Genome-wide isolation of resistance gene analogs in maize (Zea mays L.).
Conserved domains or motifs shared by most known resistance (R) genes have been extensively exploited to identify unknown R-gene analogs (RGAs). In an attempt to isolate all potential RGAs from the maize genome, we adopted the following three methods: modified amplified fragment length polymorphism (AFLP), modified rapid amplification of cDNA ends (RACE), and data mining. The first two methods involved PCR-based isolations of RGAs with degenerate primers designed based on the conserved NBS domain; while the third method involved mining of RGAs from the maize EST database using full-length R-gene sequences. A total of 23 and 12 RGAs were obtained from the modified AFLP and RACE methods, respectively; while, as many as 109 unigenes and 77 singletons with high homology to known R-genes were recovered via data-mining. Moreover, R-gene-like ESTs (or RGAs) identified from the data-mining method could cover all RACE-derived RGAs and nearly half AFLP-derived RGAs. Totally, the three methods resulted in 199 non-redundant RGAs. Of them, at least 186 were derived from putative expressed R-genes. RGA-tagged markers were developed for 55 unique RGAs, including 16 STS and 39 CAPS markers.
Wenkai
Xiao
X
National Maize Improvement Center of China, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100094, People's Republic of China.
Mingliang
Xu
X
Jiuren
Zhao
Z
Fengge
Wang
W
Jiansheng
Li
L
Jingrui
Dai
D
D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D021141:Nucleic Acid Amplification Techniques; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology / Q000469:parasitology; D011110:Polymorphism, Genetic; D003313:Zea mays / Q000235:genetics* / Q000382:microbiology / Q000469:parasitology
D017931:DNA Primers; D018744:DNA, Plant