A Cleaved Amplified Polymorphic Sequence Marker to Detect Variation in Wx Locus Conditioning Translucent Endosperm in Rice

doi:10.1016/S1672-6308(08)60065-7

Abstract

Abstract: The translucent endosperm trait in a japonica rice variety ‘Kantou 194’ is controlled by a Wx-mq gene which is allelic to Wx locus by genetic analysis and allelic test. The amylose content analysis showed that an intermediate amylose content between those of glutinous and non-glutinous rice existed in endosperm of homozygous Wx-mq genotype. The slight changes of amylose content in different varieties and F₁ grains with an identical Wx-mq genotype might be influenced by dissimilar genetic background. To identify the Wx-mq genotype simply and rapidly, a cleaved amplified polymorphic sequence (CAPS) marker was designed. The result from the molecular detection indicated that it could be used for marker-assisted selection for low amylose content varieties in rice breeding.

Key words: rice, amylose content, translucent endosperm mutant, waxy gene, molecular marker-assisted selection, cleaved amplified polymorphic sequence marker

CHEN Tao, ZHANG Ya-dong, ZHAO Ling, ZHU Zhen, LIN Jing, ZHANG Suo-bing, WANG Cai-lin. A Cleaved Amplified Polymorphic Sequence Marker to Detect Variation in Wx Locus Conditioning Translucent Endosperm in Rice[J]. RICE SCIENCE, 2009, 16(2): 106-110 .

References

1 Zhu C L, Shen W B, Zhai H Q, Wan J M. Advance in research of the application of low-amylose content rice gene for breeding. Sci Agric Sin, 2004, 3(2): 81–88. (in Chinese with English abstract)
2 Satoh H, Omura T. New endosperm mutations induced by chemical mutagenes in rice, Oryza sativa L. Jpn J Breeding, 1981, 31(3): 316–326.
3 Kaushik R P, Khush G S. Endosperm mutants in rice: Gene expression in japonica and indica backgrounds. Cereal Chem, 1991, 68(5): 487–491.
4 Yano M, Okuno K, Satoh H, Omura T. Chromosomal location of genes conditioning low amylose content of endosperm starches in rice, Oryza sativa L. Theor Appl Genet, 1988, 76(2): 183–189.
5 Sato H. Heredity and breeding of good taste rice: Present state and prospects of rearing low amylose rice. Agric & Hort, 2002, 77(5): 556–564. (in Japanese with English abstract)
6 Koh H J, Cha K W, Heu M H. Inheritance and some physicochemical properites of newly induced low-amylose endosperm mutants in rice. Korean J Breeding, 1997, 29(3): 368–375. (in Korean with English abstract)
7 Kaushik R P, Khush G S. Genetic analysis of endosperm mutants in rice Oryza sativa L. Theor Appl Genet, 1991, 83(2): 146–152.
8 Sato H, Suzuki Y, Sakai M, Imbe T. Molecular characteri- zation of Wx-mq, a novel mutant gene for low-amylose content in endosperm of rice. Breeding Sci, 2002, 52(2): 131–135.
9 Zeng D L, Yan M X, Wang Y H, Liu X F, Qian Q, Li J Y. DU1, encoding a novel Prp protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice. Plant Mol Biol, 2007, 65(4): 501–509.
10 Yan C J, Tian S, Zhang Z Q, Han Y P, Chen F, Li X, Gu M H. The source of genes related to rice grain starch synthesis among cultivated varieties and its contribution to quality. Sci Agric Sin, 2005, 39(5): 865–871. (in Chinese with English abstract)
11 Dellaporta S L, Wood J, Hicks J B. A plant DNA mini- preparation: Version II. Plant Mol Biol Rep, 1983, 1(1): 19– 21.
12 Chen X, Temnykh S, Xu Y, Cho Y G, McCouch S R. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet, 1997, 95(4): 553–567.
13 Sato H, Suzuki Y, Okuno K, Hirano H, Imbe T. Genetic analysis of low-amylose content in a rice variety, ‘Milky Queen’. Breeding Res, 2001, 3(1): 13–19. (in Japanese with English abstract)
14 Okuno K, Fuwa H, Yano M. A new mutant gene lowering amylose content in endosperm starch of rice, Oryza sativa L. Jpn J Breeding, 1983, 33(4): 387–394.
15 Wang Z Y, Wu Z L, Xing Y Y, Zheng F G, Guo X L, Zhang W G, Hong M M. Nucleotide sequence of rice waxy gene. Nucl Acids Res, 1990, 18(19): 5898.
16 Preiss J. Biosynthesis of starch and its regulation. In: Preiss J. The Biochemistry of Plants. San Diego, New York: Academic Press, 1988: 181–254.
17 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.
18 Isshiki M, Yamamoto Y, Satoh H, Shimamoto K. Nonsense- mediated decay of mutant waxy mRNA in rice. Plant Physiol, 2001, 125(3): 1388–1395.
19 Cai X L, Liu Q Q, Tang S Z, Gu M H, Wang Z Y. Molecular marker for screening rice cultivars with intermediate amylose content in indica. Chin Rice Res Newsl, 2002, 10(3): 7–9.
20 Sun H Q, Tian J, Zheng J K, Jiang K F, Luo K. New STS molecular markers for waxy gene of glutinous and non- glutinous rice. Chin J Appl Environ Biol, 2006, 12(4): 461– 463. (in Chinese with English abstract)
21 Isshiki M, Nakajima M, Satoh H, Shimamoto K. dull: Rice mutants with tissue-specific effects on the splicing of waxy pre-mRNA. Plant J, 2000, 23(4): 451–460.
22 Suto M, Ando I, Numaguchi K, Horisue N. Breeding of low amylose content paddy rice variety ‘Milky Queen’ with good eating quality. Jpn J Breeding, 1996, 46(suppl 1): 221.
23 Tomit K, Horiuchi H, Terada K, Tanoi M, Kobayashi A, Kanda K, Tanaka I, Minobe T, Furuta H, Yamamoto A, Shinoyama H, Aoki K, Masaki N, Minami T, Sugimoto A, Kagoshima C, Horiuchi K. ‘New-hikari’, a new rice cultivar. Bull Fukui Agric Exp Sta Ser, 2007, 44: 1–20. (in Japanese with English abstract)

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