The Vanilla Sustainability Project: Genomics Research on Vanilla planifolia for Crop Improvement and Sustainable Agriculture

Vanilla is by gram weight the world's most valuable spice crop and is widely employed as a flavor ingredient.  Vanilla is obtained from the mature fruit of the orchid Vanilla planifolia (Orchidaceae).  The vanilla fruit is special for many reasons, including that it is one of the few fruit crops that combines a natural image with a high socioeconomic value due to its traditional and sustainable mode of production and process.  Sustainable vanilla cultivation is critical for countries such as Madagascar, which has dominated world vanilla production for over 100 years, and for Mexico, the patrimonial birthplace of Vanilla planifolia.  The annual crop provides cash income to indigenous farmers in food-insecure, impoverished counties in pantropical regions.  Vanilla is not only an orphan crop but is also a niche crop, which has made it difficult to obtain funding for genomics research.  Also, although Vanilla planifolia is a diploid (2n= 32) with only rare tendency towards autopolyploidization, the genome size of Vanilla planifolia is quite large (mean diploid genome size of 5.03 pg, with C value of 2.35 Gb), which makes it approximately 18 times larger than the Arabidopsis genome, and comparable in size to maize and humans.  Thus a full genome sequence is currently unobtainable with available funding and sequencing technologies.  Here we report the development of extensive genomic resources for Vanilla planifolia during vegetative and reproductive growth and development and throughout fruit development.  The Vanilla Sustainability Project, an international initiative involving vanilla scientists and researchers (France, Madagascar, Mexico, USA and others), has been actively engaged in the development of genomic resources for Vanilla planifolia.  This presentation will share our accomplishments towards achieving three main project goals: 1) the development of an annotated reference base for Vanilla planifolia using RNA-Seq that functions as a comprehensive reference transcriptome of expressed genes for multiple lines of inquiry including analyses of gene regulation, expression, structure, and number; 2) the analysis of fruit development to understand developmental mechanisms, biosynthetic and metabolic pathways important to fruit quality characteristics (e.g., vanillin content, aroma, yield, nondehiscence, abiotic stress tolerance) and transcriptional regulation of these important fruit processes; and 3) the analysis of Vanilla root responses and root structure to understand the innate defense response to pathogen infection.  Plans will be discussed for how these genomic resources may be used to accelerate breeding of improved vanilla cultivars in collaboration with premier vanilla scientific institutions and research stations worldwide.  Breeding of improved and new vanilla cultivars that consistently produce higher quality fruits, are resistant to biotic stress (fungi, viruses) and abiotic stress (drought and heat), will significantly increase the income that small-holder vanilla farmers can receive for their harvest.  These changes are critical for survival of small-holder vanilla cultivation and the vanilla industry, particularly now with the ongoing threat of a Fusarium pandemic that is destroying vanilla vines and jeopardizing world vanilla production, and in the face of the accelerated threat of global warming that has already affected the timing of Vanilla planifolia flowering and impacted successful fertilization.