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
 Vegetable Crops Research: Madison, WI
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    ScientistsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Midwest Area Madison, Wisconsin Vegetable Crops Research 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
                                            COVARRUBIAS-PAZARAN, GIOVANNY - University Of Wisconsinitem
                                            DIAZ-GARCIA, LUIS - University Of Wisconsinitem
                                            SCHLAUTMAN, BRANDON - University Of Wisconsinitem
                                            DEUTSCH, JOSEPH - University Of Wisconsinitem
                                            SALAZAR, WALTER - University Of Wisconsinitem
                                            HERNANDEZ-OCHOA, MIGUEL - University Of Wisconsinitem
                                            GRYGLESKI, EDWARD - Valley Corporationitem
                                            Steffan, Shawnitem
                                            IORIZZO, MASSIMO - North Carolina State Universityitem
                                            Polashock, Jamesitem
                                            VORSA, NICHOLI - Rutgers Universityitem
                                            Zalapa, Juan
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 5/27/2016
                                    Publication  Date: 6/13/2016
                                    Publication URL: http://handle.nal.usda.gov/10113/62658Citation: Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Deutsch, J., Salazar, W., Hernandez-Ochoa, M., Grygleski, E., Steffan, S., Iorizzo, M., Polashock, J.J., Vorsa, N., Zalapa, J. 2016. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. Biomed Central (BMC) Genomics. 17(1):451. doi: 10.1186/s12864-016-2802-3.Interpretive Summary: The application of genotyping by sequencing (GBS) approaches is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to genetically characterize a recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of molecular markers for genetic mapping. We identified 10842 potentially mappable molecular markers in a cranberry wherein 5151 were used to construct a high-density cranberry genetic map. In addition, comparative analyses of sequence order between gene coding DNA regions of cranberry with grape, coffee, and kiwifruit were performed to explore the levels of similarity between species. To date, cranberry breeding programs have relied solely on phenotypic selection because of the limited molecular resources and information available to facilitate genetic improvement using molecular tools. The present study was conducted to further molecular crop improvement strategies in cranberry to generate genomic resources to improve cranberry genetic mapping techniques. In the future, the current high-density cranberry map can be used map traits and discover genes that could be useful to accelerate breeding through the development of molecular breeding strategies that reduce the required time, labor and financial investments and provide for increased breeding efficiency.
                                Technical Abstract: The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 5154 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 5154 point map consisted of twelve linkage groups spanning 1439 cM, which anchored 2508 nuclear scaffolds accounting for 13 Mb of the estimated 470 Mb cranberry genome. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided evidence that cranberry and the Ericaceae lack further whole genome duplications (WGDs) following the Ad-' WGD.
GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between this GBS-based genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. GBS-based SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate molecular breeding through QTL mapping and genome-wide association studies (GWAS).


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