A first look at the ability to use genomic prediction for improving ratooning ability of sugarcane

Authors: Islam, Md; CORAK, KEO - North Carolina State University; MCCORD, PER - Washington State University; Hulse-Kemp, Amanda; LIPKA, ALEXANDER - University Of Illinois

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2023
Publication Date: 8/2/2023
Citation: Islam, M.S., Corak, K., Mccord, P.H., Hulse-Kemp, A.M., Lipka, A.E. 2023. A first look at the ability to use genomic prediction for improving ratooning ability of sugarcane. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1205999.
DOI: https://doi.org/10.3389/fpls.2023.1205999

Interpretive Summary: Sugarcane ratooning ability (RA) is the most important for enhancing the productibility and profitability of sugarcane by reducing the planting cost. Genomic-assisted breeding could help breeders to improve this trait effectively. Thus, understanding the genetic components of RA is worthwhile. A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones, and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tons of cane per hectare (TCH), and tons of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and seven nonredundant single nucleotide polymorphic (SNP) markers along with linked candidate genes were associated with all five tested RA traits and appear to be unique. The prediction accuracies of genomic estimated breeding values for those tested traits were moderate and ranged from 0.21 to 0.36. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of RA in sugarcane.

Technical Abstract: The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane.