Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species.

Caneberry crops (raspberry and blackberry) are globally commercialized specialty crops with a high fresh market value. Field management of canes and harvesting of fruits can be complicated by the presence of prickles (the botanically accurate term rather than spines or thorns) on the stems, petioles, and underside of the leaves. Both field management and fruit harvesting could be simplified by the development of cultivars with prickle-free canes. Scanning electron microscopy (SEM) was used to analyze and compare prickle development in different Rubus species. Comparisons were made between prickled vs. prickle-free red raspberry ( Rubus idaeus L.), black raspberry ( Rubus occidentalis L.), blackberry ( Rubus hybrid), complex hybrid with purple fruit ( R. occidentalis × R. idaeus ), and the hairy and prickled wineberry (Rubus phoenicolasius Maxim). Samples from stems and leaves with petioles attached were used for imaging. There were distinct differences between prickled vs. prickle-free phenotypes in each species. The images of prickle development suggest that prickles either develop directly from glandular trichomes (in red raspberry and wineberry) or that the signal originates from glandular trichomes (in blackberry). Black raspberry prickle development was similar to that of blackberry, suggesting that prickles developed after a developmental signal from glandular trichomes rather than as a direct development from glandular trichomes. The prickle development in the purple hybrid was unique in the presence of one-sided lumps in the trichomes, which has not been seen in any other Rubus species to date; however, both prickled and prickle-free plants exhibited simple nonglandular trichomes. Unlike previous studies, an increase in the number of simple trichomes was not specific to prickle-free plants, but rather variability among the different genotypes was observed. This study adds to the basic understanding of prickle development in the genus Rubus as a first step in the development of prickle-free versions of important cultivars through gene-editing procedures for improving the ease of field management and harvesting.

Red raspberry (Rubus idaeus L.) is a globally commercialized specialty crop with growing demand worldwide. The presence of prickles on the stems, petioles and undersides of the leaves complicates both the field management and harvesting of raspberries. An RNA sequencing analysis was used to identify differentially expressed genes in the epidermal tissue of prickled “Caroline” and prickle-free “Joan J.” and their segregating progeny. Expression patterns of differentially expressed genes (DEGs) in prickle-free plants revealed the downregulation of some vital development-related transcription factors (TFs), including a MIXTA-like R2R3-MYB family member; MADS-box; APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and NAM, ATAF1/2 and CUC2 (NAC) in prickle-free epidermis tissue. The downregulation of these TFs was confirmed by qRT-PCR analysis, indicating a key regulatory role in prickle development. This study adds to the understanding of prickle development mechanisms in red raspberries needed for utilizing genetic engineering strategies for developing prickle-free raspberry cultivars and, possibly, other Rubus species, such as blackberry (Rubus sp.) and black raspberry (R. occidentalis L.).

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

A hydroponic method was developed and tested for screening red raspberry genotypes for resistance to Phytophthora fragariae var. rubi, the most common causal agent of Phytophthora root rot in raspberry. Plants of `Titan' and `Encore' exhibited typical disease symptoms, with the latter developing significantly smaller stem lesions and fewer petiole lesions. The resistant cultivar, `Latham', regenerated healthy root tissue from the crown and older-order roots after initial infection and necrosis of young roots and exhibited no other symptoms beyond minor leaf chlorosis. This component of the resistance reaction has not been documented previously. A segregating F <sub>1</sub> population from the cross of `Latham' × `Titan' had a survival rate of 56% with 42% classified as resistant, exhibited minimal symptoms, and produced varying amounts of healthy root tissue. This screening method allows multiple observations of all plant tissues, including roots, under repeatable and definable growth chamber conditions. It should be useful for classifying the phenotype of individuals in segregating red raspberry populations to investigate the inheritance of Phytophthora root rot resistance using molecular markers.

Annual plasticulture production of strawberries promises superior weed control, fruit quality and yields. However, strawberry varieties adapted for perennial, matted-row production and local markets in cold climate regions have not been widely tested for adaptation to an annual production cycle. Productivity of seven short-day varieties developed for matted-row and/or annual production was examined in an annual plasticulture system in two consecutive trials in central NY (lat. 42.87° N, long. 76.99° W) harvested in 2013 and 2014. ‘Flavorfest’ demonstrated good performance in Trial 1 with high yield (390 g/plant) and large fruit size (13.9 g mean berry weight). ‘Jewel’ was shown to be well adapted to the annual plasticulture system with consistently high yields (330 and 390 g/plant) that equaled or surpassed other varieties and had moderate fruit size. ‘Chandler’ performed similarly to previous trials conducted in warmer regions with yield (340 g/plant) and fruit size (9.8 g mean berry weight) similar to ‘Jewel’. ‘Clancy’ yielded less but was consistent from year to year. The late season varieties Seneca and Ovation showed marked variability between years, possibly due to drastically different temperatures during flowering and fruit development in Trial 1 compared to Trial 2. High temperatures in Trial 1 likely caused higher early fruit yield, a compressed season and a precipitous decline in fruit size in the later season, thus reducing yield in the late season. Survival after a second dormant period was poor resulting in a small second harvest and reduced fruit size. Overall, the system demonstrated many of the expected benefits but may be more sensitive to weather conditions in the region. While many varieties developed for matted-row production may work well in an annual plasticulture system, not all varieties are equally adapted. Performance of each variety should be determined independently before large scale adoption by growers.