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Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.)

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Abstract

Apparent amylose content (AAC) is a key determinant of eating and cooking quality in rice and it is mainly controlled by the Wx gene which encodes a granule-bound starch synthase (GBSS). In this study, sixteen single-segment substitution lines harboring the Wx gene from 16 different donors and their recipient HJX74 were used to detect the naturally occurring allelic variation at the Wx locus. The AAC in the materials varied widely and could be grouped into glutinous, low, intermediate, and two high AAC sub-classes, high I (24.36–25.20%) and high II (25.81–26.19%), under different experimental environments, which showed a positive correlation with the enzymatic activity of GBSS. One insertion/deletion (InDel) and three single nucleotide polymorphisms in the Wx gene were detected and their combinations resulted in the variation of five classes of AAC. Based on the results of AAC phenotypes, GBSS activities and cDNA sequences, five Wx alleles, wx, Wx t, Wx g1, Wx g2, and Wx g3, were identified, two of which, Wx g2 and Wx g3, are separated for the first time in this study. Under different cropping seasons, the AAC differed significantly for the Wx t and Wx g1 alleles, with higher AAC in the fall season than in the spring season, but did not differ significantly for the wx, Wx g2, and Wx g3 alleles. In conclusion, the present results might contribute to our understanding of the naturally occurring allelic variation at the Wx locus and will facilitate the improvement of rice quality by marker-assisted selection.

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References

  • Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109:630–639

    Article  PubMed  CAS  Google Scholar 

  • Asaoka M, Okuno K, Fuwa H (1985) Effect of environmental temperature at the milky stage on amylose content and fine structure of amylopectin of waxy and nonwaxy endosperm starches of rice (Oryza sativa L.). Agric Biol Chem 49:373–379

    Article  CAS  Google Scholar 

  • Asaoka M, Okuno K, Konishi Y, Fuwa H (1987) The effects of endosperm mutations and environmental temperature during development on the distribution of molecular weight of amylose in rice endosperm. Agric Biol Chem 51:3451–3453

    Article  CAS  Google Scholar 

  • Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773–781

    Article  CAS  Google Scholar 

  • Bao JS, Corke H, Sun M (2002) Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theor Appl Genet 105:898–905

    Article  PubMed  CAS  Google Scholar 

  • Bao JS, Kong XL, Xie JK, Xu LJ (2004) Analysis of genotypic and environmental effects on rice starch. 1. apparent amylose content, pasting viscosity, and gel texture. J Agric Food Chem 52:6010–6016

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Bao JS, Shen SQ, Sun M, Corke H (2006b) Analysis of genotypic diversity in the starch physicochemical properties of nonwaxy rice: apparent amylose content, pasting viscosity and gel texture. Starch/Starke 58:259–267

    Article  CAS  Google Scholar 

  • Bergman CJ, Delgado JT, McClung AM, Fjellstrom RG (2001) An improved method for using a microsatellite in the rice Waxy gene to determine amylose class. Cereal Chem 78:257–260

    Article  CAS  Google Scholar 

  • Bligh HFJ, Till RI, Jones CA (1995) A microsatellite sequence closely linked to the Waxy gene of Oryza sativa. Euphytica 86:83–85

    Article  CAS  Google Scholar 

  • Bligh HFJ, Larkin PD, Roach PS, Jones CA, Fu H, Park WD (1998) Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38:407–415

    Article  PubMed  CAS  Google Scholar 

  • Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) 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 14(4):459–465

    Article  PubMed  CAS  Google Scholar 

  • Cai XL, Liu QQ, Tang SZ, Gu MH, Wang ZY (2002) Development of a molecular marker for screening the rice cultivars with intermediate amylose content in Oryza sativa subsp. indica. J Plant Physiol Mol Biol (China) 28:137–144

    CAS  Google Scholar 

  • Champagne ET, Bett-Garber KL, McClung AM, Bergman C (2004) Sensory characteristics of diverse rice cultivars as influenced by genetic and environmental factors. Cereal Chem 81:237–243

    Article  CAS  Google Scholar 

  • Chen MH, Bergman CJ, Pinsona SRM, Fjellstrom RG (2008a) 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

    Article  CAS  Google Scholar 

  • Chen MH, Bergman CJ, Pinsona SRM, Fjellstrom RG (2008b) Waxy gene haplotypes: associations with pasting properties in an international rice germplasm collection. J Cereal Sci 48:781–788

    Article  CAS  Google Scholar 

  • Chen MH, Fjellstrom RG, Christensen EF, Bergman CJ (2010) Development of three allele-specific codominant rice Waxy gene PCR markers suitable for marker-assisted selection of amylose content and paste viscosity. Mol Breed 26:513–523

    Article  CAS  Google Scholar 

  • Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang QF (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110:1445–1452

