Abstract
Prickle-free blackberry (Rubus subgenus Rubus) canes are strongly preferred by growers due to food and worker safety concerns and damage to fruit from mechanical injury by prickles. This project was conducted to identify the genetic region responsible for prickle-free canes derived from the recessive "Merton Thornless" source in autotetraploid blackberry using a genome-wide association study, develop diagnostic Kompetitive Allele-Specific PCR markers for prickle-free canes, and determine the effects of allele dosage at the prickle-free locus on prickle density in 2 biparental populations. The prickle locus was located on chromosome Ra04 from 30.48 to 36.04 Mb in an extensive LD block, with the peak single-nucleotide polymorphism located at 33.64 Mb. Five potential candidate genes with functional annotations related to epidermal, trichome, or prickle development were identified within the prickle-free locus. One missense mutation in the third exon of the HOX3 homolog Ra_g19498, which resulted in a serine to leucine substitution at position 91 in the amino acid sequence, was discovered using whole-genome sequence data of 17 tetraploid blackberry genotypes. Three diagnostic Kompetitive Allele-Specific PCR markers were developed targeting the missense mutation in Ra_g19498 and the 2 single-nucleotide polymorphisms most strongly associated with the prickle-free trait in the genome-wide association study. These 3 markers each correctly predicted the phenotype of between 96 and 97% and of 626 diverse fresh-market blackberry genotypes from multiple breeding programs, respectively. Allele dosage at the prickle-free locus had a significant impact on prickle density, with duplex prickly genotypes having significantly higher prickle density than simplex genotypes in both biparental populations studied.