Semester of Graduation

Summer 2025

Degree

Master of Science (MS)

Department

School of Plant, Environmental, and Soil Science

Document Type

Thesis

Abstract

Heritable genetic variation is an essential raw ingredient of variety development programs. This variation is acted upon via selection by identifying elite progeny that can be utilized agronomically or exploited as parents. Sugarcane breeders are tasked with creating optimal genetic variation through crossing. Prior knowledge of pedigree and parental performance allows breeders to discern which crosses to prioritize, since the time to make crossing decisions and the space to evaluate tens and thousands of progenies are both limited resources in sugarcane variety development programs. In this project, we have updated and validated the U.S. sugarcane pedigree data and developed a user-friendly, web-based platform called CaneCestry that provides a wide range of tools utilizing pedigree information. CaneCestry can be utilized to generate family trees for parents involved in a potential cross, enabling the breeder to efficiently display and visualize the lineages of the genotypes contained within the cross. These family trees are also available as an in-field tool to aid selection, due to the web-based nature of the software. Kinship matrices are a powerful numerical representation of relationships between individuals in a population. While the calculation of kinship matrices can be computationally intensive, CaneCestry is built upon a framework allowing for efficient cloud-based computation. These numerical representations of kinship elucidate the relatedness of potential parents, allowing the breeder to make the most informed crossing decisions while avoiding inbreeding depression (Stevenson, 1954). Parental phenotypic information can be paired with these estimates of relatedness to assist the breeder to plan optimal crosses. Kinship matrices can also be utilized to enhance prediction models by adding the relatedness of the involved genotypes as a covariate, accounting for additive genetic control of traits. CaneCestry provides a comprehensive, web-based set of tools available in the office or field, enabling sugarcane breeders to utilize pedigree information in all stages of their breeding program.

Date

7-18-2025

Committee Chair

Kimbeng, Collins A.

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