Sacch5A1a489bp: Candidate molecular marker associated with smut tolerance in modern sugarcane genotypes

Abstract

Sugarcane smut, which is caused by the fungus Sporisorium scitamineum, is one of the most detrimental diseases affecting the sugarcane crop and has been shown to significantly reduce productivity. Evidence indicates that chromosome 5 is the main origin of most resistance gene analogs (RGAs) involved in pathogenic responses in modern sugarcane cultivars. The present study aimed to identify RGAs that segregate according to the presence of smut, with the goal of using them as molecular markers associated with tolerance. A total of 81 RGAs from S. spontaneum were selected; these RGAs were previously characterized by the presence of conserved regions or sequences similar to the leucine-rich repeat (LRR) domain, indicating their potential roles in plant defense. From these sequences, 147 primer pairs were designed and hybridized in silico with 77 of the selected RGAs, of which 18 pairs were subsequently evaluated in vivo. Sequencing of the 489-bp amplicon and subsequent genomic analyses indicated that the Sacch5A1a locus may be a strong candidate molecular marker associated with sugarcane smut tolerance, which was supported by in silico and in vivo findings in the contrasting genotypes analyzed: RB86-7515 (tolerant) and LCP85-384 × MP (susceptible).