Abstract：In order to develop a molecular marker for the detection of alien chromatin, an allele-specific primer targeting pyruvate dehydrogenase (PDHA1) gene was used to analyze 12 taxa representing different basic genomes in Triticeae. Amplification products with different sizes were generated among species. The sequence alignments indicated that the PDHA1 genes contained some deletions/insertions of Miniature Inverted-repeat Terminal Elements (MITE) and simple sequence repeats (SSRs), thus suggesting that the Triticeae genomes have been rapidly evolving during speciation. The genome-specific amplicons and chromosomal location of PDHA1 gene on Triticeae genomes can be used to trace the corresponding alien chromatins from Aegilops, Secale and Dasypyrum species in wheat background.
Blanco A, Simeone R, Resta P, Pace C D, Delre V, Caccia R, Mugnozza G T, Frediani M, Cremonini R, Cionini P G (1996). Genomic relationships between Dasypyrum villosum (L.) Candargy and D. hordeaceum (Cosson et Durieu) Candargy. Genome, 39: 83–92 doi: 10.1139/g96-012
Børglum A D, Flint T, Hansen L L, Kruse1 T A (1997). Refined localization of the pyruvate dehydrogenase E1α gene (PDHA1) by linkage analysis. Human Genetics, 99: 80–82
von Bothmer R, Claesson L (1990). Production and meiotic pairing of intergeneric hybridsof Triticum and Dasypyrum species. Euphytica, 51: 109–117
Brunel D, Froger N, Pelletier G (1999). Development of amplified consensus genetic marker (ACGM) in Brassica napus from Arabidopsis thaliana sequences of known biological function. Genome, 42: 387–402 doi: 10.1139/gen-42-3-387
Bustos A D, Jouve N (2002). Phylogenetic relationships of the genus Secale based on the characterisation of rDNA ITS sequences. Plant Syst Evol, 235: 147–154 doi: 10.1007/s00606-002-0215-z
Chantret N, Cenci A, Sabot F, Anderson O, Dubcovsky J (2004). Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol Genet Genomics, 271: 377–386 doi: 10.1007/s00438-004-0991-y
Dewey D R (1984). The genomic system of classificationas a guide to intergeneric hybridization with the perennial Triticeae. In: Gastafson J P, ed. Gene Manipulation in Plant Improvement. New York: Plenum Press, 209–279
Fan X, Sha L N, Yang R W, Zhang H Q, Kang H Y, Ding C B, Zhang L, Zheng Y L, Zhou Y H (2009). Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copynuclear gene encoding plastid acetyl-CoA carboxylase. BMC Evolutionary Biology, 9: 247–261 doi: 10.1186/1471-2148-9-247
Faris J, Sirikhachornkit A, Haselkorn R, Gill B, Gornicki P (2001). Chromosome mapping and phylogenetic analysis of thecytosolic acetyl-CoA carboxylase loci in wheat. Mol Biol Evol, 18: 1720–1733
Felsenstein J (1985). Confidence limits on phylogenies:an approach using the bootstrap. Evolution, 39: 783–791 doi: 10.2307/2408678
Fourmann M, Barret P, Froger N, Baron C, Charlot F, Delourme R, Brunel D (2002). From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for constructionof a gene map. Theor Appl Genet, 105: 1196–1206 doi: 10.1007/s00122-002-1040-z
Gielly L, Yuan Y M, Küpfer P, Taberlet P (1996). Phylogenetic use of noncoding regions in the genus Gentiana L.: chloroplast trnL (UAA) intron versus nuclear ribosomal internal transcribed spacersequences. Mol Phylogenet Evol, 5: 460–466 doi: 10.1006/mpev.1996.0042
Huang S X, Sirikhachornkit A, Faris J D, Su X J, Gill B S, Haselkorn R, Gornicki P (2002). Phylogenetic analysis of the acetyl-CoA carboxylaseand 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Mol Biol, 48: 805–820 doi: 10.1023/A:1014868320552
Ishikawa G, Nakamura T, Ashida T, Saito M, Nasuda S, Endo TR, Wu J, Matsumoto T (2009). Localization of anchor loci representing five hundredannotated rice genes to wheat chromosomes using PLUG markers. Theor Appl Genet, 118: 499–514 doi: 10.1007/s00122-008-0916-y
Ishikawa G, Yonemaru J, Saito M, Nakamura T (2007). PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and Dgenomes. BMC Genomics, 8: 135–146 doi: 10.1186/1471-2164-8-135
Käss E, Wink M (1997). Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (rbcL)and ncDNA (ITS 1 and 2). Mol Phylogenet Evol, 8: 65–88 doi: 10.1006/mpev.1997.0410