    Article  PubMed  CAS  Google Scholar 

  • Han YP, Xu ML, Liu XY, Yan CJ, Korban SS, Chen XL, Gu MH (2004) Genes coding for starch branching enzymes are major contributors to starch viscosity characteristics in waxy rice (Oryza sativa L.). Plant Sci 166:357–364

    Article  CAS  Google Scholar 

  • He P, Li SG, Qian Q, Ma YQ, Li JZ, Wang WM, Chen Y, Zhu LH (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502–508

    Article  CAS  Google Scholar 

  • He FH, Xi ZY, Zeng RZ, Zhang GQ (2005) Developing single segment substitution lines (SSSLs) in rice (Oryza sativa L.) using advanced backcrosses and MAS. Acta Genet Sin (China) 32(8):825–831

    Google Scholar 

  • Hirano HY, Sano Y (1998) Enhancement of Wx gene expression and the accumulation of amylose in response to cool temperature during seed development in rice. Plant Cell Physiol 39:807–812

    Article  CAS  Google Scholar 

  • Hirano HY, Eiguchi M, Sano Y (1998) A single base change altered the regulation of the Waxy gene at the posttranscriptional level during domestication of rice. Mol Biol Evol 15:978–987

    Article  PubMed  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of rice genome. Nature 436:793–800

    Article  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J 15:133–138

    Article  PubMed  CAS  Google Scholar 

  • Isshiki M, Nakajima M, Satoh H, Shimamoto K (2000) dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. Plant J 23:451–460

    Article  PubMed  CAS  Google Scholar 

  • Isshiki M, Yamamoto Y, Satoh H, Shimamoto K (2001) Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol 125:1388–1395

    Article  PubMed  CAS  Google Scholar 

  • Juliano BO (1985) Criteria and test for rice grain quality. In: Juliano BO (ed) Rice chemistry and technology. American Association of Cereal Chemists, Inc., St. Paul, Minnesota, pp 443–513

    Google Scholar 

  • Kaushik RP, Khush GS (1991) Genetic analysis of endosperm mutants in rice (Oryza sativa L.). Theor Appl Genet 83:146–152

    Article  Google Scholar 

  • Larkin PD, Park WD (1999) Transcript accumulation and utilization of alternate and non consensus splice sites in rice granule bound starch synthase are temperature sensitive and controlled by a single nucleotide polymorphism. Plant Mol Biol 40(4):719–727

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Lin SK, Chang MC, Tsai YG, Lur HS (2005) Proteomic analysis of the expression of proteins related to rice quality during caryopsis development and the effect of high temperature on expression. Proteomics 5:2140–2156

    Article  PubMed  CAS  Google Scholar 

  • Liu GF, Zhang ZM, Zhu HT, Zhao FM, Ding XH, Zeng RZ, Li WT, Zhang GQ (2008) Detection of QTLs with additive effects and additive-by-environment interaction effects on panicle number in rice (Oryza sativa L.) with single-segment substitution lines. Theor Appl Genet 116:923–931

    Article  PubMed  CAS  Google Scholar 

  • Liu GF, Zeng RZ, Zhu HT, Zhang ZM, Ding XH, Zhao FM, Li WT, Zhang GQ (2009) Dynamic expression of nine QTLs for tiller number detected with single segment substitution lines in rice. Theor Appl Genet 118:443–453

    Article  PubMed  Google Scholar 

  • Marone M, Mozzetti S, Ritis DD, Pierelli L, Scambia G (2001) Semiquantitative RT-PCR analysis to assess the expression levels of multiple transcripts from the same sample. Biol Proc Online 3:19–25

    Article  CAS  Google Scholar 

  • Mikami I, Aikawa M, Hirano HY, Sano Y (1999) Altered tissue specific expression at the Wx gene of opaque mutants in rice. Euphytica 105:91–97

    Article  CAS  Google Scholar 

  • Mikami I, Dung LV, Hirano HY, Sano Y (2000) Effects of the two most common Wx alleles on different genetic backgrounds in rice. Plant Breed 119:505–508

    Article  CAS  Google Scholar 

  • Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y, Sano Y (2008) Allelic diversification at the wx locus in landraces of Asian rice. Theor Appl Genet 116(7):979–989

    Article  PubMed  CAS  Google Scholar 

  • Nishi A, Nakamura Y, Tanaka N, Satoh H (2001) Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol 127:459–472

    Article  PubMed  CAS  Google Scholar 

  • Okuno K, Fuwa H, Yano M (1983) A new mutant gene lowering amylose content in endosperm starch of rice, Oryza sativa L. Jpn J Breed 33:387–394

    CAS  Google Scholar 

  • Peleman JD, van der Voort JR (2003) Breeding by design. Trends Plant Sci 8:330–334

    Article  PubMed  CAS  Google Scholar 

  • Prathepha P, Baimai V (2004) Variation of Wx microsatellite allele, waxy allele distribution and differentiation of chloroplast DNA in a collection of Thai rice (Oryza sativa L.). Euphytica 140:231–237

