2019 ASHS Annual Conference

Demand for all-natural vanilla flavor is increasing, but its botanical source, Vanilla planifolia, faces critical challenges arising from a narrow germplasm base and supply limitations. Genomic tools are the key to overcoming these limitations by enabling advanced genetics and plant breeding for new cultivars with improved yield and quality. Vanilla has been cultivated in the United States since the early 1900s. An original V. planifolia introduction into Puerto Rico in the early 1900’s from Mexico was followed by another introduction from Florida in 1909. The Puerto Rico Vanilla industry grew until the 1950s when it quickly declined, though material from the former plantings are still cultivated by growers and hobbyists. Vanilla cultivation in Hawaii started with introductions from Mexico, Tahiti, Samoa, and Fiji before 1900, and is mostly focused on the tourism industry today. Commercial production of V. planifolia in southern Florida is still being established as a new, high-value industry. Florida, Puerto Rico, and Hawaii all have naturalized V. planifolia, and Florida and Puerto Rico have a number of native Vanilla species. The establishment of modern Vanilla breeding programs could leverage increasingly accessible technologies including advances in genomics and biotechnology to rapidly improve this species for high priority traits like disease resistance, total bean yield, pod uniformity, vigor, non-splitting pods, flower longevity, extract quality, and flowers that are able to self-pollinate without manual intervention. The objective of this work was to establish the genomic resources needed to facilitate analysis of diversity among Vanilla accessions and to provide a resource to analyze other Vanilla collections. A V. planifolia draft genome was assembled and used to identify 521,732 single nucleotide polymorphism (SNP) markers using Genotyping-By-Sequencing (GBS). The draft genome had an estimated size of 2.40 Gb representing 97% of the estimated genome size. A filtered set of 5,082 SNPs was used to genotype a living collection of 112 Vanilla accessions from 23 species including native Florida species. Principal component analysis of the genetic distances, population structure, and the maternally inherited rbcL gene identified putative hybrids, misidentified accessions, significant diversity within V. planifolia, and evidence for 12 clusters that separate accessions by species. These results validate the efficiency of genomics-based tools to characterize and identify genetic diversity in Vanilla and provide a significant tool for genomics-assisted plant breeding. While plant breeding is generally a long-term prospect, the potential benefits are justified by the increasing demand for premium ingredients like natural vanilla extract. In the future, genetic improvement of this species could result in more resilient cultivars that reduce price volatility and excite modern consumers through innovative solutions applied to Vanilla.