Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant

Theor Appl Genet. 2020 Jan;133(1):163-177. doi: 10.1007/s00122-019-03448-4. Epub 2019 Oct 18.

Abstract

An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F1, F2, and F2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.

MeSH terms

  • Alleles
  • Alternative Splicing / genetics*
  • Amino Acid Sequence
  • Base Sequence
  • Chromosome Mapping
  • Chromosomes, Plant / genetics
  • Genes, Plant*
  • Genetic Association Studies
  • Genetic Markers
  • Homozygote
  • Hordeum / anatomy & histology*
  • Hordeum / genetics*
  • INDEL Mutation / genetics
  • Mutation / genetics*
  • Phenotype
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Quantitative Trait, Heritable
  • Reproducibility of Results
  • Synteny / genetics

Substances

  • Genetic Markers
  • Plant Proteins