U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 National Clonal Germplasm Repository: Corvallis, OR
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Plant Collections
                        Home
                                    Plant Collecting Expeditions
                                    Germplasm CGC Reports
                                    GRIN-Global
                                    Outreach
                                    Documents
                    USDASearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Pacific West Area Corvallis, Oregon National Clonal Germplasm Repository Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications

Title:   Author  item
                                            BRYANT, DOUG - Danforth Plant Science Centeritem
                                            Bushakra, Jillitem
                                            DOSSETT, MICHAEL - Pacific Agri-Food Research Centeritem
                                            VINING, KELLY - Oregon State Universityitem
                                            FILICHKIN, SERGEI - Oregon State Universityitem
                                            Weiland, Gerald

                                                         - *Jerry*item
                                            Lee, Jungminitem
                                            Finn, Chaditem
                                            Bassil, Nahlaitem
                                            MOCKLER, TODD - Danforth Plant Science Center
  Submitted to: American Society of Horticulture Science Meeting
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 4/20/2014
                                    Publication  Date: 4/20/2014
                                    Citation: Bryant, D., Bushakra, J., Dossett, M., Vining, K., Filichkin, S., Weiland, G.E., Lee, J., Finn, C.E., Bassil, N.V., Mockler, T. 2014. Building the genomic infrastructure in black raspberry [abstract]. American Society for Horticultural Science Annual Conference.Interpretive Summary: A concerted effort is being conducted to breed improved cultivars of black raspberry. We are using a variety of genomic and genetic tools to sequence the genome and construct a linkage map that is a representation of the chromosomes. We have identified specific DNA sequences that we will test to determine if they are associated with the expression of important traits. This information will be used to assist breeders in parent selection to develop cultivars that satisfy the demands of the growers and the marketplace, adding to the profitability and sustainability of the industry.
                                Technical Abstract: Cultivar improvement of black raspberry (Rubus occidentalis L.) has been stagnant for the past 75 years, with only a handful of new releases to date. The most commonly grown elite cultivars are susceptible to aphid-transmitted viruses and soil-borne pathogens that lead to a rapid decline in plant health necessitating frequent stand replacement by the growers. Recent research supporting the anti-cancer effects of black raspberries, has led to a resurgence of interest in this fruit and a renewal of breeding efforts. Genomic tools we are developing will be applied to the identification of quantitative trait loci and alleles important for breeding objectives regionally and nationally. We applied high-throughput genome sequencing of a highly homozygous accession to generate 2,200 scaffolds of approximately 240 Mbp, with 353 kbp N50, and 0.06% per-basepair variation. We employed genotyping by sequencing on the full-sibling population ORUS 4305 (115 progeny) to generate more than 900 single nucleotide polymorphic (SNP) markers to construct a linkage map. The consensus linkage map consists of seven linkage groups spanning 613.1 cM with the longest group spanning 101.7 cM with 103 markers (G1) and the shortest spanning 77.6 cM with 61 markers (G7). The linkage map was used to place over 50% of the genomic sequence into linkage groups. In addition, RNA-seq data from seven replicated libraries of five tissue types were assembled by de novo and reference-guided approaches, forming the basis for our empirically-based structural annotation (~26,000 transcription units). ORUS 4305 and a second population (ORUS 4304, 192 progeny) are being evaluated across production regions for a number of economically important traits. The genomic data and the phenotype information will be used to develop markers to assist plant breeders in parent selection with the goal of developing cultivars that satisfy the demands of the growers and the marketplace, adding to the sustainability and profitability of the industry.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov