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United States Department of Agriculture

Agricultural Research Service

Research Project: Developing the Genomic Infrastructure for Breeding Improved Black Raspberries

Location: Horticultural Crops Research

2013 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.


3.Progress Report:

This research was conducted in support of NP301 sub-objective 3A "Sequence novel viruses of small fruit crops and develop assays for rapid detection" of the parent project. We planted two groups of black raspberry seedlings in the spring and fall of 2012 at the National Clonal Germplasm Repository, Corvallis, Oregon, and replicated them in commercial fields in Oregon (4 sites) and eastern Washington (1 site). The two groups are siblings which mean they share the same parents. The replication of the groups in the different locations will help us to determine how the environment influences their traits. We can assess the environmental influences by visual appraisal of specific traits at each of the locations then use DNA technology to determine how the traits are inherited. We began collecting information on approximately 30 traits in fall of 2012 and have continued assessment through the 2013 growing season. Some of the traits that we are evaluating are plant vigor and growth habits, flowering and fruiting season, yield, cane and spine density, disease and pest tolerance, and fruit quality characteristics. We collected fruit from individuals within both groups and sent them to the Plants for Human Health Institute in North Carolina for fruit quality evaluation. We extracted DNA from leaf tissue from one group and developed and used DNA information to assess the genetic variation and to construct representative chromosomes. These representative chromosomes will allow us to identify the genes that control the traits of interest. Outreach activities in Oregon included hiring a summer intern to assist in gathering and evaluation of data, and presentation of our research results at the following meetings: Caneberry Field Day, North Willamette Research Center, Canby, Oregon; Oregon Raspberry & Blackberry Commission annual meeting, Woodburn, Oregon; North American Raspberry & Blackberry Assoc. annual meeting, Portland, Oregon; Northwest Center for Small Fruits Research, Kennewick, Washington; the Plant & Animal Genome Conference, San Diego, California; and the American Society for Horticultural Science, Palm Desert, California.


Last Modified: 9/10/2014
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