2012 Annual Report
1a.Objectives (from AD-416):
The overall goal of this proposal is to develop and make available genomic tools for the improvement of black and red raspberry (Rubus, subgenus Idaeobatus) and begin the application of these tools in using wild black raspberry germplasm for crop improvement. To achieve our overall goal, we have organized a diverse team of researchers from a variety of disciplines including plant breeders, molecular biologists, genomicists and analytical chemists, who have been an integral part of laying the foundation for modern red and black raspberry research and breeding nationwide, and who are capable, with the proper funding and resources, of making significant gains in breeding new superior cultivars that support the industry. This goal will be accomplished through seven major objectives:
A) Transcriptome sequencing and high throughput genomic sequencing.
B) Developing molecular markers from genomic and EST sequences.
C) Studying genotype by environment interaction on specific traits of interest in crosses involving diverse wild black raspberry germplasm.
D) Using molecular markers for mapping specific traits of interest in crosses involving diverse wild black raspberry germplasm.
E) Evaluate transferability of SSR markers developed in black raspberry to red raspberry.
F) Better understanding of consumer preferences for market expansion.
G) Delivering research results and training in molecular breeding to the industry, breeders, and students through a multifaceted outreach program.
1b.Approach (from AD-416):
1: Transcriptome sequencing and high throughput genomic sequencing. ESTs will be generated from leaves, stems, buds, and fruit and aligned into contigs and sequences assembled with identities assigned based on similarities to other GenBank sequences. 2: Developing molecular markers from EST and genomic sequences. Generated ESTs and genomic sequences will be mined for SSRs using the Genomic Database for the Rosaceae pipeline. SNPs will be detected after genomic sequencing with a Oregon Lab pipeline. 3: Studying genotype by environment interaction on specific traits of interest in crosses involving diverse wild germplasm. Mapping populations that segregate for a variety of traits have been generated using germplasm from the edges of the species native range. The populations will be planted and evaluated in New York, North Carolina and Oregon. Analyses of fruit chemistry will be made to examine total anthocyanins and phenolics. 4: Using molecular markers for mapping specific traits of interest in these crosses. We will place traits of interest on generated linkage maps, anchored with SSR markers from red raspberry and blackberry as well as ones generated from transcriptome and genomic sequencing. SSR markers will be tested on the parents of the mapping populations for amplification and polymorphism. Maps will be saturated with SNP markers that are developed from genomic sequencing of the SNP detection panel. Phenotypic evaluations will be used to study genotype by environment interactions and to place QTL on the maps. A detailed analysis of fruit phenolic components will be performed. These populations will be grown by commercial growers to supplement data, to provide information about performance in large-scale mechanized production systems, to generate feedback, and to educate them about the project. Linkage maps will be generated that will show QTL for traits of interest specific to locations. 5: Better understanding of consumer preferences for market expansion. A consumer panel will determine fruit attributes important in making purchasing decisions. This may identify additional characteristics to include in mapping studies. Panels will be performed with fresh fruit harvested during the peak of the season with off-season evaluations of pureed fruit. 6: Evaluate transferability of SSR markers developed in black raspberry to red raspberry. SSR markers mined from black raspberry EST and genomic sequences will be evaluated for amplification and polymorphism in red raspberry by capillary electrophoresis. Polymorphism will be determined and added to linkage maps for those populations by UK collaborators. 7: Delivering research results and training in molecular breeding to the industry, breeders, and students through a multifaceted outreach program. Research results will be communicated to the scientific community and the commercial industry at regional, national and international meetings. A workshop will be held to educate stakeholders and extension specialists in MAB as well as a one-day short course for students and scientists. Throughout the project, post-docs and graduate, undergraduate, and high school students will be participating.
Black raspberries (Rubus occidentalis) are well known for their health-promoting properties. Despite this, they remain a minor crop because they are difficult to grow and are primarily processed as opposed to a fresh market crop. The overall goal of the project is to develop genetic information to hasten the development of the superior black raspberry cultivars that will fuel industry growth. In addition to being horticulturally superior, new berry cultivars will need to possess quality traits that invoke greater consumer demand if this industry expansion is to occur.
Towards this goal, two mapping populations of black raspberry were developed and propagated. They were planted at 11 locations (Oregon [5 sites], Washington , North Carolina , New York  and Ohio ) this past spring. We were responsible for all propagation and organization and planting the Oregon and Washington sites. The plants will be grown for 2 years until they fruit. The plants will be phenotyped with vegetative traits being assessed beginning at the end of this season through the trials completion and reproductive traits related to flowering and fruiting being evaluated as soon as we have mature floricanes.
DNA was isolated from parents and each individual in the mapping populations. One hundred and thirty eight simple sequence repeat (SSR) primer pairs developed from expressed sequence tags (ESTs) of ‘Bristol’ were screened for amplification and polymorphism in parents of both mapping populations. Thirty four and 28 SSRs were polymorphic in parents of the ORUS 4304 and ORUS 4305 mapping populations, respectively. Twenty-one primer pairs generated polymorphic PCR products in both populations. These SSRs are being used to genotype progeny of both populations and construct a linkage map in R. occidentalis. This research was conducted in support of objective 3A of the parent project.