Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection

Authors: FICKETT, NATHANAEL - LSU Agcenter; GUTIERREZ, ANDRES - LSU Agcenter; VERMA, MOHIT - LSU Agcenter; PONTIF, MICHAEL - LSU Agcenter; Hale, Anna; KIMBENG, COLLINS - LSU Agcenter; BAISAKH, NIRANJAN - LSU Agcenter

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2018
Publication Date: 12/7/2018
Citation: Fickett, N., Gutierrez, A., Verma, M., Pontif, M., Hale, A.L., Kimbeng, C., Baisakh, N. 2018. Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection. Genomics. Available: https://doi.org/10.1016/j.ygeno.2018.12.002.
DOI: https://doi.org/10.1016/j.ygeno.2018.12.002

Interpretive Summary: Sugarcane is an economically important crop for both the food and biofuel industries. Because of sugarcane's genetic complexity, DNA markers associated with important economic traits have been difficult to identify in the past. Because of advances in technology and the recent identification of markers linked with disease resistance, DNA-based marker assisted breeding is finally becoming a reality in this crop. Newer techniques involve the use of large and diverse populations derived from a multitude of parents as opopsed to single families as was done in the past. This new approach is better for identifying markers associated with important agronomic traits. This process, termed Genome Wide Association Studies (GWAS) was applied to a group of Louisiana varieties that represent much of the variability found in the genepool used for sugarcane variety development in the state. Associations were identified between DNA markers 11 cane yield and sucrose traits. These markers explained up to 15% of the total variation seen for these traits. Validation of these markers on more diverse populations could lead to their use in marker-assisted selection of varieties of sugarcane in Louisiana and elsewhere.

Technical Abstract: Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (SWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits. GWAS was conducted on a Louisiana core collection to identify marker-trait associations (MTA) for 11 cane yield and sucrose traits using single nucleotide polymorphism (SNP) and instertion-deletion (Indel) markers. Significant (P<0.05) MTAs were identified for all traits where the top ranked markers explained up to 15% of the total phenotypic variation. High correlations (0.732 to 0.999) were observed between sucrose traits and 56 markers were found consistent among multiple traits. These markers following validation in more diverse populations could be used in marker-assisted selection of clones in sugarcane breeding in Louisiana and elsewhere.