Patrick P. Moore

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation.

BackgroundRapid 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.ResultsGenotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison.ConclusionsGBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species.

Developments in raspberry production, cultivar releases, and intellectual property rights: a comparative study of British Columbia and Washington State.

The Pacific Northwest (PNW) raspberry industry has undergone substantial structural changes over the last two decades driven by shifts in production and trade and strengthened intellectual property rights to protect cultivars. Since the mid-1980s, Washington raspberry production has increased substantively while British Columbia (BC) production has exhibited a downward decline. Plant breeding in the PNW has been affected by the increased globalization of the raspberry trade and the increased emphasis on plant patents and plant breeders rights to protect cultivars. The increased emphasis on intellectual property rights to protect cultivars is likely to affect the accessibility of germplasm and the transaction costs of procuring planting material from European breeding programs. Raspberry research in BC has concentrated its efforts in developing improved cultivars with little research on the effects of management practices on fruit yields. The development of improved cultivars in the PNW has relied on conventional or classical breeding approaches. With reduced public support for raspberry breeding research in the PNW, breeding programs rely more heavily on support from industry associations. Future prosperity of the PNW raspberry industry would require developing competitive cultivars and promoting intellectual property protection to stimulate market development and the world-wide dissemination of improved cultivars.