About

Ana Caicedo is a Professor of Biology at the University of Massachusetts Amherst, specializing in Plant Molecular Evolution and Evolutionary Genomics. Her research aims to understand the genetic basis of adaptation and the population and genomic context in which adaptive evolution occurs. Her work spans disciplines including population genetics, molecular evolution, evolutionary ecology, phylogeography, and evolutionary genomics, focusing on loci contributing to traits of ecological or evolutionary importance and the processes governing diversification within and between closely related plant species. Her research involves studying model organisms such as Arabidopsis thaliana, wild relatives of crop species like Solanum spp. and Oryza spp., and domesticated plants including cultivated rice (O. sativa). She investigates the genes underlying adaptive traits, the distribution of variation at these genes, the evolutionary forces acting upon them, and their molecular signatures. Her work also explores the role of genomic context in the evolution of ecologically important genes. A particular focus is on the process of domestication, providing insights into rapid evolution and adaptive responses under strong selection, by comparing domesticated species with their wild and weedy relatives. Current projects include studying the molecular evolution of genes associated with weedy phenotypes in red rice and identifying genes involved in diversification and stress tolerance in the wild tomato relative, S. cheesmaniae.

Research topics

• Biology
• Genetics
• Environmental planning
• Ecology
• Computational biology
• Agronomy
• Biotechnology
• Botany
• Evolutionary biology
• Environmental resource management

Selected publications

• Genome-wide meta-QTL approach identifies consensus loci associated with agriculturally important tomato fruit traits

  Theoretical and Applied Genetics · 2025-09-23

  articleSenior author
  PublisherDOI

• Comparative tissue‐specific transcriptomics reveals the regulatory control of convergent seed shattering in independently evolved weedy rice lineages

  The Plant Journal · 2025-03-01

  articleSenior authorCorresponding

  The repeated evolution of high seed shattering during multiple independent de-domestications of cultivated Asian rice (Oryza sativa) into weedy rice (Oryza spp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low-shattering cultivars of aus and temperate japonica domesticated groups and in two genotypes of their derived high-shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de-domestication of SWR than BHA, fewer genes exhibited a comparable AZ-region exclusive expression pattern between weed and crop in the temperate japonica lineage than in the aus lineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as, OsWRKY102 and OsXND-1-like, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ-region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages.

  PublisherDOI

• The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History

  Molecular Ecology · 2025-07-15

  articleOpen accessSenior author

  Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A 'cost of domestication' has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the domesticated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in the commonly cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavour regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 potentially deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

  PublisherDOI

• Assessment of genetic diversity in Pakistani date palm (Phoenix dactylifera L.) cultivars by genotyping and SSR markers

  Pakistan Journal of Botany · 2025-12-19

  articleSenior author
  PublisherDOI

• Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

  Molecular Ecology · 2024-04-27 · 7 citations

  articleOpen accessSenior author

  Abstract Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop‐weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide‐resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping‐by‐sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy‐related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase ( ALS ) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS‐inhibiting herbicides with a high frequency of the ALS mutation (A 122 T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica , indica and aus while weeds were mostly aus or aus‐indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus‐like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.

  PublisherOA PDFDOI

• Fungal effectors: past, present, and future

  Current Opinion in Microbiology · 2024-08-24 · 32 citations

  reviewOpen access

  Fungal effector proteins function at the interfaces of diverse interactions between fungi and their plant and animal hosts, facilitating interactions that are pathogenic or mutualistic. Recent advancements in protein structure prediction have significantly accelerated the identification and functional predictions of these rapidly evolving effector proteins. This development enables scientists to generate testable hypotheses for functional validation using experimental approaches. Research frontiers in effector biology include understanding pathways through which effector proteins are secreted or translocated into host cells, their roles in manipulating host microbiomes, and their contribution to interacting with host immunity. Comparative effector repertoires among different fungal–host interactions can highlight unique adaptations, providing insights for the development of novel antifungal therapies and biocontrol strategies. • Fungi can be symbionts and pathogens of both plant and animal hosts. • Fungal effectors are key players involved in all host–fungal interactions. • Apoplastic or cytoplasmic effectors function outside or inside host cells, respectively. • Tools continue to be developed to predict effector functions and localizations. • Challenges remain in defining effectors involved in host-specific interactions.

  PublisherDOI

• Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice

  Journal of Experimental Botany · 2024-07-08 · 13 citations

  articleSenior author

  The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.

  PublisherDOI

• The evolutionary dynamics of genetic mutational load throughout tomato domestication history

  2024-08-28

  preprintOpen accessSenior authorCorresponding

  Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A “cost of domestication” has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the cultivated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in fully cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavor regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

  PublisherDOI

• Comparative tissue-specific transcriptomics reveal the genetic bases underlying evolutionary convergence of seed shattering in two independently evolved weedy rice lineages

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-29

  preprintSenior authorCorresponding

  Summary The repeated evolution of high seed shattering during multiple independent de-domestications of cultivated Asian rice ( Oryza sativa ) into weedy rice is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low-shattering cultivars of aus and temperate japonica domesticated varieties and in two genotypes of their derived high-shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de-domestication of SWR than BHA, fewer genes exhibited a comparable AZ-region exclusive expression pattern between weed and crop in the japonica lineage than in aus lineage. Transcription factors related to the repression of lignin and secondary cell deposition, such as, OsWRKY102 and OsXND-1-like , along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ-region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages. Significance statement Exploring the extent of genetic convergence that underlies the morphological convergence - specifically, the recurrent evolution of complete abscission zones in independently evolved weedy rice populations originating from different cultivated rice populations with varying degrees of disrupted abscission zones - can improve our understanding not only of the genetic mechanisms behind convergent evolution, but also of the genetics underlying the agriculturally importance trait of seed shattering.

  PublisherDOI

• Current status of community resources and priorities for weed genomics research

  Genome biology · 2024-05-27 · 36 citations

  articleOpen access

  Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

  PublisherOA PDFDOI

Recent grants

• Genomic Structure and Contemporary Evolution of Weediness in Red Rice

  NSF · $2.6M · 2010–2017

Frequent coauthors

• Kenneth M. Olsen

  Washington University in St. Louis

  56 shared

• Yulin Jia

  Harbin Medical University

  39 shared

• Michael D. Purugganan

  New York University Abu Dhabi

  38 shared

• Thomas P. Brutnell

  24 shared

• Todd C. Mockler

  Donald Danforth Plant Science Center

  20 shared

• David R. Gealy

  Dale Bumpers National Rice Research Center

  20 shared

• Shao Jian Zheng

  East China University of Technology

  20 shared

• Richard Sibout

  Laboratoire D'étude des Résidus et Contaminants Dans les Aliments

  20 shared

Education

• B.S., Colombia

  Universidad de los Andes

  1996

• Ph.D., St. Louis

  Washington University

  2003

• Other

  North Carolina State University

  2003