Research by Crop

SIPS faculty are engaged in a broad range of research activities. A substantial number concentrate their activities on specific crop plants.  Some of the ongoing research activities related to specific crops are highlighted here, with more detailed descriptions and publications listed on the individual faculty web pages. See Extension and Outreach for research-based solutions to plant and agriculture questions, for growers, educators, and the general public.

Apples

Forages

Maize

Rice

Vegetables

Biofuels

Fruits and Berries

Ornamentals

Small Grains

 

Cassava

Grape

Potato

Tomato

 

Apples

  • Susan Brown’s research group studies apple genetics and uses marker assisted breeding and transgene technology to develop new apple varieties including the recently released SnapDragon and RubyFrost.
  • Lailiang Cheng's research group is finding new ways to manipulate the sugar and acid content in apples in ways that enhance fruit quality.
  • Kerik Cox’s research group investigates fungal pathogens of fruit crops such as apples, stone fruit, and bush berries, and how different management practices alter the pathogen life cycle 
  • Terence Robinson’s program is dedicated to improving fruit production through identification of rootstocks most suitable for New York growers and development of orchard management practices that improve fruit size and quality
  • Kenong Xu’s program is focused on characterization of regulatory networks in apple with an emphasis on those involved in stress resistance and fruit quality and longevity
  • Chris Watkins, in addition to his responsibilities as Director of Cornell Cooperative Extension, researches management strategies for extending post-harvest storage of apples.

Biofuels

  • Larry Smart’s research group investigates cultivation of willow and the genetics of biomass and yield to maximize its potential as a source of bioenergy
  • Jerome Cherney investigates the profitable and sustainable production of forage crops for use as biofuels and livestock feed
  • Don Viands’ research focuses on genetics of perennial, herbaceous plant species for both feedstock and biofuels
  • Julie Hanson’s work is focused on enhancing the potential of switchgrass and other perennial grasses as biofuels by breeding for biomass yield, low seed dormancy, and pest resistance
  • Joss Rose's research is directed at various aspects of plant cell wall biology and the formation and structure of cellulose microfibrils (the source of cellulosic ethanol).  His program has screened a range of perennial grasses for cell wall diversity.

Cassava

  • Lukas Mueller's group coordinates the SOL Genomics Network which provides resources for genome analysis and genomic selection of solanaceous crop plants including tomato, potato, pepper, and eggplant.
  • Jean-Luc Jannink’s primary focus is on developing statistical methods to use DNA markers in public sector small grains breeding
  • Tim Setter’s research group looks at the genetic sources of drought tolerance in cassava and maize with the goal of developing cultivars better able to grow in drought-prone parts of the world

Fruits and Berries

  • Kerik Cox’s research group investigates fungal pathogens of fruit crops such as apples, stone fruit, and bush berries, and how different management practices alter the pathogen life cycle 
  • Juliet Carroll coordinates Integrated Pest Management (IPM) for tree fruit berry and grape growers, working closely extension educators, faculty and growers to minimize pesticide use
  • Marvin Pritts’ research group focuses on berry production and how cultivation practices such as environment management with high and low tunnels can enhance growth in colder climates
  • Courtney Weber's research group develops improved berry varieties with emphasis on disease and insect resistance, fruit quality, and beneficial phytochemicals

Grape

  • Tom Burr's research group has identified virulence factors in bacterial pathogens of grape. Mutagenesis of factors required for colonization and movement has been used to produce biocontrol agents that outcompete the pathogen but do not themselves cause disease.
  • Marc Fuchs’ program focuses on the biology, spread, and control of virus diseases of grapevine and assists with management of virus diseases of fruits and vegetables
  • Justine Vanden Heuvel’s group researches how light and temperature influence flavor and aroma in wine grapes and how these environmental variables can be optimized during vineyard management to improve fruit quality
  • Keith Perry’s program has developed macroarrays for virus detection in potato and grapevine, facilitating the screening of plant material for large numbers of pathogens and having applications in quarantine and clean seed programs
  • Jason Londo’s research group looks to genetic sources of drought and cold tolerance in wild grapes species for use in breeding with cultivated grapes to produce no varieties that can be grown in more diverse environments. 
  • Bruce Reisch specializes in development of new grape varieties with the aid of marker-assisted breeding technology. Wine quality, disease resistance, and cold tolerance are among the traits of greatest interest.
  • Michael Milgroom's group is is using molecular markers to characterize population structure of powdery mildew fungus on grape. This work is providing insights into patterns of disease spread worldwide.
  • Wayne Wilcox’s research program focuses on biology and management of grapevine fungal diseases addressing questions such as what factors contribute to disease susceptibility and how cultural practices alter disease development
  • Tim Martinson, Northern Grapes Project leader,is focused on how best to integrate varieties and cultural practices to maximize productivity and fruit quality in the New York environment
  • Lance Cadle-Davidson works on development of new grape varieties that are healthy, delicious, and resistant to grapevine fungal and oomycete diseases

