The putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness

Area of Science:

• Plant Genetics
• Agricultural Science
• Molecular Biology

Background:

• Wheat pith-thickness (PT) is crucial for stem mechanical strength, particularly in basal internodes supporting upper plant structures.
• A quantitative trait locus (QTL) for PT was previously identified on chromosome 3BL in a specific wheat cross ('Westonia' × 'Kauz').

Purpose of the Study:

• To identify candidate genes and develop single nucleotide polymorphism (SNP) markers associated with wheat pith-thickness within the 3BL QTL region.
• To screen differentially expressed genes (DEGs) and analyze allelic polymorphisms in genes within the identified QTL interval.

Main Methods:

• Bulked segregant RNA-sequencing (BSR-seq) was employed to identify DEGs and high-probability SNPs.
• Quantitative real-time PCR (qRT-PCR) and sequencing were used to confirm gene associations with PT.
• Allelic polymorphism analysis was performed on mRNA sequences from high and low PT wheat samples.

Main Results:

• Sixteen DEGs were identified within the 3BL QTL interval.
• Twenty-four high-probability SNPs were found in eight genes, with six genes confirmed to be associated with PT.
• The vacuolar processing enzyme gene, TaVPE3cB, was identified as a strong candidate gene for PT in Australian wheat ('Westonia').

Conclusions:

• The gene TaVPE3cB is a candidate for wheat pith-thickness, and a robust SNP marker was developed for its introgression in breeding programs.
• Other DEGs may play roles in pith development and programmed cell death (PCD).
• A five-level hierarchical regulation mechanism for stem pith PCD in wheat was proposed.