The Evolution and Domestication Genetics of the Mango Genus, Mangifera (Anacardiaceae)

Domesticated species are vital to global food security and have also been foundational to the formulation and advancement of evolutionary theory. My dissertation employs emerging molecular genomic tools to provide an evolutionary context for crop improvement. I begin by providing a contemporary perspective on two components of domestication biology that have long been used to improve crop production: wild relatives of crop species and grafted rootstocks. First, I propose a method to systematically introgress crop wild relative diversity into crop breeding programs. Then, I explore rootstocks, the lesser-known half of the perennial crop equation, documenting prevalence and diversity, cataloging rootstock traits under selection, and discussing recent advances in rootstock biology. Both crop wild relatives and rootstocks remain largely underutilized resources and hold great promise for agricultural innovation. While humans have domesticated thousands of plant species, research has largely focused on annual crops, to the exclusion of perennials. To improve our understanding of how tree species respond to domestication, I examine the evolution and domestication of one of the world’s most important perennial tropical fruit crops, the mango, Mangifera indica, and its wild and semi-domesticated relatives. I generated a dataset suitable for studying Mangifera across evolutionary time using double digest restriction site associated DNA sequencing (ddRADseq). I present a multilocus phylogeny that informs the classification of Mangifera and reveals, for the first time, the evolutionary relationships of wild, semi-domesticated, and domesticated species in the genus. Narrowing my focus to the intraspecific level, I examine how the introduction of M. indica into regions of the world impacted its genetic diversity. My results show M. indica maintained high levels of genetic diversity during its introduction into the Americas. However, the novel diversity I detect in Southeast Asian mango cultivars suggests that M. indica has a more complex domestication history than previously assumed. I also find evidence that M. indica hybridized with multiple congeners following its introduction into Southeast Asia, forming two hybrid lineages that may be maintained by clonal polyembryonic reproduction. Collectively, my research provides a comprehensive framework for understanding the evolution and domestication of a tropical tree crop of global economic importance

Neotropical Anacardiaceae (cashew family)

Anacardiaceae is an ecologically and economically important plant family of about 200 species in 32 genera in the Neotropics. The family is particularly diverse in leaf architecture and fruit morphology, making it a model family to study the evolution of structural diversity as it correlates with lineage diversification. This fruit diversity is the primary reason 11 of the Neotropical genera are monotypic and that so many genera are recognized in the Anacardiaceae. The economic value of the family is driven by the global markets for cashews, mangoes, and pistachios, but there is great potential value in its medicinal properties. At least 10 Neotropical genera cause contact dermatitis, which is a rich area for research in the family. Here presented is a review of the systematics and structural diversity of the family. Particular attention is given to the morphology, economic botany, paleobotany, ecology, and taxonomy of native and naturalized genera. Keys to Neotropical Anacardiaceae subfamilies and genera are provided along with descriptions of native genera

Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method

Mango is a globally important tropical fruit but lacks genomic tools to support cultivar identification and to enable breeding efforts. Assessing the genetic diversity and relatedness of mango germplasm is essential for identifying genetically distant parents with favorable agronomic traits to produce hybrid populations enabling selection of improved cultivars. We thus genotyped 1915 mango accessions from the United States, Senegal, Thailand, and Australia with 272 single nucleotide polymorphism (SNP) markers identifying over 520,000 genotypes. These accessions represent the available diversity from both public and private germplasm collections in these countries, as well as accessions from smaller international collections. The study included Mangifera indica, other Mangifera species, and accessions from half sibling populations. Genotype data were analyzed using an affinity propagation method to define 258 groups. Using a simple visual method, no more than 30 SNPs are needed to distinguish a single cultivar of interest from all other cultivars in the dataset enabling the accurate identification of important commercial cultivars. As these SNP markers provided accurate genotype data for accessions from different genera as well as half siblings, the majority of the genetic diversity of the mango germplasm and related species that were genotyped has been captured. The dataset contains a large collection of open-pollinated half siblings from known maternal parents. A simple visual method can also be used to identify self-pollinated individuals among the half siblings of known maternal parents and, in some cases, to infer likely candidates for the paternal parent. Identification of self-pollinated individuals is particularly important in terms of selection of improved cultivars, as due to high levels of heterozygosity, self-pollinated progeny are likely to uncover deleterious recessive alleles. Genotyping of progeny at the seedling stage and removal of self-pollinated progeny can increase the efficiency and decrease the costs of selection of improved cultivars from open-pollinated populations

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species

From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs. Being able to access and share this data in standard formats is essential. The adoption of a common informatics platform for crops that may have limited resources brings economies of scale, allowing common informatics components to be used across multiple species. The close integration of such a platform with commonly used breeding software, visualization, and analysis tools reduces the barrier for entry to researchers and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing prebreeding data for 14 crops as part of the project ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on these species compliments data already publicly available in Germinate. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop TrustCropWildRelatives project demonstrates the usefulness of the system and the benefits a shared informatics platform provides. These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harness new data as it becomes available, and benefit collectively from future developments of the Germinate platform

Building a feral future: Open questions in crop ferality.

The phenomenon of feral crops, that is, free-living populations that have established outside cultivation, is understudied. Some researchers focus on the negative consequences of domestication, whereas others assert that feral populations may serve as useful pools of genetic diversity for future crop improvement. Although research on feral crops and the process of feralization has advanced rapidly in the last two decades, generalizable insights have been limited by a lack of comparative research across crop species and other factors. To improve international coordination of research on this topic, we summarize the current state of feralization research and chart a course for future study by consolidating outstanding questions in the field. These questions, which emerged from the colloquium “Darwins' reversals: What we now know about Feralization and Crop Wild Relatives” at the BOTANY 2021 conference, fall into seven categories that span both basic and applied research: (1) definitions and drivers of ferality, (2) genetic architecture and pathway, (3) evolutionary history and biogeography, (4) agronomy and breeding, (5) fundamental and applied ecology, (6) collecting and conservation, and (7) taxonomy and best practices. These questions serve as a basis for ferality researchers to coordinate research in these areas, potentially resulting in major contributions to food security in the face of climate change

Fruit in focus: A sampler platter of research

Few plants have captured the imagination and palettes of the world like those which bear edible fruits, providing novel insights into the relationships between plants and people. This special collection of reviews and research highlights the unique challenges and opportunities we face when studying, breeding, and working to conserve these species. The 18 articles included here examine fruiting plants across diverse scales and topics, from the genome to global sustainability, and from fruit morphology to species' geographic distributions, yet they showcase only a fraction of the immense evolutionary, phenotypic, and genomic diversity present in fruit‐bearing plants. Across the special collection, our hope is to not only offer highlights of fruit diversity and importance but also provide a taste of future research in this area. We hope you enjoy the fruits of our labor

Mangos and Mango Trees

Many Miami homes have mango trees in their yards, a legacy of past agricultural development, housing promoters’ efforts to create a tropical paradise, and global plant exploration spearheaded by people like David Fairchild, whose home is preserved as The Kampong. Everyone has a story to tell about their mangos, and the trees themselves have stories to tell. Their seasonal rhythms change in response to changing temperature and rainfall; their trunks and branches show the legacy of past natural disasters. Neighbors share fruit with each other and with the birds, squirrels, and insects that pass through our region. Hear more about what can mangos and mango trees can tell us about the changing city and our place in it. Consider what we’ve lost and found as we’ve remade South Florida from the original everglades to a major metropolitan area