Open AccessBioinformatics analysis of candidate sequences between two flanking markers linked with resistance gene <I>Ht1</I> to <I>Exserohilum turcicum</I> in maize
Author(s) -
Eun-Young Yang,
Feng Lin,
Chunyu Zhang,
Na Cui,
Yang Xu
Publication year - 2009
Publication title -
yichuan
Language(s) - English
Resource type - Journals
ISSN - 0253-9772
DOI - 10.3724/sp.j.1005.2009.00638
Subject(s) - open reading frame , genetics , gene , biology , phylogenetic tree , exserohilum , blight , peptide sequence , computational biology , botany
In order to get Ht1 candidate sequence(s), bioinformatics method was employed to analyze sequences between two flanking markers umc22a and umc122a linked with Ht1. Sixty-three open reading frame (ORF) sequences were found, fourteen of which encoded protein domains. The amino acid sequences encoded by these ORF sequences were blasted with the 24 cloned resistance gene amino acid sequences, and a phylogenetic tree was constructed. Among the fourteen ORF sequences, gpm565a with nucleotide binding site (NBS), containing a lot of random coils, had both high identity and close relationship with Xal resistant to bacterial blight, and was predicted to be related with Ht1. The remaining thirteen ORF sequences had no enough evidence to show any relationships with Ht1 due to lack of conserved domains, low identity or distant relationships.