About

Alan B. Bennett is a Distinguished Professor and Director of PIPRA at the Department of Plant Sciences, UC Davis. He holds a Ph.D. in Plant Biology from Cornell University, obtained in 1982, and a B.S. in Plant Physiology from the University of California, Davis, earned in 1977. His research interests and expertise include the molecular biology of tomato fruit development and ripening, cell wall disassembly, and the intersection of plant biology with intellectual property rights in agriculture. He is also engaged in university-based innovation and studies plant associations with diazotrophic microbiomes. Professor Bennett teaches courses such as Ethics in Genomics and Biotechnology, Plant Genetics and Biotechnology Laboratory, and others. His contributions to science have been recognized through awards including the Chancellor's International Engagement Achievement Award in 2017 and being named a Fellow of the American Association for the Advancement of Science in 2005. He is involved in international programs and research initiatives, contributing to advancements in postharvest biology, food safety, and sustainable agricultural practices.

Research topics

• Biology
• Agronomy
• Chemistry
• Ecology
• Medicine
• Internal medicine
• Dentistry
• Agroforestry
• Food science
• Environmental science
• Botany

Selected publications

• HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N ₂ FIXATION IN <i>ZEA MAYS</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-12

  preprintOpen access

  ABSTRACT Zea mays L. spp. mays (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of Zea entries spanning pre-domestication, post-domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits ( i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana . Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties. ARTICLE SUMMARY Zea mays aerial roots (AR) and mucilage have been implicated in diazotrophic recruitment. This study estimates heritability and identifies QTL for AR and yield components via a diverse panel of Zea entries and F2:F3 mapping populations. Genetic mapping reveals three QTL for AR and several QTL for other yield traits, both novel and previously reported. This study also compares QTL and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into a native cultivar. For AR QTL, enrichment for mexicana -derived haplotypes is greater than expected under a uniform genomic distribution, suggesting adaptive introgression from mexicana .

  PublisherOA PDFDOI

• An informed response to Kloppenburg et al. (2024)—Nagoya Protocol

  Elementa Science of the Anthropocene · 2024-01-01 · 1 citations

  articleOpen access1st authorCorresponding

  Comment on Kloppenburg, J, Calderón, CI, Ané, J-M. 2024. The Nagoya Protocol and nitrogen-fixing maize: Close encounters between Indigenous Oaxacans and the men from Mars (Inc.). DOI: https://doi.org/10.1525/elementa.2023.00115

  PublisherOA PDFDOI

• Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

  Frontiers in Plant Science · 2022-10-06 · 35 citations

  articleOpen access

  Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap's integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.

  PublisherDOI

• Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems

  Field Crops Research · 2022 · 273 citations

  • Agronomy
  • Environmental science
  • Agroforestry

  BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.

  PublisherDOI

• Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

  bioRxiv (Cold Spring Harbor Laboratory) · 2020-05-17 · 6 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and possessed multiple marker genes for mechanisms of direct plant growth promotion (PGP). In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization. Implementing in vitro colorimetric assays revealed each isolate’s potential to confer the alternative PGP activities that corroborated genotype and pathway content. We examined the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta , which led to the identification of bio-stimulant candidates that were tested for PGP by inoculating a conventional maize variety. The results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize using multiple promotion mechanisms.

  PublisherOA PDFDOI

• Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

  PLoS ONE · 2020-09-14 · 30 citations

  articleOpen accessSenior authorCorresponding

  Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N2-fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate's potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one diazotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms.

  PublisherOA PDFDOI

• The Formation of Prostaglandins and Related Substances

  2020-04-15

  book-chapter1st authorCorresponding

  There are numerous accounts of the types of prostaglandins (PGs) and related substances and how their formation is affected by drugs. PG formation is inhibited by many commonly used drugs, mainly the anti-inflammatory drugs such as aspirin, indomethacin, and other similar nonsteroidal compounds. These drugs inhibit cyclooxygenase, which is part of the enzyme complex called PG synthase. PG formation is also inhibited by corticosteroid anti-inflammatory drugs such as hydrocortisone, but in this case the mechanism is a reduction of PG precursor release. Many other compounds can be formed by the biological oxidation of arachidonate and other PG precursors by different lipoxygenases. In general, little is known about the biological activities of many of these other lipoxygenase products, and although there are experimental enzyme blockers, there are no clinically used drugs known to act via effects on these enzymes.

  PublisherDOI

• Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

  Microorganisms · 2020-12-20 · 28 citations

  articleOpen access

  Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

  PublisherOA PDFDOI

• Prostaglandins in Bone Resorption

  CRC Press eBooks · 2020 · 29 citations

  Senior authorCorresponding
  • Dentistry
  • Medicine
  • Internal medicine
  PublisherDOI

• A Model for Nitrogen Fixation in Cereal Crops

  Trends in Plant Science · 2020 · 89 citations

  1st authorCorresponding
  • Biology
  • Botany
  • Agronomy
  PublisherDOI

Frequent coauthors

• G. D. Graff

  University of California, Berkeley

  151 shared

• S. P. Kowalski

  144 shared

• R. T. Mahoney

  Texas Children's Hospital

  141 shared

• A. Krattiger

  Oak Ridge Institute for Science and Education

  140 shared

• L. Nelsen

  139 shared

• K. Satyanarayana

  139 shared

• J. A. Thomson

  East, Central and Southern Africa Health Community

  136 shared

• C. Fernández

  De La Salle University

  132 shared

Education

• B.S., Plant Physiology

  University of California Davis

• Ph.D., Plant Biology

  Cornell University

Awards & honors

• Chancellor's International Engagement Achievement Award (201…
• Fellow, American Association for the Advancement of Science…
• Senior Fellow, California Council for Science and Technology