Development of STS markers for Verticillium wilt resistance in cotton based on RGA–AFLP analysis

Abstract

Verticillium wilt (VW) is one of the most destructive diseases of cotton that decreases yield and quality. Identification of resistance gene analogs (RGAs) can provide potential candidate gene markers for marker-assisted selection (MAS) for VW resistance and cloning of VW resistance genes. The objective of this study was to convert RGA-targeted RGA–AFLP (amplified fragment length polymorphism) markers into sequence-tagged site (STS) markers. A total of 54 RGA–AFLP markers, including 28 from a backcross inbred line (BIL) population and 26 from a recombinant inbred line (RIL) population, were cloned and sequenced. Of the resulted 86 unique sequences, the majority were found to be homologous to genes, some of which showed similarity to genes encoding resistance-related products. A total of 163 STS primer pairs were designed and screened in the BIL population, 72 of which were also screened in the RIL population, resulting in 21 polymorphic STS markers in the BIL population and seven in the RIL population. Twelve STS markers were mapped onto eight chromosomes or linkage groups in the BIL population, six of which were mapped on the same chromosomes with their original RGA–AFLP markers including two STS markers on c4 flanking two VW resistance quantitative trait loci. These STS markers will be useful in MAS in breeding cotton for VW resistance. This study represents the first attempt to successfully convert RGA–AFLP markers into STS for mapping resistance genes in cotton.