[Bioinformatics analysis of candidate sequences between two flanking markers linked with resistance gene Ht1 to Exserohilum turcicum in maize].
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.
E
Yang
Y
Biological Science and Technology College, Shenyang Agricultural University, Shenyang 110161, China. isaiah1983@163.com
Lin
Feng
F
Zhang
Chun-Yu
CY
Cui
Na
N
Xu
Yu-Feng
YF
D024509:3' Flanking Region / Q000235:genetics; D024506:5' Flanking Region / Q000235:genetics; D001203:Ascomycota / Q000145:classification / Q000235:genetics / Q000472:pathogenicity*; D015415:Biomarkers / Q000032:analysis; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000502:physiology; D018744:DNA, Plant / Q000032:analysis; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000502:physiology*; D007113:Immunity, Innate / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D003313:Zea mays / Q000235:genetics* / Q000382:microbiology
D015415:Biomarkers; D018744:DNA, Plant