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The cultivated eastern U.S. blackberry (Rubus L. subgenus Rubus Watson) has gone through tremendous strides in both trait improvement and market outreach at the University of Arkansas System Division of Agriculture (UA System). What began as primarily a pick-your-own local fruit found mostly in the wild, has become a commercialized year-round product in most major U.S. grocery retailers. This could not have been achieved without decades of diligent breeding efforts. Although the genetic improvement of fresh-market blackberries has advanced, there are still issues that need to be addressed. One issue is the prevalence of red drupelet reversion (RDR), a physiological disorder where the drupelets of a fully black berry begin to turn red after harvest. A two-year study was done at the UA System to discover if harvesting at different times of day and/or harvesting genotypes with different levels of firmness might influence the incidence of RDR in blackberries after one week of cold storage (5 °C). Less RDR occurred when fruit was harvested at earlier times in the day, especially at 7:00 AM, when there is cooler ambient temperature. RDR was also sharply reduced when fruit was harvested from firmer selections such as A-2453. Another pressing issue is the lack of molecular breeding strategies provided for blackberries. The cultivated blackberry is an autotetraploid where there are four sets of homologous chromosomes that follow a multisomic pattern of inheritance. As a result, blackberries have high heterozygosity and lack saturated molecular maps reliable for gene discovery. An F1 population and the parents were genotyped with new strategies optimized for autopolyploids to yield two saturated genetic linkage maps of the parents with 3,942 markers in total across 65 linkage groups. The blackberry population was aligned to a recently released diploid ‘Hillquist’ (R. argutus Link.) reference genome and showed a high degree of collinearity, highlighting its potential as a new tool for future comparative analyses of Rosaceous crops in molecular research.