Kellogg E A, Appels R (1995). Intraspecific and interspecific variation in 5sRNA genesare decoupled in diploid wheat relatives. Genetics, 140: 325–343
Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 21: 2947–2948 doi: 10.1093/bioinformatics/btm404
Li G R, Liu C, Zeng Z X, Jia J Q, Zhang T, Zhou J P, Ren Z L, Yang Z J (2009). Identification of α-gliadin genes in Dasypyrum in relation to evolution and breeding. Euphytica, 165: 155–163 doi: 10.1007/s10681-008-9780-8
Linde L I, Frederiksen S (1991). Comparison of the giemsa C-banded karyotypes of Dasypyrum villosum (2×) and D. breviaristatum (4×) from Greece. Hereditas, 114: 237–244 doi: 10.1111/j.1601-5223.1991.tb00330.x
Liu Q L, Ge S, Tang H B, Zhang X L, Zhu G F, Lu B R (2006). Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on thenuclear ribosomal internal transcribed spacer and chloroplast trnL-Fsequences. New Phytologist, 170: 411–420 doi: 10.1111/j.1469-8137.2006.01665.x
Patel M S, Korotchkina L G (2006). The biochemistry of the pyruvate dehydrogenase complex. Biochemistry and Molecular Biology Education, 31: 5–15 doi: 10.1002/bmb.2003.494031010156
Petersen G, Seberg O (1997). Phylogenetic analysis of the Triticeae (Poaceae) basedon rpoA sequence data. Mol Phylogenet Evol, 7: 217–230 doi: 10.1006/mpev.1996.0389
Petersen G, Seberg O, Yde M, Berthelsen K (2006). Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of commonwheat (Triticum aestivum). Mol Phylogenet Evol, 39: 70–82 doi: 10.1016/j.ympev.2006.01.023
Qi L L, Echalier B, Chao S, Lazo G R, Butler G E, Anderson O D, Akhunov E D, voák J D, Linkiewicz A M, Gill B S (2004). A chromosome bin map of 16,000 expressedsequence tag loci and distribution of genes among the three genomesof polyploid wheat. Genetics, 168: 701–712 doi: 10.1534/genetics.104.034868
Rajeev K V, Ralf S, Andreas B, Viktor K, Nils S, Mark E S, Peter L, Andreas G (2004). Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye andrice. Plant Science, 168: 195–202
Ramakrishna W, Dubcovsky J, Park Y J, Busso C, Emberton J, SanMiguel P, Bennetzen J L (2002). Different types and rates of genome evolution detected by comparative sequence analysis of orthologoussegments from four cereal genomes. Genetics, 162: 1389–1400
Randall D D, Rubin P M, Fenko M (1977). Plant pyruvate dehydrogenase complex purification, characterization and regulation by meta. Biochim Biophys Acta, 485: 336–349
Song W, Xie C J, Du J K, Xie H, Liu Q, Ni Z F, Yang T, Sun Q X, Liu Z Y (2008). A ‘one-marker-for-two-genes’ approach forefficient molecular discrimination of Pm12 and Pm21 conferring resistanceto powdery mildew in wheat. Molecular Breeding, 23: 357–363 doi: 10.1007/s11032-008-9235-x
Sun G L, Ni Y, Daley T (2008). Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation ofH genome, and the relationship of the Y genome to other genomes in Elymus species. Mol Phylogenet Evol, 46: 897–907
Sun G L, Daley T, Ni Y (2007). Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species. Plant Mol Biol, 64: 645–665 doi: 10.1007/s11103-007-9183-6
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 doi: 10.1093/molbev/msm092
Wang C M, Li L H, Zhang X T, Gao Q, Wang R F, An D G (2009). Development and application of EST-STS markers specific to chromosome 1RS of Secale cereale. Cereal Research Communications, 37: 13–21 doi: 10.1556/CRC.37.2009.1.2
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003). Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA, 100: 6263–6268 doi: 10.1073/pnas.0937399100
Yang Z J, Li G R, Feng J, Jiang H R, Ren Z L (2005). Molecular cytogenetic characterization and disease resistance observation ofwheat-Dasypyrum breviaristatum partial amphiploid and its derivatives. Hereditas, 142: 80–85 doi: 10.1111/j.1601-5223.2005.01918.x
Zhang W, Qu L J, Gu H, Gao W, Liu M, Chen J, Chen Z (2002). Studieson the origin and evolution of tetraploid wheats based on the internaltranscribed spacer (ITS) sequences of nuclear ribosomal DNA. Theor Appl Genet, 104: 1099–1106 doi: 10.1007/s00122-002-0887-3
