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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.<\/p>\n
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.<\/p>\n
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.<\/p>\n
Carmen A Johns, Alexander Silva, Thomas Mason Chizk, Lacy Nelson, John R Clark, Rishi Aryal, Hudson Ashrafi, Ellen Thompson, Michael Hardigan, Margaret L Worthington, Genetic control of prickles in tetraploid blackberry, G3 Genes|Genomes|Genetics, Volume 15, Issue 6, June 2025, jkaf065, https:\/\/doi.org\/10.1093\/g3journal\/jkaf065<\/a> <\/p>\n