About

Christopher Brian Watkins is a professor in the School of Integrative Plant Science, Horticulture Section. His research program is focused on postharvest science with a major emphasis on apple fruit. He conducts statewide research and extension activities that include the development and implementation of harvest maturity management, postharvest handling, and storage technology from both basic and applied perspectives. His recent research involves developing knowledge for the use of 1-methylcyclopropene (1-MCP), an ethylene-binding inhibitor that extends apple storage life, and extending this work to preharvest applications. Additionally, he researches new apple cultivars important to New York growers, the effects of postharvest techniques on fruit nutritional quality, and the mechanisms underlying fruit responses to storage conditions such as temperature, atmosphere, and 1-MCP, as well as their interactions with storage disorders. Watkins is responsible for developing and conducting components of a statewide fruit extension program related to harvest maturity, postharvest handling, and storage technology, working in cooperation with extension faculty, regional fruit specialists, educators, storage operators, and marketers.

Research topics

• Biology
• Biochemistry
• Horticulture
• Botany
• Chemistry
• Food science
• Ecology
• Toxicology

Selected publications

• Assembly and Function of Fruit Microbiomes and Insights into Management

  Journal of the American Society for Horticultural Science · 2026-04-15

  articleOpen accessSenior author

  The study of fruit microbiomes, defined as the microbial community in and on fruit, is a novel frontier that provides the potential for contextualizing pathogen infection and biocontrol in a more holistic and ecological approach. Differences in sample year tend to explain the greatest variation in fruit microbiome studies, with geography, preharvest management regime, and cold storage also resulting in pronounced shifts. However, effects of cultivar and fungicides can be more subtle, with some studies identifying minor or no shifts. This highlights that while agricultural management is important in shaping fruit microbiomes, environmental and spatiotemporal factors are also important to consider. Additionally, there is a need for more studies that delve deeper into the functional roles of the fruit microbiome, which require extension of ‘omics technologies such as shotgun metagenomics and metabolomics to move beyond taxonomic composition and begin to determine what important roles fruit microbial communities can play. Some studies are investigating the role of native microbiota in biocontrol and how native fruit microbiomes influence the fermentation process, and the field must build on these experiments to gain a more complete understanding of how the fruit microbiome is related to pathogen dynamics and modulation of fruit quality.

  PublisherDOI

• Cultivars and Curing Conditions Affect Sweetpotato Chilling Injury Responses

  HortScience · 2026-02-24

  articleOpen accessSenior author

  Sweetpotato roots develop chilling injury (CI) when exposed to storage temperatures below 10 °C. Curing, a standard postharvest practice for sweetpotato that promotes suberization and healing of cut surfaces, may also enhance resistance of roots to CI, but research has been limited. In this study, we screened five sweetpotato cultivars, Bellevue, Bonita, Bayou Belle, Japanese, and Covington, for their susceptibility to CI. Based on high susceptibility to CI, ‘Bellevue’ was selected to investigate the effects of curing on CI. The roots were cured at 28 °C and 90% relative humidity for 7 days and then stored at 5 °C for 40 days. During the curing process, sweetpotato respiration rates increased transiently but eventually decreased to the same level as in noncured roots. Curing also transiently increased weight loss in roots, but by day 7 weight loss in cured roots was the same as that of noncured roots. Sugar and starch concentrations were unaffected by curing. After cold storage, cured roots had a 34% lower CI index and visibly less severe surface pitting than noncured roots. Furthermore, cured roots accumulated 34% and 15% less malondialdehyde and hydrogen peroxide than noncured roots, respectively. However, curing did not affect electrolyte leakage or internal tissue darkening, suggesting that it only marginally reduced CI in ‘Bellevue’ and may need to be combined with other treatments for greater effectiveness.

  PublisherDOI

• Effects of vacuum packaging on sugar and acid metabolism and flavor of persimmons

  LWT · 2026-03-06

  articleOpen access

  The effects of vacuum packaging (VAC) on the flavor quality of "Mopan" persimmon fruit stored at 20 °C for eight days have been investigated. VAC accelerated de-astringency, delayed ripening, and maintained appearance. VAC-treatment maintained higher soluble solid and soluble sugar contents, and reduced total titratable acid of the fruit, thereby enhancing the sugar acid ratio and overall taste profile. VAC enhanced sucrose accumulation, correlated with suppressed neutral invertase and enhanced sucrose phosphate synthase activities, while the rise in malic acid and decline in citric acid aligned with elevated activities of NAD-malate dehydrogenase, NADP-malic enzyme, and phosphoenolpyruvate carboxylase, alongside reduced citrate synthase activity. VAC enhanced the levels of ethyl acetate and ethylbenzene, contributing to fruity and fresh aromas, while reducing compounds like methyl acetate and 2,2,4,6,6-pentamethylheptane, which are associated with fatty and pungent off-flavors. Collectively, these findings indicate that VAC promotes de-astringency and preserves the desirable flavor profile of persimmon fruit, thereby improving its storage quality. • •VAC accelerated deastringency, increased the sugar acid ratio. • •Sucrose level was significantly greater in VAC-treated fruit. • •VAC promoted malic acid accumulation and reduced citric acid synthesis. • •VAC elevated levels of ethyl acetate and ethylbenzene, enhancing fruity and fresh aromas.

