EVALUATING PAST PROGRESS AND ASSESSING PREDICTION BREEDING STRATEGIES FOR SUSTAINED GENETIC GAINS IN THE LOUISIANA SUGARCANE VARIETY DEVELOPMENT PROGRAM
Authors:   , Blanchard Brayden 
Published: July 2024

"The aim of this dissertation is to outline important considerations for the Louisiana Sugarcane Variety Development Program (LSVDP) as it pertains to historical progress, impact, goal setting, and new strategies for continued genetic gains. Industry progress was evaluated with robust regression models to quantify rates of productivity gains. Over the last 50 years, statistically significant productivity gains were identified in sucrose content (45%), cane yield (32.2%), and sugar yield (93%) while pairwise comparisons of decades showed that progress was incremental rather than rapid and sustained once achieved. The decade from 1990-1999 was identified as the only decade with a significant year-to-year rate of gain for all three traits, and contributing factors are discussed. Historical perspectives and retrospective analyses such as this are important for breeders to learn and understand the needs of their industries and what adaptations of the breeding efforts may have contributed to progress in certain ways. The contribution of ‘LCP 85-384,’ a cultivar known to be highly impactful on the continued success of the LSVDP, was quantified with thorough analyses that further considered the physiological benefits, ratoon ability, and genetic contribution of the variety. The phenotypic performance throughout the selection stages of the program repeatedly demonstrated the merit of its selection and eventual recommendation to the commercial industry. Using late-stage trial data, its sugar yield was compared to the leading check variety at the time of evaluation using a difference-in-differences analysis that provides a better approach to including the ratoon ability of the variety in statistical comparisons. The further impact of ‘LCP 85-384’ was reported as the number of elite progenies contributed to the breeding pipeline, the high degree of relatedness with modern experimental clones and cultivars, the increase in the overall ratoon ability of the industry, and its heavy adoption in Tucuman, Argentina. Evaluating the impact of a prominent cultivar provides insight into the extensive impact of a variety development program on the industries that it serves. The recent growth and migration of the industry further into northern and western territories has prompted questions regarding the reality of genotype-by-environment interaction effects. A multi-environment family appraisal trial was conducted in three locations to represent this movement and evaluate the presence of significant family-by-environment interactions to consider in seedling selection stages. Family-by-crop, family-by-year, and family-by-location interactions along with other relevant sources of variation displayed significant (p As the industry evolves, so too do the underlying genetics of breeding populations. Advances in genomic strategies are continually providing valuable tools and understanding of the genes responsible for developing successful cultivars. A genome-wide association study was conducted on a diverse panel of sugarcane clones to identify QTL statistically associated with traits of interest for the breeding program. A total of 55 genetic markers were identified as highly significantly (p Finally, prediction modeling strategies were assessed for their efficacy in addressing specific aspects of sugarcane breeding that, if ignored, can have detrimental effects on certain components of the breeder’s equation and consequent genetic gains. We used actual breeding trials, experiments, and datasets to demonstrate 1) enhancements to linear mixed model analysis, 2) a novel approach to site-specific multi-trait selection, 3) a selection index that better accounts for the ratoon ability of experimental clones, 4) the optimization of late-stage variety trials by the use of enviromics, and 5) machine learning predictions for parent genetic values that are used in crossing. This study encompasses different experiments that were organized to inform, enhance, and optimize the breeding effort of the LSVDP, and each topic meticulously addresses how modern concepts of plant breeding and quantitative genetics can be applied to the improvement of sugarcane."