Forages

  • Jerome Cherney’s research group is focused on finding ways to manage forage crops profitably and sustainably.  His work also includes exploration of forage crops for use as bioenergy
  • Don Viands research group develops improved cultivars of alfalfa and birdsfoot trefoil with traits beneficial to needs of growers in the Northeast
  • Julie Hansen’s research involves variety development and genetic improvement of forage crops, with emphasis on improved yield, quality, and pest resistance
  • Gary Bergstrom’s program conducts research on the biology, host resistance, and epidemiology of forage legume diseases and provides recommendations for their management

Maize

  • Michael Gore’s research group engages in genetic dissection of metabolic seed traits related to nutritional quality, and contribute to the development and application of field-based, high-throughput phenotyping tools for plant breeding and genetics research
  • Mike Scanlon's research group investigates the developmental biology of leaves, revealing new strategies for optimizing leaf angles so light is more efficiently captured by the whole plant.
  • Ed Buckler’s research group uses genomics and statistical genetics to understand and dissect complex traits in maize and other crops, and develops software for relating genotype to phenotype
  • Gary Bergstrom’s group conducts research on disease of small grains, maize, and soybean focusing on factors that increase the risk and spread of disease, and the efficacy of different control methods for fungal diseases
  • Tim Setter’s research group looks at the genetic sources of drought tolerance in cassava and maize with the goal of developing cultivars better able to grow in drought-prone parts of the world
  • Margaret Smith’s program focuses on genetic improvement of maize with an emphasis on traits that enhance performance in marginal environments
  • Rebecca Nelson's program explores and characterizes natural genetic diversity for quantitative disease resistance in maize
  • William Cox conducts field trials throughout New York State to identify top performing soybean varieties and corn silage hybrids and management practices best suited for production in New York
  • Leon Kochian’s research group investigates genetic sources of stress tolerance to acid soils and associated aluminum toxicity.
  • David Stern’s research group investigates assembly of RuBisCO, the enzyme that catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere
  • Wojtek Pawlowski's research group studies meiotic recombination using genetics, biochemistry and several advanced microscopy methods, such as restorative deconvolution, multiphoton excitation, and structured illumination microscopy.
  • Klaus van Wijk’s research group investigates the development and repair of photosynthetic apparatuses in plants using different photosynthetic pathways

Ornamentals

  • Taryn Bauerle's research group images very fine-scale spatial relationships between competing tree roots in a 3D space using X-ray computed tomography
  • Neil Mattson’s program investigates how different environmental variables affect the growth of greenhouse crops.  Given that flower growers frequently grow many different cultivars and species in the same greenhouse, there is particular interest in identifying variables that benefit a wide range of plants.
  • Nina Bassuk’s research program is focused on improving the quality of urban life by enhancing the functions of plants within the urban ecosystem
  • Thomas Whitlow’s research concerns restoration of ecosystem functions to cities and other human impacted landscapes
  • Frank Rossi’s research program addresses practical problems in turfgrass management with emphasis on environmental compatibility and economic feasibility
  • Bill Miller’s program addresses floricultural crop production and postharvest physiology, especially with flower bulbs
  • Mark Bridgen, Director of the Long Island Horticultural Research and Extension Center, focuses on new plant development, breeding, and propagation of herbaceous ornamentals and flowers

