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United States Department of Agriculture

Agricultural Research Service

Title: Use of TILLinG/EcoTILLinG as an efficient SNP discovery tool to survey genetic variation in different peanut populations

Authors
item Ramos, M - UNIV OF GA
item Chu, Ye - UNIV OF GA
item Holbrook, C
item Ozias-Akins, Peggy - UNIV OF GA

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: October 15, 2006
Publication Date: N/A

Interpretive Summary: not required

Technical Abstract: Single Nucleotide Polymorphisms (SNPs), the most common type of sequence difference between alleles, may alter amino acid sequence and affect gene function. TILLinG (Targeting Induced Local Lesions in Genomes) is a recently developed method for detecting mutations in a high-throughput manner available to plant geneticists. We are exploring for these mutations specifically to alter the allergen content and composition in peanut seeds. Therefore, these functional SNPs also would be valuable markers for breeding purposes. A TILLinG peanut population generated by EMS, a peanut mini-core collection representing the global geographic range, and wild relative accessions (A-genome Arachis duranensis) were used in this study to survey variation in the ara h 2 gene, a seed storage protein gene that encodes one of the most powerful peanut allergens. The mutation rate observed in the EMS-generated mutant population was similar to that reported for Arabidopsis. EcoTILLinG allowed the identification of five different allelic variants distributed in the signal peptide region or in the mature protein. Three of them could have a potential damaging effect on the protein as reported by SIFT (Sorting Intolerant From Tolerant). One allelic variant showed a mutation that altered the immunodominant DPYSPS epitope. Preliminary computational modeling of predicted proteins supported changes in the secondary structure associated with this kind of mutation. Indels and SNPs also were identified in the promoter and 3’ UTR. Thus, in the quest for a hypoallergenic peanut, these methods represent an efficient approach to identify mutants without the production of genetically modified organisms.

Last Modified: 11/24/2014
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