biostudies-literatureLiu QMurdoch UniversityGrains Research and Development Corporation138https://www.ebi.ac.uk/biostudies/studies/S-EPMC10219903biostudies-literatureUnknown136(6)<h4>Key message</h4>The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of 'Westonia' × 'Kauz'. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and diffTAG. Theoretical and applied genetics. Theoretische und angewandte GenetikThe putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness.PMC10219903UMU00048Liu HIslam SZhang JRahman SMa HLiu QYang RZhao YShe MO'Hara GVarshney RKMa WfalseThe putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness.<h4>Key message</h4>The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of 'Westonia' × 'Kauz'. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and diff2023-01-01T00:00:00Z2023 May2025-04-04T20:57:25.18Z2025-04-04T20:57:25.18ZS-EPMC102199033723382510.1007/s00122-023-04372-4