a. So that the National Plant Disease Recovery System (NPDRS) steering committee can begin to pull together information on the degree of uniformity of the “standing crops”, identification and ranking of the highest impact crop diseases (and insects or other threats to production), and identification of the crop genetic diversity “in reserve” that might be mobilized in a crop disease-associated emergency.
Mike ____ presented information about the NPDRS. Funding level at $5-6 M was proposed; $1.2 M was budgeted. The NPDRS was created in response to HSPD #9. Objectives include developing capacity to recover from major plant disease incidents within one year. Personnel have been working with the EPA to get permits for emergency fungicide use. Aphis selects priority disease organisms. Chemical, genetic and greenhouse resources are to be identified and their roles defined, by disease, by crop. The roles of the public and private sectors need to be defined.
Threats are to be identified, and plans developed for recovery actions.
Summary of discussion: Worldwide screening opportunities are available thru industry partners (Bill Dolezal). There is a need to look at base germplasm, and to use testers endemic to each area for testing, not US hybrids. There are issues with the list of diseases and organisms developed; Septoria maydis, for example, does not belong on the list. Mildews could get into the US, but would not likely become established in the Corn Belt due to a lack of the environmental conditions they require. Aphis permits are required to collect and bring some organisms into the US. It would be helpful if industry was informed as to types of diseased materials intercepted at ports of entry. Industry and the public sector need a focal point to report monitoring results; a communications trees, easy database entry, and scanning are needed. Peter Bretting indicated that ARS, as the lead agency for the NPRS, can leverage development of a communications tree.
Knowing the genetics of diseased material is important; for example, whether gray leaf spot is on susceptible or resistant genetic material could indicate pathogen shifts. Tropical rust incidence is increasing in Central American; a central infection source is lacking. Within the US, distribution of various pathogen types varies; internal US monitoring for pathogen biotypes is needed. Discussion of terrorism threats centered around potential distribution of Striga spores, agents which would selectively attack Roundup Ready beans, introduction of insects which are resistant to a particular Bt event, or other factors which would cause resistance to be overcome. Single gene events pose a vulnerability risk, as they can be used as a threat pathway; examples included sudden death susceptibility of early Roundup Ready soybean varieties; Fusarium susceptibility linked with original varieties used as donor gene parents.
It was agree that monitoring of race differential sets is needed.
Ease of virus migration from grasses to maize was discussed; most require specialized vector transmission. Unknown vector introduction is a potential threat.
CIMMYT has no formal threat reporting system; IPGRI has an early warning system for emerging threats; this has focused primarily on insect threats to date. Dr. Taba indicated that in Mexico, if winter production planted in July or August is threatened by corn stunt virus, delayed planting until September provides a solution.
It was pointed out that continual, stable funding to the international CGIAR centers helps preserve genetic diversity reserves to combat threats to production. Coordination of reporting from industry sources, US and foreign production areas, would be helpful.
Bill Dolezal moved that a clear reporting structure be developed to receive and record perceived plant disease and insect threats and incident reports. This requires clear communication channels for use by public and private sector members, with designated contact people. The motion carried.
Industry needs to be involved in pest/risk analysis; currently there is no industry involvement in the Plant Diagnostic Network team. Margaret Smith pointed out the importance of including the CGIAR’s on communication lists.
Bill Tracy indicated that the CGC should develop lists of potential threat and then discuss germplasm resources vs. the threats.
The American Phytopathological Society produces a list; APS reports and the CABI database define known pathogen threats; this is distributed every six months. The ICBR and CAST lists were circulated to the NCR25 membership.
Mark Millard provided an annual report on NCRPIS maize curatorial activities. He described the plan and process for incorporating Major Goodman’s 1800 member racial collection into the NCRPIS maize collection, and for imaging seeds of the collection. Dr. Taba indicated that maybe 400 of these 1800 populations will be unique accessions. Major accessioned material based on its source in addition to the material’s collection id. The materials were derived from country of origin banks, CIMMYT, USDA collections, and many researchers who obtained seed in various ways. Discrepancies were noted between various sources of some populations; each seed lot will be maintained separately. Attempts will be made to procure additional seed from the institutions of origin where supplies are limiting. Regeneration prioritization will be given to accessions from rare races with low seed supply. See NCRPIS report for details.
