Comparative transcriptome analysis reveals candidate gene for flowering time QTL HvHeading in barley

Area of Science:

• Plant genetics and genomics
• Crop science
• Molecular biology

Background:

• Flowering time is crucial for crop adaptation and productivity.
• Understanding the genetic basis of flowering time in barley (Hordeum vulgare) is essential.
• The quantitative trait locus (QTL) HvHeading is known to influence barley flowering time.

Purpose of the Study:

• To identify the specific gene(s) responsible for the flowering time variation associated with the HvHeading QTL in barley.
• To investigate the molecular mechanisms underlying the delayed-flowering effect of HvHeading.

Main Methods:

• Utilized spring barley MAGIC DH lines with distinct HvHeading alleles and controlled epistatic backgrounds.
• Performed phenotyping of apex development to assess flowering time differences.
• Conducted RNA sequencing on apex and leaf tissues to analyze gene expression.
• Integrated recombination analysis with differential gene expression data.
• Performed full-length sequencing of candidate genes.

Main Results:

• Phenotypic analysis revealed contrasting effects of different HvHeading alleles on flowering time.
• RNA sequencing and recombination mapping identified a 3.94 Mbs interval containing 22 differentially expressed genes.
• The transcription elongation factor HvSpt6 (HORVU1Hr1G067820) was identified as a strong candidate gene.
• Two promoter mutations in the HvSpt6 allele from delayed-flowering genotypes were discovered, creating a binding site for the flowering-suppressing transcription factor TEM1.

Conclusions:

• This study provides initial insights into the gene regulating flowering time at the HvHeading locus in barley.
• HvSpt6 is proposed as a key candidate gene involved in flowering time regulation, with promoter mutations potentially driving delayed flowering.
• The combined approach of leveraging epistatic locus knowledge and RNA sequencing is effective for gene discovery in complex crop genomes.