Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: OAT SNP DEVELOPMENT & IDENTIFICATION OF LOCI AFFECTING KEY TRAITS IN N. AMER OAT GERMPLASM USING ASSOC GENETICS; MARKER DEV & KARYOTYPING
2011 Annual Report


1a.Objectives (from AD-416)
The objective of this research will be to: i) develop a set of oat anueploid hybrids with the Ogle1040 and TAM O-301 parental lines, ii) use the oat anueploid hybrids to anchor newly developed single nucleotide polymorphism (SNP) and DArT markers onto oat chromosomes, and iii) determine the genomic translocations in the AFRI oat association mapping population. iv) clone the Cslf6 gene that controls beta glucan fiber in oat grain.


1b.Approach (from AD-416)
(i) Putative oat aneuploids and aneuploid-hybrids will be screened using microspore analysis and C-banding (if necessary) to verify aneuploidy and to identify the monosome (if necessary); (ii) DNA from nullisomics and aneuploid-hybrids will be extracted in conjunction with ARS researchers at Aberdeen as needed for hybridization to DArT arrays, and PCR-based SNP markers will be assayed using DNA from these aneuploids/aneuploid-hybrids to assign markers to syntenic groups; (iii) AFRI oat mapping population lines will be karyotyped using C-banding and, if necessary, in situ hybridization with pAs120a (A-genome clone) and pAm1 (C-genome clone) probes, to determine the presence and identity of chromosomal rearrangements, particularly the 7C-17A race-specific intergenomic translocation. (iv, supplemental) Novel SNP markers will be developed based on reduced-complexity genomic DNA sequence from allotetraploid wild oat (A. magna) and mapped to Ba 13-13 x #169 A. magna (4x) and Ogle 1040 x TAM 0-301 (6x) populations. (v) Genomic librairies for the Cslf6 gene in twenty differnet oat varieties will be generated and sequenced. The complete gene structure will be assembled and compared between Cslf6 gene seuqence in Rice and Barley. In addition, gene structures will be compared within oat varieties to determine copy number and between varieties to identify function SNP mutation that can be used as markers.

Documents Grant with Brigham Young University.


3.Progress Report

Over the past 48 years world-wide oat production has declined 58%, while production of crops like corn and soybean have drastically increased. Research groups in North America actively working on oat have also declined from 28 (1998) to 11 (2008). The Collaborative Oat Research Enterprise was recently established by the USDA ARS in Aberdeen, Idaho as an international scientific collaboration to reverse these trends. As part of the project, ARS Aberdeen enlisted the help of Brigham Young University to develop new “molecular” tools and evaluate the physical structure of oat chromosomes from 685 oat lines. Over the last year (2010 – 2011), 80,000 oat genetic “mile” markers have been identified of which, 1,100 have been used to build the first complete genetic “road” map. Using a new strategy, the map was physically anchored to the appropriate genetic “state” know as a chromosome. In addition, 300 oat lines have been evaluated and new abnormalities have been discovered. This information will allow oat breeders to use marker-assisted breeding and select oat lines with good chromosome structure for crossing and varietal development. This work will allow target development of high beta glucan lines possible in oat. This work directly relates to objective 3 of the current ARS Aberdeen project plan (5366-21000-024-00D) “Develop improved barley and oat cultivars meeting the needs of conventional and specialty markets for both dryland and irrigated production systems.” Monitoring of the project is accomplished via site visits, phone conversations, e-mail and written reports.


Last Modified: 10/21/2014
Footer Content Back to Top of Page