Peter Bretting discussed need to determine whether individual PVP lines should be retained in the collection, and asked if it could be determined whether a line represented a substantial contribution, and whether the line changed. Marlin Edwards indicated that the PVPs will provide future resources for genetic investigation, just as the long-term Illinois selection populations have, and should be retained.
Ed Buckler is proving quality assurance testing via use of SSR markers to verify quality of 89 accessions, inbred lines in the Goodman diversity set. The intent is to compare previously regenerated samples (by NCRPIS) with Goodman samples to verify quality and potentially save regeneration resources if SSR profiles are identical.
Hiring of a federal IT specialist within the NCRPIS has relieved the maize curator from acting-network administration duties. Two maize thesis projects are focused on describing landraces of maize native to the US Southwest.
The collection is approximately 65% available, and continues to grow at a rate of about 3% per year. Over 17% of the collection was distributed in 2004; expired PVP lines (45) continue to be in high demand. Mark M was asked to provide a note to the Maize Genetics Newsletter listing newly expired PVP lines each year. Approximately 74% of the collection is backed up at the NCGRP. Regenerations were attempted on 466 accessions in 2004, including 317 in Ames, one annual teosinte in the winter greenhouse using Bonzi® growth regulator, two accession of Zea perennis, 100 accessions in Puerto Rico (by Golden Harvest), 42 in St. Croix, and four tropical maize inbreds sent to Hebron Smith at Guthrie, KY for greenhouse increase.
Plans for FY05 include completing inventory and image documentation of the Goodman collection, prioritizing acquisition and regeneration activities, distributing the completed Races of Maize CD’s, identifying collaborators for regeneration in PR, hiring of an additional full time permanent maize curator position, releasing over 10,000 maize images to GRIN, loading existing molecular marker information and frequencies on collections held at NCRPIS, and working with Wilfredo Salhuana to develop a consolidated list of holdings of the world’s maize collections.
Candice Gardner provided an update on NCRPIS personnel and financial resources, facilities changes and project progress. The digital capture project of the volumes of the Races of Maize was completed for the English versions; lack of a high quality, pristine copy of the Spanish version of the Races of Maize of Mexico prevents completion. Major Goodman offered to provide his hard-bound copy, which includes Spanish versions of multiple volumes. A new 6,000 sq ft machinery storage shed will be built in 2005. The germplasm viability testing lab renovations will be completed in January.
A document prepared for the 2002 meeting on maize curation objectives, issues, obstacles and/or opportunities was distributed and reviewed. Significant additional funding will be required to increase the rate at which maize accessions are regenerated, or alternative means need to be identified.
Additional financial resources became available to the project in the past year, due to Congressional action and the efforts of GEM stakeholders.
Nine GEM lines from the Ames program (25% tropical) and seven lines from the Raleigh program (50% tropical) were recommended for release. Two stress tolerant lines derived from GEM germplasm were released from TAMU (Xu). Inbred UW EX01 will be released in 2005 by the Univ of WI (Coors), for superior silage productivity and milk production per acre. GEMS-0002 was submitted for Crop Science registration (Pratt, Pollak, and Montgomery). Univ. of Delaware (Hawk) and GEM Ames (Blanco) initiated a cooperative study on breeding methodology utilizing SS and NSS breeding crosses to compare GEM protocol, mass selection, and modified single seed descent procedures.
See the GEM website, http://www.public.iastate.edu/~usda-gem/, for reports on pathology/entomology evaluations and other breeding collaborations, and public cooperator reports, and the results of a web-based survey of individuals who had familiarity with GEM and/or exotic germplasm research.
The GEM TSG organized a successful interactive meeting in June, 2004 in Raleigh, NC on application of genomic technologies and strategies for partnering to enhance success of identifying allelic diversity for key target traits.
a. Allelic Diversity project
b. Core CollectionsRandy Holley described the protocol and population crosses being made to provide 100-200 racially derived lines for allelic diversity cvomparison. Accession populations (200) are used as donor parents and crossed to four PVP inbred lines, using 5 donor populations per racial classification, 10 contributing parent plants per population. The lines will be compared for allelic diversity; if native diversity is found, it can be utilized. If no diversity is found for a given gene, an alternative transgenic strategy would be feasible. The challenges do not include obtaining markers or SNP data, but the resources for plant phenotyping. Currently, field assessment is more costly than genomic assessment.
