This study aimed to validate the use of two SNP markers associated to a sdw1 allele identified previously in a short barley genotype (ND23049) with an adequate peduncle extrusion which reduces predisposition to fungal disease development. First, the GBS SNP were converted in a KASP marker but only one of them, named TP4712, correctly amplified all allelic variations and had a Mendelian segregation in a F2 population. To corroborate the association between TP4712 allele with plant height and peduncle extrusion, a total of 1221 genotypes were genotyped and evaluated for both traits. Out of the 1221 genotypes, 199 were F4 lines, 79 were a diverse panel, and 943 were two complete breeding cohorts of stage 1 yield trials. To corroborate the association between the sdw1 allele and the short plant height with adequate peduncle extrusion, contingency tables were created, grouping the 2427 data points into categories. Based on the contingency analysis, it was demonstrated that the higher proportion of short plants with adequate peduncle extrusion were present in genotypes carrying the SNP allele of ND23049 regardless the population and the sowing date. This study develops a marker-assisted selection tool to accelerate the introgression of favourable alleles for plant height and peduncle extrusion in adapted germplasm. © 2023, The Author(s), under exclusive licence to Springer Nature B.V.