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Molecular characterization and genomic organization of low molecular weight glutenin subunit genes at the Glu-3 loci in hexaploid wheat (Triticum aestivum L.)

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Abstract

In this study, we report on the molecular characterization and genomic organization of the low molecular weight glutenin subunit (LMW-GS) gene family in hexaploid wheat (Triticum aestivum L.). Eighty-two positive BAC clones were identified to contain LMW-GS genes from the hexaploid wheat ‘Glenlea’ BAC library via filter hybridization and PCR validation. Twelve unique LMW glutenin genes and seven pseudogenes were isolated from these positive BAC clones by primer-template mismatch PCR and subsequent primer walking using hemi-nested touchdown PCR. These genes were sequenced and each consisted of a single-open reading frame (ORF) and untranslated 5′ and 3′ flanking regions. All 12 LMW glutenin subunits contained eight cysteine residues. The LMW-m-type subunits are the most abundant in hexaploid wheat. Of the 12 LMW-GS, 1, 2 and 9 are i-type, s-type and m-type, respectively. The phylogenetic analysis suggested that the LMW-i type gene showed greater differences to LMW-s and LMW-m-type genes, which, in turn, were more closely related to one another. On the basis of their N-terminal sequences, they were classified into nine groups. Fingerprinting of the 82 BAC clones indicated 30 BAC clones assembled into eight contigs, while the remaining clones were singletons. BAC end sequencing of the 82 clones revealed that long terminal repeat (LTR) retrotransposons were abundant in the Glu-3 regions. The average physical distance between two adjacent LMW-GS genes was estimated to be 81 kb. Most of LMW-GS genes are located in the d-genome, suggesting that the Glu-D3 locus is much larger than the Glu-B3 locus and Glu-A3 locus. Alignments of sequences indicated that the same type (starting with the same N-terminal sequence) LMW-GS genes were highly conserved in the homologous genomes between hexaploid wheat and its donors such as durum wheat and T. tauschii.

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Acknowledgments

We would like to thank Travis Banks for bioinformatics support, and Elsa Reimer and Andrzej Walichnowski for technical assistance. X.Q. Huang received a visiting fellowship from the National Science and Engineering Research Council of Canada (NSERC). This research was supported by the Canadian Crop Genomics Initiative (CCGI). This is Agriculture and Agri-Food Canada publication number 1962.

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  1. Xiu-Qiang Huang

    Present address: Department of Plant Science, University of Manitoba, 66 Dafoe Road, R3T 2N2, Winnipeg, MB, Canada

Authors and Affiliations

  1. Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, R3T 2M9, Winnipeg, MB, Canada

    Xiu-Qiang Huang & Sylvie Cloutier

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Correspondence to Sylvie Cloutier.

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Communicated by J. Snape.

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Fig. S3 162 BAC end sequences (DOC 115 kb)

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Table S1 Primer sequences and annealing temperatures of primers used for PCR and sequencing of LMW-GS genes in Glenlea (DOC 68 kb)

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Table S2 Distribution of 82 BAC clones containing LMW-GS sequences based on the number of gene(s) and pseudogene(s) per BAC clone (DOC 28 kb)

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Table S3 Pairwise percentage similarity of the coding region (below the diagonal) of 12 LMW-GS genes and their deduced amino-acid sequences (above the diagonal) isolated from Glenlea (DOC 46 kb)

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Table S4 Similarity scores of the coding regions of the 12 LMW-GS genes from Glenlea obtained by MegaBLAST search of the non-redundant NCBI database (DOC 163 kb)

Table S5 Chromosome-specific primers and chromosome assignment of LMW-GS genes (DOC 41 kb)

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Huang, XQ., Cloutier, S. Molecular characterization and genomic organization of low molecular weight glutenin subunit genes at the Glu-3 loci in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 116, 953–966 (2008). https://doi.org/10.1007/s00122-008-0727-1

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