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
 Plant Stress and Germplasm Development Research: Lubbock, TX
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Projects
                        NP 301Search small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Plains Area Lubbock, Texas Cropping Systems Research Laboratory Plant Stress and Germplasm Development 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
                                            Chopra, Ratanitem
                                            Burow, Gloriaitem
                                            Sattler, Scottitem
                                            Acosta-Martinez, Veronicaitem
                                            Hayes, Chaditem
                                            Burke, Johnitem
                                            Xin, Zhanguoitem
                                            EMENDACK, YVES - Orise Fellow
  Submitted to: Meeting Abstract
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 8/6/2015
                                    Publication  Date: 9/1/2015
                                    Citation: Chopra, R., Burow, G.B., Sattler, S.E., Acosta Martinez, V., Hayes, C.M., Burke, J.J., Xin, Z., Emendack, Y. 2015. Translational genomics and marker assisted selection in sorghum case study using brown midrib (bmr) trait [abstract]. Sorghum Improvement Conference of North America, September 1-3, 2015, Manhattan, Kansas. p. 1.Interpretive Summary:
                                Technical Abstract: 
Translational genomics is a critical phase in harnessing the rich genomic data available for sorghum.   There is a need to transform  nucleotide variation data between sorghum germplasm such as that derived from RNA seq, genotype by sequencing (gbs) or whole genome resequencing thru translation and validation of Single Nucleotide Polymorphism (SNP) into easy access DNA markers for molecular and marker assisted breeding. Here, we use genes for lignin biosynthesis and the brown midrib phenotype, an important trait, which is associated with reduced lignin content as a case study for translational genomics. In this study SNP markers were developed from previously identified mutations in monolignol biosynthetic genes that affect the lignin content. In sorghum, there are three genes - caffeic acid O-methyltransferase (COMT), cinnamyl alcohol dehydrogenase (CAD) and 4-coumaroyl CoA ligase (4CL) that when mutated lowered the lignin content and produce the brown midrib phenotype. Twenty mutations are known in these three genes and nineteen of them were converted into SNP molecular markers that can easily be assayed using endpoint genotyping technology. The SNP markers were assayed in a pool of germplasm, which consisted of commercial varieties, bmr6-ref and bmr12-ref inbred lines and 6 new bmr mutants from EMS populations. We observed that the 6 new bmr mutants did not contain any of the known natural or induced mutations in three genes, which suggests the presence of new mutations in monolignol biosynthetic genes causing bmr phenotype. The SNP molecular markers for bmr described here provide a platform to screen for the variations present in diverse lines and provide an opportunity to identify new alleles for crop improvement.


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