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
 Corn Insects and Crop Genetics Research: Ames, IA
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Database Projects
                        MaizeGDB
                                    SoyBase
                                    PeanutBase
                                    Legume Information System
                                    Maize Newsletter
                                    Maize Mutant Phenotypes
                                    Maize Genetics Conference
                                    Shiny Soybase CNV
                                    Shiny Soybase SNP
                                    Common Bean and Alfalfa - PvGEA
                                    Common Bean and Alfalfa - AGEDSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Midwest Area Ames, Iowa Corn Insects and Crop Genetics 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
                                            LUO, Z - UNIV. OF BIRMINGHAM, UKitem
                                            POTOKINA, E - UNIV. OF BIRMINGHAM, UKitem
                                            DRUKA, A - SCOTTISH CROP RES. INST.item
                                            Wise, Rogeritem
                                            WAUGH, R - SCOTTISH CROP RES. INST.item
                                            KEARSEY, M - UNIV. OF BIRMINGHAM, UK
  Submitted to: Genetics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 3/18/2007
                                    Publication  Date: 6/15/2007
                                    Citation: Luo, Z.W., Potokina, E., Druka, A., Wise, R.P., Waugh, R., Kearsey, M.J. 2007. SFP genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics. 176:789-800.Interpretive Summary: Several recent studies have explored the possibility of using transcript abundance data from cRNA hybridizations to Affymetrix microarrays (Affymetrix, Santa Clara, CA) to reveal genetic polymorphisms that can be used as markers to genotype individuals in mapping populations. 

This article reports two new statistical methods for identifying single feature polymorphisms (SFPs) by modeling expression data from replicated Affymetrix microarrays on the Steptoe and Morex barley varieties and for mapping these SFPs in a doubled-haploid population from a cross of these two parental lines.  The expression analysis was performed on Affymetrix Barley1 GeneChips using RNA taken from two tissues, seedling leaves and embryo-derived tissue from the germinating grain.  The major aim was to define and validate a robust procedure for fast and reliable SFP genotyping in mapping populations that is appropriate to model organisms as well as agriculturally important but less tractable species.  The availability of such an approach has wide value in genetical analysis of crop plants and farm animals and also in complementing information available in sequenced model organisms for researchers working in the field of genomics.
                                Technical Abstract: The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data.  SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves.  However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and unsequenced genomes.  To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny.  The methods were compared in terms of numbers of SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes, and to match existing maps and individual haplotypes.  We identified >4000 separate SFPs that accurately predicted the SNP genotype of >98% of the doubled-haploid (DH) lines.  They were highly enriched for features containing sequence polymorphisms, but all methods uniformly identified a majority of SFPs (approximately 64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that "SFPs" mainly represent polymorphism in cis-acting regulators.  All methods are efficient and robust at predicting markers for gene mapping.


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