Resistance gene analogue markers are mapped to homeologous chromosomes in cultivated tetraploid cotton

Abstract

Degenerate primers designed from conserved motifs of known plant resistance gene products were used to amplify genomic DNA sequences from the root-knot nematode (Meloidogyne incognita) resistance genetic source, Upland cotton (Gossypium hirsutum) cultivar Auburn 634 RNR. A total of 165 clones were isolated, and sequence analysis revealed 57 of the clones to be novel nucleotide sequences, many containing the resistance (R)-protein nucleotide-binding site motif. A cluster analysis was performed with resistance gene analogue (RGA) nucleotide sequences isolated in this study, in addition to 99 cotton RGA nucleotide sequences already deposited in GenBank, to generate a phylogenetic tree of cotton R genes. The cotton RGA nucleotide sequences were arranged into 11 groups and 56 sub-groups, based on genetic distances. Multiple sequence alignments were performed on the RGA sequences of each sub-group, and either the consensus sequences or individual RGA sequences were used to design 61 RGA-sequence-tagged site primers. A recombinant inbred line (RIL) population of cultivated tetraploid cotton was genotyped using RGA-specific primers that amplified polymorphic fragments between the two RIL parents. Nine RGA markers were mapped to homeologous chromosomes 12 and 26, based on linkage to existing markers that are located on these chromosomes.

Targeting and genotyping RGAs in a mappingpopulation of the AA genome of wild Arachis

“…The identification of molecular markers tightly linked to genes of interest, in this case, of pathogen resistance, would allow the implementation of a Marker-Assisted Selection program (MAS), which can increase the effectiveness of the back-crosses, overcome linkage drag, and reduce the time for selection of resistant lines. In such cases, the resistance mechanism may be unknown, but the resistance-related loci can be selected through generations of selection by simple PCR (Hinchliffe et al 2005). This would greatly speed up and optimize the development of improved peanut varieties with incorporation of new wild diseaseresistance genes.…”

Use of Tyramide-Fluorescence in situ Hybridization and Chromosome Microdissection for Ascertaining Homology Relationships and Chromosome Linkage Group Associations in Oats

“…2 d, e and 3 b). Other authors, using genetic analysis, have shown that RGA markers map to homoeologous chromosomes in different species [Spielmeyer and Lagudah, 2003;Irigoyen et al, 2004;Hinchliffe et al, 2005]. Differences in the hybridization intensity of duplicated loci, such as those detected by III2.18 in A. strigosa , plus their relative positions on chromosomes, provide evidence of homology between the diploid and hexaploid species ( fig.…”

Mapping resistance gene analogs (RGAs) in cultivated tetraploid cotton using RGA-AFLP analysis

“…Degenerate primers have been designed from these R gene products and extensively used to isolate resistance gene analogs (RGAs) from diverse plant species by simple PCR reactions (Leister et al 1996;Yu et al 1996;Chen et al 1998;Collins et al 1998;Mago et al 1999;Madsen et al 2003;Hinchliffe et al 2005). The recent reports of RGA studies in cotton were focused on a limited number of PCR amplification products for isolation and sequencing of putative R genes.…”