Freedom to operate and its relationship to phenotypic and genotypic diversity in an open source carrot breeding framework

The intellectual property rights (IPR) landscape for plant germplasm has changed dramatically over the past 50 years, with germplasm moving from the public domain into proprietary structures. Using carrot as a model crop, this dissertation explores the freedom to operate (FTO) -- the ability for plant breeders to access and use crop genetic diversity -- with the diversity present in 140 commercially available carrot cultivars in the United States. The first chapter presents the historical forces and trends that have led to various types of biological and intellectual property protections and how this has potentially limited plant breeders' FTO and farmers' sovereignty over seed. It introduces the Open Source Seed Initiative (OSSI), which is providing an alternative to other IPR for crop plants and working to maintain open access to crop germplasm through the OSSI-Pledge.;The second chapter presents the phenotypic and genotypic diversity analysis of carrot cultivars commercially available in the US and how this diversity is protected by IPR. For the phenotypic analysis, 140 commercially available carrot cultivars were grown on two organic farms in the Madison, WI area in 2013 and 2014 and a variety of phenotypic traits were measured in each environment and in each year. Illumina sequencing was used to conduct genotyping by sequencing analysis on all cultivars to understand the range of genetic diversity present. About one-third of the commercially available US carrot cultivars are restricted through IPR, but the genetic and phenotypic variability of the protected cultivars does not represent unique variation compared to cultivars with FTO. These findings suggest that the genetic diversity present in carrot cultivars that have FTO is large enough to support carrot breeding efforts in all market classes given present levels of IPR.;The third chapter discusses the development of eight open source carrot composite populations which represent the diversity from 87 cultivars of carrot that were not restricted by IPR. These populations are being released under the Open Source Seed Initiative Pledge (www.osseeds.org). This is the first example of crop germplasm that has been collected, characterized, and bred specifically for entry into an open source protected commons.