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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
2012 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.


3.Progress Report:

Progress was made on the objective, which fall under National Program 301, Component 1, Plant and Microbial Genetic Resource Management, and Component 2, Crop Informatics, Genomics, and Genetic Analyses. Progress on this project focuses on the problem of assessments of cytogenetic characterization of oat lines. To date, we have C-banded the first 156 of the core lines and another 14 peripherally associated with the study. We reported our results thus far on Friday, June 22, at the 9th International Oat Conference in Beijing, China. Four undergraduate students have helped with this work in my lab at Brigham Young University. Thus far we have identified nine lines having the non-translocation forms of chromosomes 7C and 17A; the remaining lines are homogeneous for the 7C-17A translocation. The nine non-translocation lines, which presume Avena byzantina ancestry based on previous work (Jellen & Beard 2000), are the following: HiFi (line #16), La Prevision (line #21), Jerry (line #29), Pusa Hybrid (line #87), Fulghum (line #92), Red Rustproof (line #106), Victoria (line #108), Coker 234 (line #54), heterogeneous for the 7C-17A translocation, Kanota (line #19), heterogeneous for the 7C-17A translocation. These results support Objective 1 in the parent project plan, development of molecular tools for oat. This is the final report for the project. Total of 156 core oat lines were analyzed using C-Banding technology. The genomic relationships among the materials was evaluated using the C-Banding data. The results were reported in the Oat International Conference in June 2012. The translocation between chromosome 7C and 17A was analyzed in the 156 lines. Nine of the lines had the non-translocation type of genome and rest had the translocation type. This information will be useful in selecting parents for future genetic mapping experiments.


Last Modified: 10/23/2014
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