Marker trait association and candidate gene identification for brown rust disease in sugarcane

Authors: Islam, Md; QIN, LIFANG - Guangxi University; MCCORD, PER - Washington State University; Sood, Sushma; ZHANG, MUQING - Guangxi University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Brown rust is one of the most devastating diseases of sugarcane and causes up to 50% yield loss. Host plant resistance appears to be the most desirable approach to control the disease through breeding. A genome-wide association study uncovered seven, nine, and seven nonredundant marker-trait associations for plant cane, first ratoon, and across two crop cycles, respectively. Six putative candidate genes were identified and linked with brown rust resistance in sugarcane. This research has identified new sources of brown rust resistance that can be exploited to enhance the durability of the trait in the Florida sugarcane breeding program and identified candidate genes that can be studied further in efforts to elucidate the mechanism(s) of resistance to this economically important sugarcane pathogen.

Technical Abstract: Brown rust (caused by Puccinia melanocephala H. & P. Sydow) is one of the most devastating diseases in commercial sugarcane production. It could reduce sugarcane yield by up to 50% depending on the susceptibility levels of cultivars. Breeding disease-resistant cultivars is the most effective, economical, and environmentally friendly option to control brown rust. A genome-wide association study was conducted on a field trial using 432 sugarcane clones following an augmented design with two replications. Brown rust was screened using the whorl inoculation method over two crop cycles. The genotype data were obtained through target enrichment sequencing technologies. The gene actions considering six different models and marker dosage effects were included during the marker-trait analysis. A total of seven, nine, and seven nonredundant marker-trait associations were identified for plant cane, first ratoon, and across two crop cycles, respectively. The most significant (p-value 6.17e-20) marker (chr01p59833543) has the additive effect of -0.63 for the Diplo-additive model and reduced disease severity the most (41.35%) due to heterozygote (AG) over homozygote allele (AA) combination in the tested clones. Gene annotation of the monoploid sugarcane genome R570 suggested that six putative candidate genes were co-located with significant markers associated with brown rust resistance in sugarcane. The putative candidate genes regulated the formation of a cell wall barrier that plays a crucial role in controlling brown rust pathogen infection. The results of this study will open the path to exploit new resistance sources for brown rust resistance in commercial sugarcane.