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Characterization of the waxy gene in diploid Triticum L. and Aegilops L. species and its geographic distribution

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Abstract

Waxy gene plays a key role for amylose synthesis in wheat seeds. The study evaluated the Waxy gene variability in 59 accessions of six diploid Triticum and Aegilops species. The percentages of variable sites, singleton variable sites, and parsimony informative sites were 16.38, 5.59, and 10.79 %, respectively. A total of 22 amino acid changes in the transit peptide and the remaining in the mature protein were observed. Moreover, 17 amino acid changes between Triticum and Aegilops species were also detected. Specially, Gla 14 and Phe 153 was observed in diploid Triticum, compared with Thr 14 and Tyr 153 in diploid Aegilops. Two types of amino acids, Gla 5/Val 5 and Ile 140/Val 140, were identified in T. urartu, as well as Val 22/Phe 22, Thr 52/Lys 52, and Gln 54/delete in A. tauschii. The insertion/deletions (InDels) had high frequency in intron region, but very low in transit peptide and exon region. Neighbour-joining tree showed that 146 sequences from 23 species could be clustered into eight groups with the species characterizations. The Wx-B1 of polyploid Triticum were grouped with A. sharonensis, A. longissima, A. searsii, A. speltoides, while Wx-D1 of T. aestivum and T. spelta together with A. umbellulata, A. markgrafii, A. comosa, and A. tauschii. The Wx-A1 of polyploid Triticum were separated clearly with the diploid species. The Wx-B1 could be divided into two subgroups and maybe had two phylogenetic origins, but most of them were related to A. speltoides. Waxy gene of A. tauschii also had two subgroups, and the sequences from southern Caspian (Mazandaran, Iran) were more closed with Wx-D1. The variability of 5′ Un-Translation Region (UTR) of waxy was stronger than intron and exon region based on genetic distance. Phylogeography analysis showed that geography affected strongly the distribution of all accessions along the north–south axis based on the partial open reading fragment (ORF) of waxy gene, A. speltoides and A. longissima along the west–east axis and north–south axis based on exon, and A. tauschii along the west–east axis based on 5′ UTR, respectively. Our results suggest that diploid Triticum and Aegilops have new waxy gene resources; waxy gene could play a more important role in genetic exploitation, genetic relationship evaluation and phylogeography investigation.

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References

  • Ainsworth C, Clark J, Balsdon J (1993) Expression, organisation and structure of the genes encoding the waxy protein (granule-bound starch synthase) in wheat. Plant Mol Biol 22:67–82

    Article  CAS  PubMed  Google Scholar 

  • Avise JC (1998) The history and purview of phylogeography: a personal reflection. Mol Ecol 7:371–379

    Article  Google Scholar 

  • Baumel A, Ainouche ML, Bayer RJ, Ainouche AK, Misset MT (2002) Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae). Mol Phylogenet Evol 22(2):303–314

    Article  CAS  PubMed  Google Scholar 

  • Domon E, Saito A, Takeda K (2002) Comparison of the waxy locus sequence from a non-waxy strain and two waxy mutants of spontaneous and artificial origins in barley. Genes Genet Syst 77(5):351–359

    Article  CAS  PubMed  Google Scholar 

  • Dvorak J, Pantaleo DT, Zhang HB, Resta P (1993) The evolution of polyploid wheats: identification of the A genome donor species. Genome 36:21–31

    Article  CAS  PubMed  Google Scholar 

  • Dvorak J, Luo MC, Yang ZL, Zhang HB (1998) The structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat. Theor Appl Genet 97:657–670

    Article  CAS  Google Scholar 

  • Dvorak J, Deal KR, Luo MC, You FM, von Borstel K, Dehghani H (2012) The origin of spelt and free-threshing hexaploid wheat. J Hered 103:426–441

    Article  CAS  PubMed  Google Scholar 

  • Evans RC, Alice LA, Campbell CS, Kellogg EA, Dickinson TA (2000) The granule-bound starch synthase (GBSS) gene in the Rosaceae: multiple loci and phylogenetic utility. Mol Phylogenet Evol 17:388–400

    Article  CAS  PubMed  Google Scholar 

  • Fortune PM, Schierenbeck KA, Ainouche AK, Jacquemin J, Wendel JF, Ainouche ML (2007) Evolutionary dynamics of waxy and the origin of hexaploid Spartina species (Poaceae). Mol Phylogenet Evol 43:1040–1055

    Article  CAS  PubMed  Google Scholar 

  • Guzmán C, Alvarez JB (2012) Molecular characterization of a novel waxy allele (Wx-A u 1a) from Triticum urartu Thum. ex Gandil. Genet Resour Crop Evol 59(6):971–979

    Article  Google Scholar 

  • Guzmán C, Caballero L, Alvarez JB (2009) Variation in Spanish cultivated einkorn wheat (Triticum monococcum L. ssp. monococcum) as determined by morphological traits and waxy proteins. Genet Resour Crop Evol 56:601–604

