Publication Date

8-2023

Date of Final Oral Examination (Defense)

3-2-2023

Type of Culminating Activity

Dissertation

Degree Title

Doctor of Philosophy in Ecology, Evolution, and Behavior

Department

Biology

Supervisory Committee Chair

Sven Buerki, Ph.D.

Supervisory Committee Member

Stephen Novak, Ph.D.

Supervisory Committee Member

Marcelo Serpe, Ph.D.

Supervisory Committee Member

Félix Forest, Ph.D.

Abstract

Conserving the genetic diversity of crop species and their wild relatives has become a mounting concern as the detrimental effects of climate change, habitat destruction, and genetic erosion are being realized. In this epoch of unprecedented biodiversity loss, the genetic resources needed to improve crops may be at risk of extinction. Even one of the most iconic spices, vanilla, is threatened. Wild populations of the main vanilla producing species, Vanilla planifolia Andrews (Orchidaceae), are being rapidly extirpated due to deforestation and illegal harvesting in their native range. On top of that, clonal propagation methods within cultivated plants are hypothesized to have limited their genetic diversity and decreased their ability to cope with changing environmental conditions and respond to pathogens. Although the vanilla spice is so well-known, there is an unexpected lack of knowledge on its natural history and the ecological and evolutionary processes that have shaped its genetic resources, overall hindering its effective preservation and sustainability. To mitigate this gap of knowledge and help ensure the sustainability of this globally important spice, this thesis aimed to unravel the cultivation and domestication processes that have affected V. planifolia in its cultivated center of origin, Mexico, by answering the fundamental questions: What is the native distribution of V. planifolia? What are its crop-wild relatives and how should their conservation be prioritized? How many vanilla species are cultivated in its center of origin? What domestication processes have shaped its genetic resources? and What is the genomic origin of cultivated vanilla? By answering these questions, this thesis aimed to distinguish between cultivated wild populations, regionally domesticated landraces, and globally domesticated cultivars using a range of approaches, from ecological to taxonomic to comparative phylogenetic to genomic. Analyses used samples collected from vanilla’s cultivated center of origin, Mexico, along with publicly available genetic sequences of Vanilla spp. and a haplotype-phased reference genome of the global “Daphna” cultivar. Results indicated that V. planifolia occurs within a larger distribution than previously expected, from Mexico to northern Brazil, along with ten crop-wild relatives. Occurrences from Mexico encompassed the range of climatic niches exhibited by all occurrences within the entire distribution. Due to this high climatic variability, along with recorded morphological variability in V. planifolia, Mexico was used as a focal region to assess vanilla’s genetic resources. In addition to the predominantly cultivated V. planifolia, two other crop-wild relatives, V. pompona and V. insignis, were found to be cultivated in Mexico based on DNA barcoding of ITS sequences. Ten haplotypes were identified within Mexican accessions of V. planifolia and two were identified within V. pompona. Genetic variability and high levels of genome-wide heterozygosity found within Mexican V. planifolia and the “Daphna” cultivar revealed the occurrence of multiple domestication events and past hybridization within cultivated vanilla. Signatures of introgressive hybridization between V. planifolia and V. pompona were discovered in the “Daphna” cultivar based on comparative chromosomal analyses (e.g. incongruence along the terminal region of chromosome two). A parental origin for the highly heterozygous Mexican accessions, however, has yet to be identified. Considering the high levels of crop-wild relative diversity and the long history of cultivation by different cultural groups in Mexico, these results might provide evidence for regionally cultivated landraces produced from regional domestication events. These may provide important sources of genetic diversity to potentially increase crop resilience in the face of climate change. Findings from this thesis provide a clearer illustration of vanilla’s genetic resources and support the urgent prioritization of biodiversity within this important region through the conservation of V. planifolia’s crop-wild relatives and landraces. These recommendations will help to benefit the livelihoods of farmers, encourage the protection of biological and cultural diversity in Mexico, and ultimately help to ensure the sustainable cultivation of this iconic spice.

DOI

https://doi.org/10.18122/td.2102.boisestate

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