Randy’s strategy is an overall diversity assessment; if four out of five alleles are lost in fixing one collection it is not an issue if, over many accessions, diversity of sampling is achieved.
Discussion points included a question about further reductionism of allelic diversity, once the resource is available to molecular researchers. Industry researchers are not likely to use this material unless it has demonstrated significant positive, desirable attributes.
Concern was expressed about GEM Project funding that would be diverted to this project; Jim Coors indicated that 6% of the molecular research community currently utilizes GEM germplasm vs. 30% of maize genetic resources. Randy indicated that the allelic diversity project could be incorporated in the Raleigh group’s current program.
Marty Sachs presented details of the Stock Center’s activities. To date in 2004, 4,330 seed samples were supplied in response to 257 requests. Over 90% of the requests are received via electronic mail or their website order form. Popular stock requests include the IBM RIL mapping populations, Hi-II lines, ig1 lines, transposable element lines, Maize Gene Discovery Project lines, and Chromatin stocks. Over 10.5 acres of nursery planting were devoted to several categories of stocks; allelism tests of several categories of mutants with similar phenotype or chromosome location were conducted; the Spotted-dilute and Fcu controlling element systems were characterized; propagation of a large collection of cytological variants, including A-A translocation stocks and inversions; stocks from the NSF project “Maize Gene Discovery, Sequencing and Phenotypic Analysis.”
ICIA continues to provide winter nursery services, and this is going well. Over 45, 260 available seed stocks that were generated by the above NSF project; emphasis is increasing on materials produced by the ‘Regulation of Inflorescence Architecture in Maize’ project. Dr. Gerry Neuffer has provided 1644 B73 and B73 x Mo17 lines from this project. Torbert Rocheford provided about 1200 lines of A619 EMS materials. Karen McGinnis provided 43 lines of Functional Genomics or Chromatin Project stocks.
Over 300 lines of Neuffer’s materials were screened for ear and kernel mutations in the lab, and grown for field observation during summer ’04 at the U of IL. Rocheford’s 1200 lines and Tom Brutnell’s 1700 Ac lines were planted also and observed for phenotype variation.
IT specialist Jason Carter completed the first version of curation tools being used to maintain collection data. Monthly uploads are being provided to MaizeGDB. Revised tools will connect directly to Maize GDB in the near future.
Kay Walker Simmons provided information that the tropical germplasm CRIS project at Mayaguez, PR is responsible for overseeing the quarantine growouts in St. Croix for sorghum and maize, and is in critical need of additional funding support.
Peter Bretting provided additional detail to the NPS 2004 Report for the NPGS on the International Treaty for Plant Genetic Resources for Food and Agriculture, and continuing development of an MTA for plant genetic resource exchange.
Kay discussed the White House Interagency initiative on Genomes, particularly the large maize initiative to sequence the entire genome, not only gene-rich areas. The Maize Genetic Stocks Center will archive the materials from this NSF project.
Southern US maize geneticists have formed an aflatoxin working group.
In response to HSPD #9 of January 30, 2004, which is concerned with national polity to defend the agriculture and food system from terrorist attacks, major disasters, and other emergences, the NPDRS is being designed and implemented. THE NPDRS will utilize the genetic resources contained in the NPGS and the scientific capabilities of the Federal-State-industry agricultural research and extension system. Its current objectives are to develop and implement a system to ensure a coordinated Federal, State, local levels, and private sector response and recovery plan to minimize the impact of high-consequence plant diseases. All Crop Germplasm Committees have been asked to update the crop vulnerability/crop reports to include recent information on the degree of uniformity of the ‘standing crop(s)”, to identify and rank the highest impact crop diseases and other relevant threats to production, and to identify the crop genetic diversity in reserve that could be mobilized in response to a crop disease-associated emergency.
A new Institute of Food and Agriculture, under the umbrella of the USDA, separate and in addition to ARS and CSREES, is planned to provide a science-based structure to get more rigorous science out of agriculture; its structure would be similar to that of NIH.
