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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #340407

Research Project: Genetic Dissection of Traits for Sugar Beet Improvement

Location: Sugarbeet and Bean Research

Title: Leveraging long sequencing reads to investigate R-gene clustering and variation in beet

item Funk, Andrew - Michigan State University
item Mcgrath, J Mitchell - Mitch

Submitted to: Annual Beet Sugar Development Foundation Research Report
Publication Type: Research Notes
Publication Acceptance Date: 3/31/2017
Publication Date: 4/1/2017
Citation: Funk, A., McGrath, J.M. 2017. Leveraging long sequencing reads to investigate R-gene clustering and variation in beet. Annual Beet Sugar Development Foundation Research Report. Denver, Colorado: Beet Sugar Development Foundation. [CD-ROM].

Interpretive Summary:

Technical Abstract: Proteins containing nucleotide binding site-leucine rich repeat (NBS-LRR) motifs have been implicated in gene-for-gene resistance to many different pathogens. An initial set of predicted proteins containing this domain was used to obtain the nucleotide sequence underlying the protein coding region. These nucleotide sequences were aligned using MAFFT software and used to build a Hidden Markov model as a tool to probe the EL10 genome. This process identified 250 signatures of NB domains. By using the genomic sequence as our search space and applying filters based on expected domain length, 194 NB domain loci were assembled into a high-confidence set. The sequence relationships of these 194 loci were assessed through phylogenetic analysis. Looking at the Rz2 locus revealed potentially biologically relevant variation between the compared samples. One locus fits the genetic criteria for involvement in Rz1 resistance. This locus contains an indel at the 3' end of the gene that alters to terminal domain and could influence its biological function. This insertion is present in the susceptible EL10 genome but is missing in the resistant genotypes. Moreover, it is segregating in the base population in a 3:1 ratio of hypothetical resistant-to-susceptible.