  PublisherDOI

• Pulsed light treatment delays softening of harvested ‘Mopan’ persimmon by modulating ethylene biosynthesis and signaling pathways

  Postharvest Biology and Technology · 2026-04-27

  article
  PublisherDOI

• Within‐tree biogeography shapes composition and diversity of apple microbiomes

  Ecosphere · 2026-05-01

  articleOpen accessSenior author

  Abstract Fundamental ecological concepts such as biogeography can help inform sustainable agricultural practices. Since distinct ecological patches can exist even if the areas in between are hospitable, we examined the potential of biogeography to shape microbiomes of apple fruit within and across the orchard canopy trees. In a 2‐year study of commercial orchard blocks, we found that canopy areas showed differences in bacterial and fungal composition and diversity. The most notable differences occurred between the lower and upper canopies, with higher diversity in the lower canopy and microbial taxonomic shifts across both harvest years. PICRUSt2 was used to predict metagenomes from taxonomy, providing functional predictions across canopy zones. The lower canopy had a higher abundance of predicted genomic elements related to secondary metabolite production and a lower abundance of predicted genomic elements related to biofilm formation. This suggests potential different patterns of growth and competition as a result of differing microbial dispersal to canopy areas. These results advance the view that fundamental ecological factors such as biogeography and dispersal are important for shaping fruit microbiomes at harvest and throughout storage. This knowledge has the potential to improve our understanding of microbiome establishment and persistence in agroecosystems.

  PublisherDOI

• Examining the effects of fruit maturity on the relationships between mineral composition and incidence of physiological disorders of apple fruit

  Acta Horticulturae · 2025-06-01 · 2 citations

  article1st authorCorresponding
  PublisherDOI

• Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones

  Genome biology · 2025-05-09 · 13 citations

  articleOpen access

  BACKGROUND: The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. RESULTS: Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction, and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single molecules with high resolution, throughout S-phase, genome-wide, and at high coverage at specific loci using targeted enrichment. We find a significant enrichment of initiation sites within the broad initiation zones identified by population-level studies. However, these focused initiation sites only account for ~ 20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature. CONCLUSIONS: We show here that single-molecule sequencing enables unbiased detection and characterization of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.

  PublisherOA PDFDOI

• Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr

  Molecular Ecology · 2025-08-26

  articleOpen access

  Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.

  PublisherOA PDFDOI

• Mineral content and maturity indices at harvest in relation to stem end flesh browning development in ‘Gala’ apples after long-term ultra-low O₂ storage

  Acta Horticulturae · 2025-06-01

  articleSenior author
  PublisherDOI

• Fruit Maturity Based on IAD Values in Relation to Preharvest 1-Methylcyclopropene Treatment and Postharvest Physiological Disorder Development in ‘Honeycrisp’ Apples

  HortScience · 2025-06-27

  articleOpen accessSenior author

  ‘Honeycrisp’ apples are prone to physiological disorder development during storage, fruit susceptibility to disorder incidence being affected by harvest date. The effects of fruit maturity from untreated trees and those sprayed at 1 week before the first harvest with 1-methylcyclopropene (1-MCP; Harvista TM ) were investigated by categorizing fruit into index of absorbance difference ( I AD ) values before storage. Maturity indices, chlorophyll, carotenoid, and sugar concentrations were assessed at harvest. The incidences of physiological disorders were assessed after 4 months plus 7 days at 20 °C. The internal ethylene concentration and the starch pattern index were lower in fruit treated with preharvest 1-MCP compared with untreated fruit, while fruit firmness was higher in preharvest 1-MCP–treated fruit. The difference was more pronounced in fruit with higher I AD values (higher chlorophyll) categories at harvests 2 and 3. Chlorophyll a and total chlorophyll concentrations were positively correlated with the I AD values in both untreated and preharvest 1-MCP–treated fruit. Acetaldehyde and ethanol were unaffected by harvest time, but preharvest 1-MCP–treated fruit had lower ethyl acetate accumulation at all harvests. Sucrose, fructose, glucose, galactose, sorbitol, and malic acid concentrations were often higher in preharvest 1-MCP–treated fruit than in untreated fruit. Soft scald incidence was higher in fruit with lower I AD values. However, the disorder was lowest in harvest 1 and 2 fruit of higher I AD values when the fruit were treated with preharvest 1-MCP. Additionally, fruit senescence was higher in late-harvested fruit. Principal components analysis, multivariate analysis, and the nonlinear iterative partial least square algorithm showed that fruit physiological disorder development after storage was correlated with fruit maturity based on the I AD value and maturity at harvest as affected by preharvest 1-MCP treatment.

  PublisherDOI

Frequent coauthors

• Jacqueline F. Nock

  106 shared

• Yosef Al Shoffe

  76 shared

• James Lipscombe

  Norwich Research Park

  34 shared

• Karim Gharbi

  Earlham Institute

  33 shared

• Naomi Irish

  Norwich Research Park

  32 shared

• Wilfried Haerty

  Norwich Research Park

  32 shared

• Burak Erdem Algül

  New York State College of Agriculture & Life Sciences

  31 shared

• Jinhua Zuo

  30 shared

Labs

• Postharvest Science Research Program, School of Integrative Plant Science, Horticulture SectionPI

Awards & honors

• Inducted into Alpha Zeta (2019)
• CALS Alumni Outstanding Faculty Award (2018)
• B.Y. Morrison Lecture invitee, American Society for Horticul…
• Fellow (2015)