Analysis of the barley bract suppression gene Trd1

Abstract

A typical barley (Hordeum vulgare) floret consists of reproductive organs three stamens and a pistil, and non-reproductive organs—lodicules and two floral bracts, abaxial called ‘lemma’ and adaxial ‘palea’. The floret is subtended by two additional bracts called outer or empty glumes. Together these organs form the basic structural unit of the grass inflorescence, a spikelet. There are commonly three spikelets at each rachis (floral stem of the barley spike) node, one central and two lateral spikelets. Rare naturally occurring or induced phenotypic variants that contain a third bract subtending the central spikelets have been described in barley. The gene responsible for this phenotype was called the THIRD OUTER GLUME1 (Trd1). The Trd1 mutants fail to suppress bract growth and as a result produce leaf-like structures that subtend each rachis node in the basal portion of the spike. Also, floral development at the collar is not always suppressed. In rice and maize, recessive mutations in NECK LEAF1 (Nl1) and TASSEL SHEATH1 (Tsh1) genes, respectively, have been shown to be responsible for orthologous phenotypes. Fine mapping of the trd1 phenotype in an F3 recombinant population enabled us to position Trd1 on the long arm of chromosome 1H to a 10 cM region. We anchored this to a conserved syntenic region on rice chromosome Os05 and selected a set of candidate genes for validation by resequencing PCR amplicons from a series of independent mutant alleles. This analysis revealed that a GATA transcription factor, recently proposed to be Trd1, contained mutations in 10 out of 14 independent trd1 mutant alleles that would generate non-functional TRD1 proteins. Together with genetic linkage data, we confirm the identity of Trd1 as the GATA transcription factor ortholog of rice Nl1 and maize Tsh1 genes.

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Acknowledgments

The work reported in this paper was funded through European Research Area Networks in plant genomics project number ERAPGFP/06.046A - Genomics-Assisted Dissection of Barley Morphology and Development awarded to RW, NS and MM via their respective funding agencies. We would like to thank Harold Bockelman at the National Small Grains Collection, Aberdeen ID USA, David Marshall who combined sequence information from Bowman and Morex NGS assemblies which allowed us to locate the promoter region of Trd1, Sean Chapman and Martin Kierans for help with SEM work, and David Harrap for generating BW069 x Barke F2 seeds.

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Correspondence to Robbie Waugh.

Additional information

Communicated by T. Close.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

. This includes all mutant lines that had previously been described as Trd1. Details of donor line cultivar, backcross stage and mutagen used to generate the line are provided. (PDF 38 kb)

Online Resource 2

. Details of the SNPs used in the 384-SNP Illumina GoldenGate oligo pool assay. The name refers to the SNP id in Close et al. (2009). (PDF 135 kb)

Online Resource 3

. Dendrogram based on bead express analysis of 384 SNPs in all lines included in this study. Where appropriate new nomenclature for the lines has been used, otherwise previous names are given. (PDF 130 kb)

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Houston, K., Druka, A., Bonar, N. et al. Analysis of the barley bract suppression gene Trd1 . Theor Appl Genet 125, 33–45 (2012). https://doi.org/10.1007/s00122-012-1814-x

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Keywords

  • Floral Meristem
  • Brachypodium
  • Gata Transcription Factor
  • Oligo Pool Assay
  • Rachis Node