    Article  CAS  Google Scholar 

  • Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467–473

    Article  CAS  Google Scholar 

  • Sano Y, Maekawa M, Kikuchi H (1985) Temperature effects on the Wx protein level and amylose content in the endosperm of rice. J Hered 76:221–222

    CAS  Google Scholar 

  • Sano Y, Katsumata M, Okuno K (1986) Genetic studies of speciation in cultivated rice. Inter-and intra-specific differentiation in the waxy gene expression. Euphytica 35:1–9

    Article  Google Scholar 

  • Shu QY, Wu DX, Xia YW, Gao MW, Ayres NM, Larkin PD, Park WD (1999) Microsatellites polymorphism on the Waxy gene locus and their relationship to amylose content in indica and japonica rice, Oryza sativa L. Acta Genet Sin (China) 26(4):350–358

    CAS  Google Scholar 

  • Smith AM, Denyer K, Martin C (1997) The synthesis of the starch granule. Annu Rev Plant Physiol Plant Mol Biol 48:67–87

    Article  PubMed  CAS  Google Scholar 

  • Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang QF (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648

    Article  CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Tetlow IJ, Wait R, Lu ZX, Akkasaeng R, Bowsher CG, Esposito S, Hashemi BK, Morell MK, Emesa MJ (2004) Protein phosphorylation in amyloplasts regulates starch branching enzyme activity and protein–protein interactions. Plant Cell 16:694–708

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Tian ZX, Qian Q, Liu QQ, Yan MX, Liu XF, Yan CJ, Liu GF, Gao ZY, Tang SZ, Zeng DL, Wang YH, Yu JM, Gu MH, Li JY (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765

    Article  PubMed  CAS  Google Scholar 

  • Traore K, McClung AM, Chen MH, Fjellstrom R (2011) Inheritance of flour paste viscosity is associated with a rice Waxy gene exon 10 SNP marker. J Cereal Sci 53:37–44

    Article  CAS  Google Scholar 

  • 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 165:1193–1199

    Article  CAS  Google Scholar 

  • Wang ZY, Zheng FQ, Shen GZ, Gao JP, Snusted 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(4):613–622

    Article  PubMed  CAS  Google Scholar 

  • Wang LQ, Liu WJ, Xu Y, He YQ, Luo LJ, Xing YZ, Xu CG, Zhang QF (2007) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 115:463–476

    Article  PubMed  CAS  Google Scholar 

  • Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49:476–484

    Article  PubMed  CAS  Google Scholar 

  • Yano M, Okuno K, Kawakami J, Satoh H, Omura T (1985) High amylose mutants of rice, Oryza sativa L. Theor Appl Genet 69:253–257

    Article  CAS  Google Scholar 

  • Yano M, Okuno K, Satoh H, Omura T (1988) Chromosomal location of genes conditioning low amylose content of endosperm starches in rice (Oryza sativa L.). Theor Appl Genet 76:183–189

    Article  CAS  Google Scholar 

  • Young ND, Tanksley SD (1989) Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet 77:95–101

    Article  Google Scholar 

  • Zeng RZ, Zhang ZM, He FH, Xi ZY, Akshay T, Shi JQ, Qin LJ, Huang CF, Zhang GQ (2006) Identification of multiple alleles at the Wx Locus and development of single segment substitution lines for the alleles in rice. Rice Sci 13(1):9–14

    Google Scholar 

  • Zhang GQ, Zeng RZ, Zhang ZM, Ding XH, Li WT, Liu GM, He FH, Tulukdar A, Huang CF, Xi ZY, Qin LJ, Shi JQ, Zhao FM, Feng MJ, Shan ZL, Chen L, Guo XQ, Zhu HT, Lu YG (2004) The construction of a library of single segment substitution lines in rice (Oryza sativa L.). Rice Genet Newsl 21:85–87

    Google Scholar 

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Acknowledgments

This research was funded by the grants from the National Natural Science Foundation of China (30870074 and U1031002).

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Authors and Affiliations

  1. Guangdong Provincial Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People’s Republic of China

    Bin Teng, Ruizhen Zeng, Yicun Wang, Ziqiang Liu, Zemin Zhang, Haitao Zhu, Xiaohua Ding, Wentao Li & Guiquan Zhang

  2. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, People’s Republic of China

    Ruizhen Zeng, Ziqiang Liu, Zemin Zhang & Guiquan Zhang

  3. Anhui Provincial Key Lab of Rice Genetics and Breeding, Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, People’s Republic of China

    Bin Teng

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  1. Bin Teng
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  2. Ruizhen Zeng
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Correspondence to Guiquan Zhang.

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Bin Teng and Ruizhen Zeng contributed equally to this work.

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Teng, B., Zeng, R., Wang, Y. et al. Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.). Mol Breeding 30, 583–595 (2012). https://doi.org/10.1007/s11032-011-9647-x

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