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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

Location: Small Grains and Potato Germplasm Research

Project Number: 5366-21000-028-19
Project Type: General Cooperative Agreement

Start Date: May 18, 2010
End Date: Aug 31, 2012

Objective:
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.

Approach:
(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.

Last Modified: 8/21/2014
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