Potato

  • Walter De Jong’s program works on genetic improvement of potato by conventional and molecular genetic means as well as identification of genes that control tuber color and shape
  • Keith Perry’s program has developed macroarrays for virus detection in potato and grapevine, facilitating the screening of plant material for large numbers of pathogens and having applications in quarantine and clean seed programs
  • Bill Fry's research group focuses on changes in Phytophthera infestans populations that influence virulence and strategies for disease control. Development and refinement of the BlightPro decision support system (DSS) helps users improve their crop protection strategy.
  • Xiaohong Wang's research group is identifying nematode virulence factors that promote parasitism in potato.  RNA-silencing of nematode parasitism genes may prove an effective strategy for generating resistant cultivars. 

Rice

  • Susan McCouch’s program is focused on genetic analysis of rice and identification of genes and quantitative trait loci in wild and exotic species that enhance productivity of modern rice cultivars
  • Adam Bogdanove's research group works on TAL effector proteins that are injected into host plants such as rice by pathogenic bacteria and activate expression of genes that determine susceptibility and resistance. TAL effectors are additionally being used as biotechnological tools for DNA modification.
  • Leon Kochian’s research group investigates genetic sources of stress tolerance to acid soils and associated aluminum toxicity.

Small Grains

  • Gary Bergstrom’s group conducts research on disease of small grains, maize, and soybean focusing on factors that increase the risk and spread of disease, and the efficacy of different control methods for fungal diseases
  • Mark Sorrells’ research group is engaged in genomic analysis of small grains and the mapping and characterization of candidate genes associated with stem rust resistance, nutritional quality and other kernel properties
  • Leon Kochian’s research group investigates genetic sources of stress tolerance to acid soils and associated aluminum toxicity.

Tomato

  • Joss Rose's research group is developing new protocols and computational tools to characterize cell wall proteins with particular emphasis on cell wall changes during fruit development and molecular interactions with pathogens
  • Jim Giovannoni, Carmen Catala and their research groups are characterizing developmental changes associated with ripening, revealing new genetic targets for improving flavor in tomatoes.
  • Lukas Mueller's group coordinates the SOL Genomics Network which provides resources for genome analysis and genomic selection of solanaceous crop plants including tomato, potato, pepper, and eggplant.
  • Greg Martin's group collaborates closely with Alan Collmer's group, identifying defense pathways and proteins in tomato that trigger resistance in response to pathogen cultivars.  By screening for variation in responses among different tomatoes, Martin's group is identifying novel sources of host resistance.
  • Chris Smart’s research program engages in detection of fungal, oomycete, and bacterial pathogens of vegetables. Genome sequences of pathogens both to identify sources of inoculum and to distinguish among pathogen isolates with different levels of virulence.
  • Martha Mutschler-Chu’s research group works on the genetic improvement of tomatoes and onion with a particular focus on pathogen and insect pest resistance.

Vegetables

  • Sarah Pethybridge’s program focuses on understanding the epidemiology and control of fungal diseases of processing vegetables including beans, beets, carrots and potatoes
  • Chris Smart’s research program engages in detection of fungal, oomycete, and bacterial pathogens of vegetables. Genome sequences of pathogens both to identify sources of inoculum and to distinguish among pathogen isolates with different levels of virulence.
  • Michael Mazourek’s program is focused in part on development of specialty vegetables such as small, extra sweet squash and peppers with altered taste profiles for enhancement of the aesthetic and culinary appeal of New York produce.
  • Steve Reiners’ research focuses on cultural practices and variety selection for the processing vegetable industry, with particular interest in using cover crops to maximize nutrient cycling and reducing disease incidence
  • Thomas Bj√∂rkman’s program is involved in development of commercial broccoli varieties from existing germplasm that are capable of thriving in growing conditions of northeastern states, thereby minimizing the flavor-killing lag between harvest and consumption that occurs when broccoli is imported from more temperate regions
  • Phillip Griffiths’ research is focused on genetic improvement of snap bean and brassica crops, with particular focus on traits conferring resistance to plant diseases.
  • Margaret McGrath’s research program is focused on management of diseases of vegetable crops grown on Long Island using both conventional and organic production