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Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.).
BMC Genomics. 2015 Oct 23; 16:844.BG

Abstract

BACKGROUND

5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous copies of the allohexaploid wheat EPSPS gene were cloned and characterized.

METHODS

Genomic and coding DNA sequences of EPSPS from the three related genomes of allohexaploid wheat were isolated using PCR and inverse PCR approaches from soft white spring "Louise'. Development of genome-specific primers allowed the mapping and expression analysis of TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1 on chromosomes 7A, 7D, and 4A, respectively. Sequence alignments of cDNA sequences from wheat and wheat relatives served as a basis for phylogenetic analysis.

RESULTS

The three genomic copies of wheat EPSPS differed by insertion/deletion and single nucleotide polymorphisms (SNPs), largely in intron sequences. RT-PCR analysis and cDNA cloning revealed that EPSPS is expressed from all three genomic copies. However, TaEPSPS-4A1 is expressed at much lower levels than TaEPSPS-7A1 and TaEPSPS-7D1 in wheat seedlings. Phylogenetic analysis of 1190-bp cDNA clones from wheat and wheat relatives revealed that: 1) TaEPSPS-7A1 is most similar to EPSPS from the tetraploid AB genome donor, T. turgidum (99.7 % identity); 2) TaEPSPS-7D1 most resembles EPSPS from the diploid D genome donor, Aegilops tauschii (100 % identity); and 3) TaEPSPS-4A1 resembles EPSPS from the diploid B genome relative, Ae. speltoides (97.7 % identity). Thus, EPSPS sequences in allohexaploid wheat are preserved from the most two recent ancestors. The wheat EPSPS genes are more closely related to Lolium multiflorum and Brachypodium distachyon than to Oryza sativa (rice).

CONCLUSIONS

The three related EPSPS homoeologues of wheat exhibited conservation of the exon/intron structure and of coding region sequence, but contained significant sequence variation within intron regions. The genome-specific primers developed will enable future characterization of natural and induced variation in EPSPS sequence and expression. This can be useful in investigating new causes of glyphosate herbicide resistance.

Authors+Show Affiliations

Department of Crop and Soil Science, Washington State University, Pullman, WA, USA. attawan.aramrak@gmail.com.Department of Crop and Soil Science, Washington State University, Pullman, WA, USA. kidwell@wsu.edu.Department of Crop and Soil Science, Washington State University, Pullman, WA, USA. csteber@wsu.edu. Wheat Genetics, Quality, Physiology and Disease Research, USDA-ARS, Pullman, WA, USA. csteber@wsu.edu.Department of Crop and Soil Science, Washington State University, Pullman, WA, USA. icburke@wsu.edu.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26492960

Citation

Aramrak, Attawan, et al. "Molecular and Phylogenetic Characterization of the Homoeologous EPSP Synthase Genes of Allohexaploid Wheat, Triticum Aestivum (L.)." BMC Genomics, vol. 16, 2015, p. 844.
Aramrak A, Kidwell KK, Steber CM, et al. Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.). BMC Genomics. 2015;16:844.
Aramrak, A., Kidwell, K. K., Steber, C. M., & Burke, I. C. (2015). Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.). BMC Genomics, 16, 844. https://doi.org/10.1186/s12864-015-2084-1
Aramrak A, et al. Molecular and Phylogenetic Characterization of the Homoeologous EPSP Synthase Genes of Allohexaploid Wheat, Triticum Aestivum (L.). BMC Genomics. 2015 Oct 23;16:844. PubMed PMID: 26492960.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.). AU - Aramrak,Attawan, AU - Kidwell,Kimberlee K, AU - Steber,Camille M, AU - Burke,Ian C, Y1 - 2015/10/23/ PY - 2015/05/08/received PY - 2015/10/14/accepted PY - 2015/10/24/entrez PY - 2015/10/27/pubmed PY - 2016/7/2/medline SP - 844 EP - 844 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous copies of the allohexaploid wheat EPSPS gene were cloned and characterized. METHODS: Genomic and coding DNA sequences of EPSPS from the three related genomes of allohexaploid wheat were isolated using PCR and inverse PCR approaches from soft white spring "Louise'. Development of genome-specific primers allowed the mapping and expression analysis of TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1 on chromosomes 7A, 7D, and 4A, respectively. Sequence alignments of cDNA sequences from wheat and wheat relatives served as a basis for phylogenetic analysis. RESULTS: The three genomic copies of wheat EPSPS differed by insertion/deletion and single nucleotide polymorphisms (SNPs), largely in intron sequences. RT-PCR analysis and cDNA cloning revealed that EPSPS is expressed from all three genomic copies. However, TaEPSPS-4A1 is expressed at much lower levels than TaEPSPS-7A1 and TaEPSPS-7D1 in wheat seedlings. Phylogenetic analysis of 1190-bp cDNA clones from wheat and wheat relatives revealed that: 1) TaEPSPS-7A1 is most similar to EPSPS from the tetraploid AB genome donor, T. turgidum (99.7 % identity); 2) TaEPSPS-7D1 most resembles EPSPS from the diploid D genome donor, Aegilops tauschii (100 % identity); and 3) TaEPSPS-4A1 resembles EPSPS from the diploid B genome relative, Ae. speltoides (97.7 % identity). Thus, EPSPS sequences in allohexaploid wheat are preserved from the most two recent ancestors. The wheat EPSPS genes are more closely related to Lolium multiflorum and Brachypodium distachyon than to Oryza sativa (rice). CONCLUSIONS: The three related EPSPS homoeologues of wheat exhibited conservation of the exon/intron structure and of coding region sequence, but contained significant sequence variation within intron regions. The genome-specific primers developed will enable future characterization of natural and induced variation in EPSPS sequence and expression. This can be useful in investigating new causes of glyphosate herbicide resistance. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26492960/Molecular_and_phylogenetic_characterization_of_the_homoeologous_EPSP_Synthase_genes_of_allohexaploid_wheat_Triticum_aestivum__L___ DB - PRIME DP - Unbound Medicine ER -