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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #331841

Title: Development of an RAPD-based SCAR marker for smut disease resistance in commercial sugarcane cultivars of Pakistan

item KHAN, MEHWISH - Collaborator
item Pan, Yong-Bao
item IQBAL, JAVED - Collaborator

Submitted to: Crop Protection
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2016
Publication Date: 1/5/2017
Publication URL:
Citation: Khan, M., Pan, Y.-B., Iqbal, J. 2017. Development of an RAPD-based SCAR marker for smut disease resistance in commercial sugarcane cultivars of Pakistan. Crop Protection. 94:166-172.

Interpretive Summary: Sugarcane smut is a fungal disease caused by Sporisorium scitamineum and can cause serious damage to the sugarcane industry. To minimize the yield loss by this disease, the most practical and effective approaches are to plant resistant cultivars. Many endeavors have been made by breeders worldwide to identify resistant germplasm to cross, select, and breed smut resistant cultivars. Nonetheless, the conventional breeding methods are time-consuming, laborious, and efficient. Therefore, molecular tools and practices such as molecular markers may help. Through a series of laboratory experiments, the researchers have developed a molecular SCAR (sequence characterized amplified regions) marker that amplifies a DNA fragment of 300 base pairs (bp) specifically from sugarcane cultivars that were rated resistant to smut. DNA samples were extracted from the leaf tissues of 12 cultivars and four bulked DNA samples were pooled from two completely resistant, two completely susceptible, four moderately resistant, and four moderately susceptible cultivars, respectively. Initial screening of these four DNA bulks with 480 generic 10-base primers revealed 44 being polymorphic. Two more rounds of screening were conducted involving both bulked and individual DNA samples identified a DNA fragment of 300 bp that was exclusively and reproducible from the smut resistance cultivars. Verification experiments with seven additional Pakistani sugarcane cultivars that react differently to smut disease infection confirmed the finding. The nucleotide sequences of this 300 bp SCAR marker shared no homology to any of the earlier identified sequences in the GenBank. This SCAR marker can be used for selection of smut resistance in sugarcane cultivars and hence presents a resourceful tool for sugarcane breeding programs.

Technical Abstract: Development of RAPD-derived Sequence Characterized Amplified Region (SCAR) marker in order to select Sporisorium scitamineum resistant and susceptible commercial cultivars of sugarcane from Pakistan was achieved. Bulked segregant and RAPD-analysis were conducted using 480 random decamers in initial screening of 12 sugarcane genotypes (two completely smut resistant, two completely smut susceptible, four moderately smut resistant, and four moderately smut susceptible). Eighty-four of these primers proved to be polymorphic while only one (B-17) produced a reproducible polymorphic fragment, which appeared to co-segregate in repulsion with sugarcane smut resistance. A SCAR marker of 300bp was generated from the sequence of B-17 product and was used to amplify all these12 given cultivars. The results of SCAR analysis confirmed the marker to be specific for two completely and four partially resistant genotypes. Furthermore, screening of seven additional sugarcane cultivars of Pakistan with SCAR marker, verified the earlier findings by showing essentially similar results. Therefore, it was precluded that the marker is linked with smut resistance trait in sugarcane. NCBI blast of SCAR marker sequence showed no homology to any of the earlier identified sequences in GenBank. The new discovered SCAR marker for resistant genotypes will facilitate sugarcane breeding programs since it can be used for marker assisted selection for smut resistance in sugarcane.