Relationship Between the First Base of the Donor Splice Site of Waxy Gene Intron 1 and Amylose Content in Yunnan Indigenous Rice Varieties

Abstract

Abstract: There exists a single nucleotide polymorphism, G or T, at the first base of the donor splice site of waxy gene intron 1 in rice. In order to study the relationship between the first base of the donor splice site of waxy gene intron 1 and amylose content in rice, the one-step PCR method was used to determine whether it is G or T in 220 Yunnan indigenous rice varieties from 14 districts, 55 towns/counties of Yunnan Province, and 101 varieties of which were validated by the PCR-Acc I method. According to the G/T polymorphism, 164 rice varieties showed GG-genotype, while the other 56 fell into TT-genotype, accounting for 74.5% and 25.5% of all the test varieties, respectively. When all the rice varieties were divided into indica and japonica subspecies, it was found that 80.5% of indica rice and 67.0% of japonica rice belonged to GG-genotype. The rice varieties with GG-genotype had significantly higher amylose content (18.95% on average) than those with TT-genotype (all below 16%), but 33 rice varieties with GG-genotype still had low amylose content ranging from 3.91% to 15.93%, and most of them came from the Dai minority area in the Southwest of Yunnan Province. However, there was no significant difference in the mean amylose content of the same GG or TT genotypes between indica and japonica rice, suggesting that different genetic backgrounds, indica or japonica, had no effect on amylose content. The coefficient of correlation between the genotype and amylose content was 0.733 (P<0.01).

Key words: Yunnan indigenous rice varieties, waxy gene, intron, the first base of donor splice site, amylose content, genotype, relationship

ZHANG Ya-li, XU Ming-hui, ZENG Ya-wen, YAO Chun-xin, CHEN Shan-na. Relationship Between the First Base of the Donor Splice Site of Waxy Gene Intron 1 and Amylose Content in Yunnan Indigenous Rice Varieties[J]. RICE SCIENCE, 2007, 14(3): 189-194 .

References

1 Juliano B O. Criteria and test for rice grain quality. In: Juliano B O. Rice Chemistry and Technology. Saint Paul, Minnesota: American Association of Cereal Chemists, Incorporated, 1985: 443-513.
2 Chen N, Luo Y K, Zhu Z W, Xie L H. Studies on the texture and palatability of cooked rice. Chinese J Rice Sci, 1999, 13(3): 152-156. (in Chinese with English abstract)
3 Jiang Y G, Pan C G. Rice quality breeding. In: Zhai F L. Crop Quality Breeding. Beijing: Agricultural Press, 1988: 242-272. (in Chinese)
4 Mo H D. Quality improvement of rice grain in China. Sci Agric Sin, 1993, 26: 8-14. (in Chinese with English abstract)
5 Okagaki R J, Wessler S R. Comparison of non-mutant and mutant waxy genes in maize. Genetics, 1988, 120: 1137-1143.
6 Shen Y Z, Min S K, Xiong Z M, Luo Y K. Genetical studies on amylose content of rice grain and modifies on the determination method. Sci Agric Sin, 1990, 23(1): 60-68. (in Chinese with English abstract)
7 Huang C W, Li R. The genetic analysis of amylose content of rice (Oryza sativa L.). J South China Agric Univ, 1990, 11(1): 23-29. (in Chinese with English abstract)
8 Wang Z Y, Zheng F Q, Shen G Z, Gao J P, Snustad D P, Li M G, Zhang J L, Hong M M. The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J, 1995, 7: 613-622.
9 Cai X L, Wang Z Y, Xing Y Y, Zhang J L, Hong M M. Aberrant splicing of intron 1 leads to the heterogeneous 5′UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J, 1998, 14(4): 459-465.
10 Cheng S J, Ge H F, Wang Z Y, Hong M M. Analysis of influence of Wx intron 1 on gene expression in transgenic rice plant. Acta Phytophysiol Sin, 2001, 27(5): 381-386. (in Chinese with English abstract)
11 Bligh H F J, Larkin P D, Roach P S, Jones C A, Fu H, Park W D. Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol, 1998, 38: 407-415.
12 Isshiki M, Morino K, Nakajima M, Okagaki R J, Wessler S R, Izawa T, Shimamoto K. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5’ splice site of the first intron. Plant J, 1998, 15(1): 133-138.
13 Hirano H Y, Eiguchi M, Sano Y. A single base change altered the regulation of the waxy gene at the post-transcriptional level during evolution of rice. Mol Biol Evol, 1998, 15: 978-987.
14 Ayres N M, McClung A M, Larkin P D, Bligh H F J. Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet, 1997, 94: 773-781.
15 Cai X L, Liu Q Q, Tang S Z, Gu M H, Wang Z Y. Development of a molecular marker for screening the rice cultivars with intermediate amylose content in Oryza sativa subsp. indica. J Plant Physiol & Mol Biol, 2002, 28(2): 137-144. (in Chinese with English abstract)
16 Mao X X, Liu Y Z, Xiao X, Chen J W, Luo W Y, Li X F. A one-step PCR method for detecting the first base of splice donor of Wx intron 1 in rice. Rice Sci, 2004, 11(5-6): 342-344.
17 Nakagahra K. The differentiation, classification and center of genetic diversity of cultivated rice (Oryza sativa L.) by isozyme analysis. Trop Agric Res Ser, 1978, 11: 77-82.
18 Chang T T. The origin, evolution, cultivation, dissemination and diversification of Asian and African rices. Euphytica, 1976, 5: 425-441.
19 Huang Y H, Sun X L, Wang X K. Study on the center of genetic diversity and its origin of cultivated rice in China. J Plant Genetic Res, 2005, 6(2): 125-129. (in Chinese with English abstract)
20 Cheng K S, Zhou J W, Lu Y X, Luo J, Huang N W, Liu G R, Wang X K. Studies on the indigenous rices in Yunnan and their utilization: Ⅱ. A revised classification of Asian cultivated rice. Acta Agron Sin, 1984, 10(4): 271-280. (in Chinese with English abstract)
21 Cheng K S, Wang X K, Lu Y X, Luo J, Huang N W, Liu G R. Studies on the indigenous rices in Yunnan and their utilization Ⅸ. China Seeds, 1988 (1): 1-5. (in Chinese with English abstract)
22 Murray M G, Thompson W F. Rapid isolation of high molecular weight plant DNA. Nucl Acids Res, 1980, 8: 4321-4325.
23 Kwok S, Chang S Y, Sninsky J J. Mismatch and degenerate primer design and application. In: Huang P T, Yu W Y, Chen T M. PCR Primer: A laboratory manual. Beijing: Science Press, 1998: 95-102. (in Chinese)
24 Zeng Y W, Li Z C, Shen S Q, Wang X K, Yang Z Y, Zhang H L, Chen Y M. Diversity and good germplasm of indigenous rice varieties in Yunnan Province. Chinese J Rice Sci, 2001, 15(3): 169-174. (in Chinese with English abstract)
25 Zhang J Y, Chen D Q, Li S G, Ma Y Q, Wang Y P. The genotype of waxy gene and their relationship to amylose content in indica and japonica rice (Oryza sativa L.). Acta Agron Sin, 2005, 31(4): 420-424. (in Chinese with English abstract)
26 Yamanaka S, Nakamura I, Watanabe K N, Sato Y. Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet, 2004, 108(7): 1200-1204.
27 He F H, Zeng R Z, Xi Z Y, Akshay T, Zhang G Q. Genetic diversity of different waxy genotypes in rice. Mol Plant Breeding, 2003, 1(12): 179-186. (in Chinese with English abstract)

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