    Article  Google Scholar 

  • Guzmán C, Caballero L, Alvarez JB (2011) Molecular characterization of the Wx-B1 allelic variants identified in cultivated emmer wheat and comparison with those of durum wheat. Mol Breed 28:403–411

    Article  Google Scholar 

  • Guzmán C, Caballero L, Martín LM, Alvarez JB (2012a) Waxy genes from spelt wheat: new alleles for modern wheat breeding and new phylogenetic inferences about the origin of this species. Ann Bot 110:1161–1171

    Article  PubMed  PubMed Central  Google Scholar 

  • Guzmán C, Caballero L, Yamamori M, Alvarez JB (2012b) Molecular characterization of a new waxy allele with partial expression in spelt wheat. Planta 235:1331–1339

    Article  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hammer K, Filatenko AA, Pistrick K (2011) Taxonomic remarks on Triticum L. and ×Triticosecale Wittm. Genet Resour Crop Evol 58:3–10

    Article  Google Scholar 

  • Huang XQ, Brûlé-Babel A (2010) Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples. BMC Res Notes 3:140

    Article  PubMed  PubMed Central  Google Scholar 

  • Jaaska V (1980) Electrophoretic survey of seedling esterases in wheats in relation to their phylogeny. Theor Appl Genet 56:273–284

    Article  CAS  PubMed  Google Scholar 

  • Kidd DM, Liao X (2006) Phylogeographic information systems: putting the geography into phylogeography. J Biogeogr 33:1851–1865

    Article  Google Scholar 

  • Kluth A, Sprunck S, Becker D, Lörz H, Lütticke S (2002) 5′ deletion of a gbssI promoter region from wheat leads to changes in tissue and developmental specificities. Plant Mol Biol 49:669–682

    Article  CAS  PubMed  Google Scholar 

  • Lagudah ES, Appels R, Brown ADH (1991) The molecular-genetic analysis of Triticum tauschii, the D genome donor to hexaploid wheat. Genome 36:913–918

    Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Li W, Gao Z, Xiao W, Wei YM, Liu YX, Chen GY, Pu ZE, Chen HP, Zheng YL (2012) Molecular diversity of restriction enzyme sites, indels and upstream open reading frame (uORFs ) of 5′ untransalted regions (UTRs) of Waxy genes in Triticum L. and Aegilops L. species. Genet Resour Crop Evol 59:1625–1647

    Article  CAS  Google Scholar 

  • Li W, Wei YM, Xu LL, Liu AJ, Sheng YZ, Pu ZE, Cheng GY, Zheng YL (2014) Evaluation of geographic distribution of high-molecular-weight glutenin subunits (HMW-GS) in wild and cultivated Triticum species. Genet Resour Crop Evol 61:1105–1119

    Article  Google Scholar 

  • Ma J, Jiang QT, Zhao QZ, Zhao S, Lan XJ, Dai SF, Lu ZX, Liu C, Wei YM, Zheng YL (2013) Characterization and expression analysis of waxy alleles in barley accessions. Genetica 141(4–6):227–238

    Article  CAS  PubMed  Google Scholar 

  • Martin C, Smith AM (1995) Starch biosynthesis. Plant Cell 7:971–985

    Article  CAS  PubMed  PubMed Central  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

    Article  CAS  PubMed  Google Scholar 

  • Mizuno N, Yamasaki M, Matsuoka Y, Kawahara T, Takumi S (2010) Population structure of wild wheat D-genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat. Mol Ecol 19:999–1013

    Article  PubMed  Google Scholar 

  • Monari AM, Simeone MC, Urbano M, Margiotta B, Lafiandra D (2005) Molecular characterization of new waxy mutants identified in bread and durum wheat. Theor Appl Genet 110:1481–1489

    Article  CAS  PubMed  Google Scholar 

  • Moore MJ, Jansen RK (2006) Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae). Mol Phylogenet Evol 39:668–687

    Article  CAS  PubMed  Google Scholar 

  • Murai J, Taira T, Ohta D (1999) Isolation and characterization of the three Waxy genes encoding the granule-bound starch synthase in hexaploid wheat. Gene 234:71–79

    Article  CAS  PubMed  Google Scholar 

  • Nakai Y (1979) Isozyme variation in Aegilops and Triticum, IV. The origin of the common wheats revealed from the study on esterase isozymes in synthesized hexaploid wheats. Jpn J Genet 54:175–189

    Article  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ortega R, Guzmán C, Alvarez JB (2014a) Wx gene in diploid wheat: molecular characterization of five novel alleles from einkorn (Triticum monococcum L. ssp. monococcum) and T. urartu. Mol Breed 34:1137–1146

    Article  CAS  Google Scholar 

  • Ortega R, Alvarez JB, Guzmán C (2014b) Characterization of the Wx gene in diploid Aegilops species and its potential use in wheat breeding. Genet Resour Crop Evol 61:369–382

