Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology (2008)

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J Examples of Interactions with Industry and Plant Breeders Reported by Principal Investigators of NPGI A subset of the 167 responses received is listed in this appendix to show the interactions between principal investigators of the National Plant Genome Initia- tive and industry and plant breeders. Some responses were redacted to remove third party names. START-UP OF BIOTECHNOLOGY COMPANIES • Our NPGI supported work has led to the formation of a spin-off company, GrassRoots Biotechnology, which is currently in discussions with two major Ag- Biotech companies. • Founder and current Science Advisory Board member, Divergence, Inc. • Two start up companies were established and are still in business: Plexigen and Array Express. • We have formed a start-up company (PhylloTech, LLC) to produce natural product fungicide alternatives and to exploit trichome produced diterpenes and sugar esters. Also, since the field trial for aphid resistance, we have had 3 additional APHIS permits (on a non-trichome project) and conducted the respective field trials. • The technology developed at the University of Chicago on centromere biology resulted in multiple patent applications. It was used as the basis to obtain venture capital financing for Chromatin, Inc in 2001. 159 

160 A pp e n d i x J PATENTS OR COMMERCIAL LICENSING AGREEMENTS • We have used a machine learning approach to identify 100 novel genes in Arabidopsis, which our analysis suggests are involved in seed development. This set of genes is being evaluated for addition to our patent portfolio by the NYU Office of Industrial Liaison. The current NYU patent portfolio on plant genes from the lab of the PI is the basis for a set of commercial licensing agreements with two major US agricultural companies working on trees, corn, alfalfa and other crop species. • We have received continuous funding from the Biotechnology Research and Development Corporation (BRDC), a consortium of industries, to develop new plant promoters, and methodologies to improve plant transformation. We have obtained 8 patents, and applied for several others that are pending. • Identified a soybean cyst nematode inducible promoter (patent 7,223,901) • A co-dominant marker was developed for pungency that has been licensed to industry breeding programs. • A segregating population has been developed for mapping that has also been licensed for private use. • Licensed genetic stocks to Syngenta and DuPont/Pioneer MATERIAL TRANSFER TO OR ACCESS TO RESOURCES BY INDUSTRY • My program has provided marker assisted selection services to the follow- ing private wheat breeding companies: WestBred, Resource Seed, Inc., and Arizona Plant Breeders. Two of these companies are releasing cultivars in 2007 developed with the help of our marker assisted selection services. • The computational tools and resources are documented at gene.genetics. uga.edu and www.fgsc.net. These websites are used to keep track of requests for software, data, and laboratory resources. Requests from companies include Pfizer, Bristol-Myers-Squib, Millenium Pharmaceuticals, MycoPharmaceuticals, Novo- zyme, Paradigm Genetics. Additionally, many academic labs have requested our tools. • The funding resulted in material transfer agreements between the Regents of the University of California and Mendel Biotech • Commercial versions of our spliced alignment software are distributed by NewLink Genetics (http://www.linkp.com/) and licensed to several big agro companies. • Released open source software (TASSEL) that implements association map- ping algorithms have helped companies get these to run in environments. It has been used by researcher’s at all major seed companies. • An experimental line that carries the two G. soja resistance QTL was released. 

A pp e n d i x J 161 Seed of this experimental line was requested by 16 private soybean breeders from 11 companies and four public soybean breeders from three universities. Seed was sent to all breeders who requested the seed. • Numerous private companies with breeding programs have accessed our web site to download our SNPs, sequence alignments and other data. These com- panies include Pioneer, General Mills, Monsanto, Keygene, Dow, AgReliant, Dupont and CoGentCo. • We have produced soybean BAC contigs for the United Soybean Board, sweet orange BAC contigs for the California Citrus Board, and are in the process of generating walnut BAC contigs for the California Walnut Marketing Board. • We have provided one seed company with gene sequences that are being used to selectively breed varieties with superior nutrition. We also trained two of their scientists in techniques in our lab. That technology is now integrated into the seed company’s internal research program. • MAGI maize genome assemblies and annotations provided to seed com- panies (BASF, Pioneer and Syngenta) for use on their internal maize genome web sites. • Our software program is used by breeders at seed companies such as Semi- nis, De Ruiter Seeds COLLABORATIONS WITH INDUSTRY • One example is a successful interaction with Cotton Incorporated (Cotton, Inc. http://www.cottoninc.com/), which provided additional funds to generate more genomic resources for the cotton genomics community. We proposed to generate 20,000 ESTs in the NSF-funded project. Using the additional funds from Cotton Inc., we were able to produce ~40,000 ESTs. Also, we were able to design and pro- duce the spotted oligonucleotide microarrays for the cotton research community. • We have extensive interaction with the Phenotype Screening Corporation, which developed one of the technologies that we are using to image roots. (GrassRoots Biotech is incorporated in DE). • We are assisting Cenicafe, a research institute in Colombia focused on coffee research, in identify genes important in coffee disease resistance and quality. • We are working with industry (Bayer Bioscience and Monsanto) to coor- dinate the effort on sequencing cotton genomes and to transfer genomics and biotechnology to the cotton field. • Through funding from NGPI and Monsanto company we have developed a series of near-isogenic lines each harboring a single mapped Ac transposable ele- ment. Stock requests for most lines may be made directly from the Maize ­Genetics Cooperation Stock Center (http://www.maizegdb.org/cgi-bin/stockcatalog.cgi) and 

