Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes

PLoS One. 2020 Apr 16;15(4):e0231704. doi: 10.1371/journal.pone.0231704. eCollection 2020.

Abstract

The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Aegilops / genetics*
  • Alleles
  • Base Sequence
  • Chromosomes, Plant
  • Genes, Plant*
  • Plant Proteins / genetics
  • Polymorphism, Genetic
  • Transcription Factors / genetics
  • Transcription, Genetic
  • Triticum / genetics*

Substances

  • 5' Untranslated Regions
  • Plant Proteins
  • Transcription Factors

Grants and funding

This research was funded by State Task 0431-2019-0004. The Ae. tauschii collection of Federal Research Center Vavilov All-Russian Institute of Plant Genetic Resources (VIR, Saint-Petersburg, Russia) is supported by grant number 0662-2019-0006 VIR. The next-generation sequencing of the amplicons was funded by Kurchatov Genomics Center of All-Russia Research Institute of Agricultural Biotechnology for support, agreement № 075-15-2019-1667. The growing, genotyping and phenotyping of the set of 20 breeding lines of bread winter wheat developed at the Lisitsyn Field Experimental Station (RSAU-MTAA) was funded by the Russian Science Foundation, grant number 17-76-20023.