    Article  CAS  Google Scholar 

  • Parks DH, Beiko RG (2009) Quantitative visualizations of hierarchically organized data in a geographic context. Geoinformatics. 17th International conference on, August 12–14, pp 1–6

  • Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG (2009) GenGIS: a geospatial information system for genomic data. Genome Res 19:1896–1904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peralta IE, Spooner DM (2001) Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon). Am J Bot 88(10):1888–1902

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Quijano M, Lucas R, Carrillo JM (2003) Waxy proteins and amylose content in tetraploid wheats Triticum dicoccum Schuld., Triticum durum L. and Triticum polonicum L. Euphytica 134:97–101

    Article  CAS  Google Scholar 

  • Rohde W, Becker D, Salamini F (1988) Structural analysis of the waxy locus from Hordeum vulgare. Nucl Acids Res 16(14B):7185–7186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sestili F, Botticella E, Bedo Z, Phillips A, Lafiandra D (2010) Production of novel allelic variation for genes involved in starch biosynthesis through mutagenesis. Mol Breed 25:145–154

    Article  CAS  Google Scholar 

  • Shapter FM, Eggler P, Lee LS, Henry RJ (2009) Variation in granule bound starch synthase I (GBSSI) loci amongst Australian wild cereal relatives (Poaceae). J Cereal Sci 49(1):4–11

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

  • Urbano M, Margiotta B, Colaprico G, Lafiandra D (2002) Waxy proteins in diploid, tetraploid and hexaploid wheat. Plant Breed 121:465–469

    Article  CAS  Google Scholar 

  • Van Slageren MW (1994) Wild wheats: a monograph of Aegilops L. and Amblyopyrum (Jaub. & Spach) Eig (Poaceae). Agricultural University Papers, Wageningen

    Google Scholar 

  • Wang JR, Wei YM, Long XY, Yan ZH, Nevo E, Baum BR, Zheng YL (2008) Molecular evolution of dimeric a-amylase inhibitor genes in wild emmer wheat and its ecological association. BMC Evol Biol 8:91

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang JR, Luo MC, Chen ZX, You FM, Wei YM, Zheng YL, Dvorak J (2013) Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New Phytol 198:925–937

    Article  CAS  PubMed  Google Scholar 

  • Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES (2002) Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci USA 99(20):12959–12962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J, Frick M, Laroche A, Ni ZF, Li BY, Lu ZX (2009a) Isolation and characterization of the rye Waxy gene. Genome 52(7):658–664

    Article  CAS  PubMed  Google Scholar 

  • Xu LL, Li W, Wei YM, Zheng YL (2009b) Genetic diversity of HMW glutenin subunits in diploid, tetraploid and hexaploid Triticum species. Genet Resour Crop Evol 56:377–391

    Article  CAS  Google Scholar 

  • Yamamori M, Guzmán C (2013) SNPs and an insertion sequence in five Wx-A1 alleles as factors for variant Wx-A1 protein in wheat. Euphytica 192:325–338

    Article  CAS  Google Scholar 

  • Yan LL, Bhave M, Fairclough R, Konik C, Rahman S, Appels R (2000) The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat. Genome 43:264–272

    Article  CAS  PubMed  Google Scholar 

  • Zhang LY, Ravel C, Bernard M, Balfourier F, Leroy P, Feuillet C, Sourdille P (2006) Transferable bread wheat EST–SSRs can be useful for phylogenetic studies among the Triticeae species. Theor Appl Genet 113:407–441

    Article  CAS  PubMed  Google Scholar 

  • Zimmer EA, Wen J (2012) Using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 65:774–785

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by The Key Project of National Natural Science Foundation of China (No. 31230053) and The International Science & Technology Cooperation Program of China (No. 2015DFA30600).

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Authors and Affiliations

  1. Key Laboratory of Crop Genetic Resources and Improvement in Southwest China, Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Wei Li, Ya-Xi Liu, Zhi-En Pu, Peng-Fei Qi, Qian-Tao Jiang, Guo-Yue Chen, Ji-Rui Wang, Yu-Ming Wei & You-Liang Zheng

  2. Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Wei Li, Bang-Bo Fu, Zhe Li, Ya-Xi Liu, Zhi-En Pu, Peng-Fei Qi, Qian-Tao Jiang, Guo-Yue Chen, Ji-Rui Wang, Yu-Ming Wei & You-Liang Zheng

  3. College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Wei Li, Bang-Bo Fu, Zhe Li & Zhi-En Pu

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  1. Wei Li
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Li, W., Fu, BB., Li, Z. et al. Characterization of the waxy gene in diploid Triticum L. and Aegilops L. species and its geographic distribution. Genet Resour Crop Evol 63, 987–1002 (2016). https://doi.org/10.1007/s10722-015-0296-5

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