162 A pp e n d i x J can be searched through the MaizeGDB Website (http://www.maizegdb.org/). These lines are freely available with no MTA required. Additional lines that we are propa- gating to increase seed stocks can be viewed on our project website (http://bti. cornell.edu/Brutnell_lab2/Projects/Tagging/BMGG_pro_currentmap.html) and seed stocks requested via email. • We have exchanged large sets of SNPs with Pioneer Hi-Bred International. Our SNPs will be used by them for marker assisted selection and for tracking germplasm. • We have initiated formal research/contract collaborations with Dow Agro- sciences (Zionsville, IN) to help them with projects involving plant transformation and protein expression in plants. • Collaboration with BASF Plant Sciences. The objective is to identify the Avr genes that match two late blight R genes that have entered the commercialization pipeline. The effector work is providing mode of action information as well as provide a tool for monitoring pathogen populations for virulence. • Work built the foundation for three independent industrial collaborations on tomato flavor (with the largest European seed company), fresh lettuce producer (largest in U.S.) and a major flower seed company. Each of those collaborations resulted in a funded research project in our lab. • Research collaboration with DuPont/Pioneer Hi-Bred to identify genes that contribute to the superior N uptake phenotype in the Illinois High Protein germplasm. • Service agreement with Monsanto Company to conduct high-throughput amino acid analysis of plant samples. • I interacted with Arcadia Biosciences to apply TILLING (a targeted reverse genetic technology) to wheat and soybean. My knowledge and understanding of allopolyploidy was instrumental in helping this biotech company in establishing TILLING in polyploidy species. • This project had a close collaboration with scientists at Pioneer Hibred. The project allowed them to identify all but two of the maize cellulose synthase genes and provisional patents also resulted. Later work after this project identified the two remaining genes and also established that over-expression of certain CesA genes led to altered stalk strength, a trait important in the more windy northern parts of the U.S.; stronger stalks resist lodging in the field. INTERACTIONS WITH BREEDERS • Working with cotton breeders in USDA-ARS in Stoneville, Mississippi, we have successfully applied microarrays to detect gene expression differences in the breeding strains that have 20 percent better fiber strength than regular cultivars. 

A pp e n d i x J 163 The gene expression data will uncover genes that are associated with cotton fiber quality. • In addition to our basic and genomic research efforts, I run a lettuce breed- ing program that utilizes the genetic information on disease resistance as well as the molecular markers for selection generated by these NPGI projects. Throughout the year I meet regularly with seed industry individuals. Markers and genetic informa- tion, particularly relating to disease resistance generated by my lab are extensively used by the lettuce breeding companies. • We are working closely with Prunus breeding programs worldwide to mark genes that control fruit quality characters, tree architecture and other important traits. • We meet once a year with other soybean breeders that work in fatty com- position (USB meeting) and share our discoveries. We share information so other breeders can use it to perform marker-assisted selection in their programs. • I collaborate with the soybean breeder of the USDA-ARS unit here in NC so when I discover QTLs and develop allele specific markers for candidate genes, I transfer this knowledge to him and either he can use it to make selections or I do the marker work for him so he can make selections. • Map and map score data for 301 recombinant inbred lines of inter-mated B73 x Mo17 (IBM), a four-fold-expanded panel of lines equivalent to over 2400 meiotic products. This resource is widely used in public and private breeding, where it provides dense and highly precise markers for marker-assisted selection. • Breeders in India, Indonesia, Bangladesh, Korea, Ghana, Mozambique, and Uganda have all requested access to both the interspecific advanced backcross NIL families and the strategy for advanced backcross breeding in rice using wild ances- tors as donors.