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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Research Project #435224

Research Project: Molecular Characterization of Leaf Scald Disease Resistance in Saccharum spp. for the Sugarcane Cultivar Improvement

Location: Sugarcane Field Station

Project Number: 6030-22000-012-002-N
Project Type: Non-Funded Cooperative Agreement

Start Date: Oct 1, 2018
End Date: Sep 30, 2023

Sugarcane is a semi perennial grass, frequently encountering numerous biotic and abiotic stresses worldwide. Among the biotic stresses, leaf scald diseases are the most widely spread major diseases in sugarcane caused by a bacterium named Xanthomonas albilineans. Leaf scald is a vascular bacterial disease and has been reported in more than 66 countries, mostly resulting from germplasm exchange, and was first detected in Louisiana in 1993. An estimated 20-30% yield loss due to leaf scald was reported in the symptomatic stalks in a moderately susceptible cultivar. Enhancement of disease resistance in host plants through breeding is the most effective and economic method to control the diseases. Due to the long breeding cycles of sugarcane, a genetic marker linked to the disease resistance gene(s) would allow for a marker assisted selection (MAS) procedure that will dramatically increase the selection efficiency. For example, the brown rust marker for resistance gene Bru1 has been successfully and effectively used in selecting brown rust resistant clones and developing resistant cultivars in many sugarcane breeding programs. The genetic markers allow the resistance to be determined before infection at an early sugarcane developmental stage without waiting for the infection after artificial inoculation or waiting for disease epidemic in the field to select the resistant clones. With the advances of molecular and genomic technologies, such as high throughput DNA extraction, next generation sequencing (NGS) technologies, sorghum genome, large amount of sugarcane transcript sequences, bioinformatics tools and so on, the success of marker development is much faster with higher likelihood of success than previously developing the markers of the Bru1 resistance (~20 years). Sugarcane genotyping has long been a difficult task due to its high polyploidy level with large number of chromosomes. The development and utilization of single nucleotide polymorphisms (SNPs) in sugarcane can overcome the current limitations as large numbers throughout the genome can be easily screened across hundreds of clones simultaneously. A quantitative trait loci study associated with leaf scald disease resistance using capture sequencing genotyping technique will allow us to identify markers linked to resistance to leaf scald disease efficiently. The identified markers will be used to select resistance parents and progeny for U.S. sugarcane breeding programs through MAS, which will allow breeders to develop new disease resistance cultivars for the growers.

Materials: A bi-parental population consisting of 201 F1 individuals originated from a cross CP01-2390 × CP72-2086 had been planted in the field in a three replicated trial in Canal Point, Florida, on January 09, 2018. CP72-2086 is resistance to leaf scald disease while CP01-2390 is susceptible. Another population derived from a reciprocal cross of these two parents will be planted to be used for validating the identified Quantitative Trait Loci (QTLs). Procedure: Leaf scald screening: The population (201 individuals x 3 replicates) will be tested for the leaf scald in a field using three stalks per individual per replication. Plants will be inoculated by injecting the freshly prepared suspension (106 cells per ml) of leaf scald bacteria Xanthomonas (X.) albilineans into the meristem. After 2-3 months plants will be rated visually for number of leaves with pencil lines symptoms, wilting or chlorosis, and death. In addition, a quantitative polymerase chain reaction (qPCR) method will be used for the quantification of bacterial population. Genotyping and QTL analysis: The DNA samples of the 201 individuals in the population and the two parents will be extracted from young leaf tissues using cetyl trimethylammonium bromide method. The good quality DNA will be genotyped using capture sequencing technique. Linkage analysis will be conducted by using JoinMap 4, and the QTL analysis will be performed by using WinQTLCart 2.5.