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Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms

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Abstract

The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r 2 in the sequenced region (exon 1–intron 1–exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K s values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication.

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References

  • Brookes AJ (1999) The essence of SNPs. Gene 234:177–186

    Article  PubMed  CAS  Google Scholar 

  • Cai CM, Van K, Kim MY, Lee S-H (2005) Optimization of SNP genotyping assay with fluorescence polarization detection. Korean J Crop Sci 50:361–367

    Google Scholar 

  • Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203–207

    Article  PubMed  CAS  Google Scholar 

  • Collines FS, Brookes LD, Charkravati A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8:1229–1231

    Google Scholar 

  • Coryell VH, Jessen H, Schupp JM, Webb D, Keim P (1999) Allele-specific hybridization markers for soybean. Theor Appl Genet 98:690–696

    Article  CAS  Google Scholar 

  • Domon E, Fujita M, Ishikawa N (2002) The insertion/deletion polymorphisms in the waxy gene of barley genetic resources from East Asia. Theor Appl Genet 104:132–138

    Article  PubMed  CAS  Google Scholar 

  • Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci USA 1495:4441–4446

    Article  Google Scholar 

  • Fisher RA (1935) The logic of inductive interference. J Roy Stat Soc Ser A 98:39–54

    Article  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374

    Article  CAS  Google Scholar 

  • Fukunaga K, Domon E, Kawase M (1997a) Ribosomal DNA variation in foxtail millet and a survey of variation from Europe and Asia. Theor Appl Genet 95:751–756

    Article  CAS  Google Scholar 

  • Fukunaga K, Kawase M, Sakamoto S (1997b) Variation of caryopsis length and width among landraces of foxtail millet, Setaria italica (L.) P. Beauv. Jpn J Trop Agric 41:235–240

    Google Scholar 

  • Fukunaga K, Kawase M, Kato K (2002a) Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype. Mol Genet Genomics 268:214–222

    Article  PubMed  CAS  Google Scholar 

  • Fukunaga K, Wang ZM, Kato K, Kawase M (2002b) Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet Res Crop Evol 49:95–101

    Article  Google Scholar 

  • Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 165:1502–1506

    Article  Google Scholar 

  • Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitutions ate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel ate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93:10274–10279

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485

    Article  PubMed  CAS  Google Scholar 

  • Hirano HY, Sano Y (1991) Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol 32:989–997

    CAS  Google Scholar 

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

    Article  Google Scholar 

  • Jusuf M, Pernes J (1985) Genetic variability of foxtail millet (Setaria italica Beauv.): electorophretic study of five isoenzyme systems. Theor Appl Genet 71:385–391

    Article  Google Scholar 

  • Kawase M (1986) Genetic variation and landrace differentiation of foxtail millet, Setaria italica, in Eurasia. Ph. D. thesis, Kyoto University, Japan

  • Kawase M, Sakamoto S (1984) Variation, geographical distribution and genetic analysis of esterase isozymes in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 67:529–533

    Article  CAS  Google Scholar 

  • Kawase M, Sakamoto S (1987) Geographical distribution of landrace groups classified by intraspecific hybrid pollen sterility in foxtail millet, Setaria italica (L.) P. Beauv. Jpn J Breed 37:1–9

    Google Scholar 

  • Kawase M, Fukunaga K, Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable elements insertions. Mol Genet Genomics 274:131–140

    Article  PubMed  CAS  Google Scholar 

  • Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 95:2005–2010

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rated of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Kuppuswamy MN, Hoffman JW, Kasper CK, Spitzer SG, Groce SL, Bajaj SP (1991) Single nucleotide primer extension to detect genetic disease: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc Natl Acad Sci USA 88:1143–1147

    Article  PubMed  CAS  Google Scholar 

  • Kwok P-Y, Gu Z (1999) Single nucleotide polymorphism libraries: why and how are we building them? Mol Med Today 5:538–543

    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 

  • Mason-Gamer RJ, Weil CF, Kellogg EA (1998) Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 15:1658–1673

    PubMed  CAS  Google Scholar 

  • Morinaga T, Nagamatu T, Kawahara E (1943) New linkage relations in rice. Jpn J Genet 19:206–208. (in Japanese with English résumé)

    Google Scholar 

  • Naciri Y, Darmency H, Belliard J, Dessaint F, Pernes J (1992) Breeding strategy in foxtail millet, Setaria italica (L. P. Beauv.), following interspecific hybridization. Euphytica 60:97–103

    Google Scholar 

  • Nakamura T, Yamamori M, Yamaguchi I (1990) Variation of starch-granule bound protein (Wx protein) in foxtail millet and Japanese barnyard millet. Jpn J Breed 40(Suppl):418–419. (in Japanese)

    Google Scholar 

  • Nakayama H, Afzal M, Okuno K (1998) Intraspecific differentiation and geographical distribution of Wx alleles for low amylose content in endosperm of foxtail millet, Setaria italica (L.) P. Beauv. Euphytica 102:289–293

