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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Publications at this Location » Publication #365291

Research Project: Development of High-Yielding, Stress Tolerant Sugarcane Cultivars Using Agronomic, Genetic, and Molecular Approaches

Location: Sugarcane Field Station

Title: Genome-wide Association Studies on Saccharum spp. Hybrid for Sugar Related Traits

item QIN, LIFANG - Guangxi University
item MCCORD, PER - Washington State University
item ZHANG, MUQING - Guangxi University
item Sood, Sushma
item YANG, XIPING - University Of Florida
item Zhao, Duli
item Islam, Md

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 6/24/2019
Publication Date: 12/20/2019
Citation: Qin, L., Mccord, P.H., Zhang, M., Sood, S.G., Yang, X., Zhao, D., Islam, M.S. 2019. Genome-wide Association Studies on Saccharum spp. Hybrid for Sugar Related Traits. American Society of Sugar Cane Technologists. 39:47.

Interpretive Summary: N/A

Technical Abstract: Genome-wide association study (GWAS) is available to synchronously scan many genotypes for genetic variation underlying various traits. This study was carried out with 432 sugarcane (Saccharum spp. hybrid) clones showing variation for different traits to determine molecular makers related to sugar content and other yield traits. These diverse clones were planted in an experimental field at the USDA-ARS Sugarcane Field Station, Canal Point, FL in November 2016. We analyzed three sugar related traits (Brix, Fiber, and Pol) from two harvests (plant cane and first ratoon). A large number of genetic variants were generated by genotyping the diverse set of clones using capture sequencing. The sequences of genetic variants were aligned to Sorghum bicolor reference genome. GWAS was conducted for each harvest separately and the combined data using the GWASpoly package in R, following the “additive” model. The threshold for significant marker trait association (MTA) was p value = 0.001. Results revealed that a total of 60, 45, and 55 MTAs were identified for the three traits using data from plant cane, first ratoon, and combination of the two crops, respectively. The most significant MTAs for Brix (Chr01P6670629), fiber (Chr02P59122919), and Pol (Chr07P57580794) were identified on chromosome 1, 2, and 7 with additive values of 0.31, -0.19, and -2.07, respectively. The MTAs identified in this study can be used to improve sugar content and sugar yield in a sugarcane breeding program.