37-46.
44. Mizuno K, Kawasaki T, Shimada H et al (1993) Alteration of the structural properties of starch components by the lack of an isoform of starch branching enzyme in rice seeds. J Biol Chem 268: 19084-19091.
45. Myers AM, Morell MK, James MG et al (2000) Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol 122: 989-997.
46. Nakamura Y, Francisco PBJ, Hosaka Y et al (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58: 213-227.
47. Naredo MEB, Juliano AB, Lu B-R et al (1997) Hybridization of AA genome rice species from Asia and Australia I. Crosses and development of hybrids. Genet Resour Crop Evol 44: 17-23.
48. Nishi A, Nakamura Y, Tanaka N et al (2001) Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol 127: 459-472.
49. Nishikawa T, Vaughan DA, Kadowaki K (2005) Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor Appl Genet 110: 696-705.
50. Ochieng JW, Muigai AWT, Ude GN (2007) Phylogenetics in plant biotechnology: principles, obstacles and opportunities for the resource poor. Afr J Biotechnol 6: 639-649.
51. Ohdan T, Francisco PB Jr, Sawada T et al (2005) Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot 56: 3229-3244.
52. Ohtsubo H, Cheng C, Ohsawa I et al (2004) Rice retroposon p-SINE1 and origin of cultivated rice. Breed Sci 54: 1-11.
53. Oka HI (1988) Origin of cultivated rice. Elsevier, Tokyo.
54. O'Shea MG, Samuel MS, Konik CM et al (1998) Fluorophore-assisted carbohydrate electrophoresis (FACE) of oligosaccharides: efficiency of labeling and high-resolution separation. Carbohydr Res 307: 1-12.
55. Peng S, Huang J, Sheehy JE, Laza RC, Visperas RM, Zhong X, Centeno GS, Khush GS, Cassman KG (2004) Rice yields decline with higher night temperature from global warming. Proc Natl Acad Sci USA 101(27): 9971-9975.
56. Rieseberg LH, Baird SJE, Gardner KA (2000) Hybridization, introgression, and linkage evolution. Plant Mol Biol 42: 205-224.
57. Saitoh K, Onishi K, Mikami I et al (2004) Allelic diversification at the C (OsC1) Locus of wild and cultivated rice nucleotide changes associated with phenotypes. Genetics 168: 997-1007.
58. Sarkar R, Raina SN (1992) Assessment of genome relationships in the genus Oryza L. based on seed-protein profile analysis. Theor Appl Genet 85: 127-132.
59. Shu X-L, Shen S-Q, Bao J-S et al (2006) Molecular and biochemical analysis of the gelatinization temperature characteristics of rice (Oryza sativa L.) starch granules. J Cereal Sci 44: 40-48.
60. Small RL, Wendel JF (2000a) Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155: 1913-1926.
61. Small RL, Wendel JF (2000b) Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae). Mol Phylogenet Evol 16: 73-84.
62. Small RL, Wendel JF (2002) Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol Biol Evol 19: 597-607.
63. Small RL, Ryburn JA, Cronn RC et al (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85: 1301-1315.
64. Small RL, Ryburn JA, Wendel JF (1999) Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Mol Biol Evol 16: 491-501.
65. Soltis DE, Soltis PS, Pires JC et al (2004) Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons. Biol J Linn Soc 82: 485-501.
66. Sun C, Sathish P, Ahlandsberg S et al (1998) The two genes encoding starch-branching enzymes IIa and IIb are differentially expressed in barley. Plant Physiol 118: 37-49.
67. Sun CQ, Wang XK, Yoshimura A et al (2002) Genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.). Theor Appl Genet 104: 1335-1345.
68. Sweeney M, McCouch S (2007) The complex history of the domestication of rice. Ann Bot 100: 951-957.
69. Tanaka N, Fujita N, Nishi A et al (2004) The structure of starch can be manipulated by changing the expression levels of strach branching enzyme IIb in rice endosperm. Plant Biotechnol 2: 507-516.
70. Tang T, Lu J, Huang J et al (2006) Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet 2: 1824-1833.
71. Tang L, Zou XH, Achoundong G et al (2010) Phylogeny and biogeography of the rice tribe (Oryzeae): evidence from combined analysis of 20 chloroplast fragments. Mol Phylogenet Evol 54: 266-277.
72. Tateoka T (1962) Taxonomic studies of Oryza II. in several species complexes. Bot Mag Tokyo 75: 165-173.
73. Tetlow IJ, Morell MK, Emes MJ (2004) Recent developments in understanding the regulation of starch metabolism in higher plants. J Exp Bot 55: 2131-2145.
74. Umemoto T, Aoki N (2005) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme. Funct Plant Biol 32: 763-768.
75. Vaughan DA, Balazs E, Heslop-Harrison JS (2007) From crop domestication to super-domestication. Ann Bot 100: 893-901.
76. Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83: 565-581.
77. Waters DLE, Henry RJ, Reinke RF et al (2006) Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant Biotechnol 4: 115-122.
78. Waters DLE, Nock CJ, Rice N, et al (2012) Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecology and Evolution 2: 211-217.
79. Yano M, Okuno K, Kawakami J et al (1985) High amylose mutants of rice, Oryza sativa L. Theor Appl Genet 69: 253-257.
80. Zhang J (2000) Rates of conservative and radical nonsynonymous substitutions in mammalian nuclear genes. J Mol Evol 50: 56-68.
81. Zhang Y, Wang J, Zhang X et al (2009) Genetic signature of rice domestication shown by a variety of genes. J Mol Evol 68: 393-402.
82. Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167: 249-265.
83. Zou X-H, Zhang F-M, Zhang J-G et al (2008) Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol 9: R49.