    Article  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nordborg M (2000) Linkage disequilibrium, gene trees, and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154:923–929

    PubMed  CAS  Google Scholar 

  • Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193

    Article  PubMed  CAS  Google Scholar 

  • Ochiai Y (1996) Minor millet in Cheju Island, Korea. Millet News Lett 8:8–10. (in Japanese)

    Google Scholar 

  • Ochiai Y, Kawase M, Sakamoto S (1994) Variation and distribution of foxtail millet (Setaria italica (L.) P. Beauv.) in mountainous areas of northern Pakistan. Breed Sci 37:413–418

    Google Scholar 

  • Olsen KM, Purugganan MD (2002) Molecular evidence on the origin and evolution of glutinous rice. Genetics 162:941–950

    PubMed  CAS  Google Scholar 

  • Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. CABIOS 12:357–358

    PubMed  CAS  Google Scholar 

  • Rafalski A (2002) Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  PubMed  CAS  Google Scholar 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Sánchez-DelBarrio JC, Messenguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  PubMed  CAS  Google Scholar 

  • Sakamoto S (1982) Waxy endosperm and perisperm of cereals and grain amaranth and their geographical distributions. J Jpn Soc Starch Sci 29:41–55

    Google Scholar 

  • Sakamoto S (1987) Origin and dispersal of common millet and foxtail millet. Jpn Agric Res Q 21:84–89

    Google Scholar 

  • SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

    Article  PubMed  CAS  Google Scholar 

  • SanMiguel P, Ramakrishna W, Bennetzen JL, Busso CS, Dubcovsky J (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am. Funct Integr Genomics 2:70–80

    Article  PubMed  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 

  • Schontz D, Rether B (1998) Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv.—RFLP using a heterologous rDNA probe. Plant Breed 117:231–234

    Article  Google Scholar 

  • Seo Y-W, Hong B-H, Ha Y-W (1998) Identification of granule bound starch synthase (GBSS) isoforms in wheat. Korean J Crop Sci 43:89–94

    Google Scholar 

  • Shure M, Wessler S, Fedoroff N (1983) Molecular identification and isolation of the Waxy locus in maize. Cell 35:225–233

    Article  PubMed  CAS  Google Scholar 

  • Takeda K, Chang C (1996) Inheritance and geographical distribution of phenol reaction-less varieties of barley. Euphytica 90:217–221

    Article  Google Scholar 

  • Takei E, Sakamoto S (1989) Further analysis of geographical variation of heading response to daylength in foxtail millet (Setaria italica (L.) P. Beauv.). Jpn J Breed 39:285–298

    Google Scholar 

  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:961–966

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Umeda M, Ohtsubo H, Ohtsubo E (1991) Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns. Jpn J Genet 66:569–586

    Article  PubMed  CAS  Google Scholar 

  • Van K, Hwang E-Y, Kim MY, Kim Y-H, Cho YI, Cregan PB, Lee S-H (2004) Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica 139:147–157

    Article  CAS  Google Scholar 

  • Van K, Hwang E-Y, Kim MY, Park HJ, Lee S-H, Cregan PB (2005) Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J Hered 96:529–535

    Article  PubMed  CAS  Google Scholar 

  • Wang ZM, Devos KM, Liu CJ, Wang RQ, Gale MD (1998) Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 96:31–36

    Article  CAS  Google Scholar 

  • Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland

    Google Scholar 

  • Yanagisawa T, Kiribuchi-Otobe C, Yoshida H (2001) An alanine to threonine change in the Wx-D1 protein reduces GBSS I activity in waxy mutant wheat. Euphytica 121:209–214

    Article  CAS  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    PubMed  CAS  Google Scholar 

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Acknowledgments

This research was also supported by a grant (code no. CG3121) from the Crop Functional Genomics Center of the twenty-first Century Frontier Research Program funded by the Ministry of Science and Technology (MOST), Republic of Korea. Dr. K. Van and K. D. Kim are recipients of a fellowship and a scholarship, respectively, from the BK21 program granted by the Ministry of Education & Human Resources Development (ME & HRD), the Republic of Korea. We also thank the National Instrumentation Center for Environmental Management at Seoul National University in Korea.

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Authors and Affiliations

  1. Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, 151-921, The Republic of Korea

    K. Van, S. Onoda, M. Y. Kim, K. D. Kim & S.-H. Lee

  2. Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, The Republic of Korea

    M. Y. Kim & S.-H. Lee

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  1. K. Van
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  2. S. Onoda
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  3. M. Y. Kim
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  4. K. D. Kim
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Correspondence to S.-H. Lee.

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Communicated by R. Hagemann.

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Van, K., Onoda, S., Kim, M.Y. et al. Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms. Mol Genet Genomics 279, 255–266 (2008). https://doi.org/10.1007/s00438-007-0310-5

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