High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryza sativa L.

Abstract

Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae ( Xoo) (Ishyama) Dye, is one of the serious diseases prevalent throughout Asia. In a previous study, a resistance ( R) locus was transferred from the tetraploid wild rice Oryza minuta to the cultivated rice species, Oryza sativa L. Here, we report the fine genetic mapping of the R locus, tentatively designated as Xa27(t). We performed disease evaluation with an Xa27(t) near-isogenic line, IRBB27, testing 35 Xoo strains collected from 11 countries. The Xa27(t) locus conferred a high level of resistance to 27 strains and moderate resistance to three strains. Resistance of the Xa27(t) gene was developmentally regulated in IRBB27 and showed semi-dominant or a dosage effect in the cv. CO39 genetic background. As a prelude to cloning Xa27(t), a molecular mapping strategy was employed with a large mapping population consisting of 3,875 gametes. Three molecular markers, M336, M1081, and M1059, closely linked to Xa27(t), were identified to facilitate the mapping of Xa27(t) to the long arm of chromosome 6. The Xa27(t) locus was confirmed by chromosome landing of M1081 and M1095 markers on the rice genome. Markers derived from the genomic sequence of O. sativa cv. Nipponbare were used to further saturate the Xa27(t) genomic region. Xa27(t) was finally located within a genetic interval of 0.052 cM, flanked by markers M964 and M1197, and co-segregated with markers M631, M1230, and M449.

High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea

“…This illustrates the utility of comparative genome mapping for map-based cloning of agronomically important genes. Gu et al (2004) also found a good syntenic relationship between the genetic map of the Xa27(t) region in the rice line IRBB27 and in O. sativa cv. Nipponbare.…”

Full-genome analysis of resistance gene homologues in rice

“…The locations of three characterized rice NBS-LRR resistance genes, Pib, Pita, and Xa1, are designated with arrows. The approximate map positions of other bacterial blight (designated Xa-) and blast (designated Pi-) resistance genes that have been mapped by phenotype by various groups Causse et al 1994;Conaway-Bormans et al 2003;Gu et al 2004;Jeon et al 2003;Jiang and Wang 2002;Li et al 1999;Liu et al 2002;Porter et al 2003;Sallaud et al 2003;Tabien et al 2002;Wang et al 1994;Yoshimura et al 1995) are shown to the right of the chromosomes NBS portions of their coding regions were compared, even between group members that were duplicated on different chromosomes. Many groups have members mapping to different chromosomes that have as little as 30% amino acid sequence identity (Table 2).…”

Genetic analysis and fine mapping of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene bph19(t)

“…Secondly, RCA enables to confirm the candidate markers for mapping the target gene on its chromosome using the homo-recessive progenies (Pan et al 2003;Zhu et al 2004a). Third, BIA allows us to adopt and/or develop molecular markers in the target region, and to construct a physical map spanning the target gene locus, in silico (Gu et al 2004;Chen et al 2005;Liu et al 2005). As a result, the bph19(t) locus was genetically defined to a chromosomal interval of 1.0 cM in length with five cosegregated markers, and physically mapped to a DNA fragment of 60-kb in length.…”

“…1, and also see subsequently). The recombination frequency between a marker and the resistance gene was calculated using the following formula: c = N r /2N, in which N is the total number of the resistant individuals tested, N r is the number of recombination events occurred at the respective locus (Pan et al 2003;Gu et al 2004). The recombination frequency was transformed into centimorgans according to the Kosambi function (Kosambi 1944).…”

“…That is, bioinformatics analysis (BIA) of the reference sequences using various software tools has enabled mapbased cloning as a routine work in the laboratories related. Doubtlessly, sequence-based map of the target gene is a crucial step for both marker-assisted gene pyramiding and cloning (Schuler 1998;Pan et al 2003;Gu et al 2004;Yang et al 2004). …”