Henry Shands provided a document which listed accessions shipped in 2004 that are held by NCGRP and not by CIMMYT, and those held in common. 784 ‘NCGRP Only’ accessions were shipped; ‘603 accessions held jointly with CIMMYT were shipped.
He also provided a summary of Zea mays holdings in the NPGS by NCGRP, Ames, and/or Urbana. Holdings include19,828 landrace materials; 51 expired PVP’s; 806 PVP voucher specimens; 7.136 genetic stocks; and 109 quarantine materials.
Dr. Kaster’s report described notably low corn insect pest problems in the Eastern US in 2004 (limited primarily to early season injury problems); common seedling insect pest problems in the central US, including southern corn leaf beetles, corn flea beetles and stinkbugs; low SW corn borer populations in the southern US due to unfavorable weather conditions for adult mating and oviposition during July; early, severe and widespread corn rootworm (Diabrotica spp.) injury in much of the central corn belt; continued expansion of the range of the western bean cutworm (Loxagrostis albicosta). Much late root lodging occurred in 2004, due to both beetle and non-beetle (wind) causes.
YieldGard Rootworm™ hybrids suffered some severe injury in scattered instances; it is thought that a gradual decline in expression of the low dose transgene enabled rootworm larvae to more readily feed and injure roots. Sub-lethal doses of rootworm toxin, due to declining production during the corn plant’s life cycle, may lead to increase larval survival rates; this could result in shortened 3effective life-cycle for the transgene technology. Native plant resistance research has not resulted in discovery of any commercially useful alleles to date. Efficacy and consistency of control by the transgenic products is still better than that achieved using insecticides on non-transgenic material.
The western bean cutworm cannot be reared in sufficient numbers for screening large numbers of germplasm varieties; extent of resistance alleles in corn germplasm is unknown. It is expected that the insect will continue to expand its range and that most of the central corn belt will be subject to injury. Corn hybrids containing the Herculex™ trait offer a degree of built-in plant protection; foliar applied insecticides are commonly used to prevent economic losses.
The third coolest summer on record across much of the Mid-western corn belt resulted in new state corn harvest record in IA, IL and OH. Few economically damaging pest outbreaks were recorded; local disease outbreaks included Gray Leaf Spot, Northern Corn Leaf Blight and Diplodia ear mold. Rainfall late in the growing season resulted in some harvest delays, this coupled with winds led to an increase in stalk lodging. A lot of down stalks did not collapse as a result of diseas, but rather from large, leavy ears with high test weight.
Low frequency seedling blights were observed generally in 2004; Pythium and other seedling blights w2ere recorded in the southern Corn Belt and in some flooded areas. Crazy top was reported from some flooded fields, particularly in MN, IA, IL and OH. Goss’ Wilt was widely reported in western NE and Eastern CO, as in 2003.
The three dominant foliar diseases reported in the MidWest included Gray Leaf Spot, Common Rust and Northern Corn Leaf Blight, the most serious. The Southern Corn Belt widely reported Southern corn rust and Southern corn leaf blight. Cool wet weather favored Diplodia ear mold from KS to OH; Giberella ear rot was also reported. Northern Leaf Blight Race 1 predominates; resistance provided by the Ht1 gene has been overcome.
No new viruses were reported in 2004; Barley yellow dwarf was reported in low levels in KS and NE, as was High Plains Virus in KS and TX.
Dr. Taba’s comments are interspersed throughout these minutes.
USDA funding helped link Tripsacum work with Cornell Univ. researchers. 955 accessions have been regenerated in the last three years. NCGRP has received 2,611 accessions from CIMMYT for secure backup. 1300 samples were sent to NCGRP this year.
Funding pressure for genebank resources continues. Concern over transgenics in the collection led to an IPGRI conference dealing with unintentional contamination. A draft policy on unintentional contamination will be posted on IPGRI’s website; Dr. Taba is requesting comments from Maize CGC members.
Dr. Jonathan Crouch is the new head of the Genetics Resources Program. Marianne Banzinger will be the African Program Director.
Genome Assembly:
Ed Coe reported that a sequencing-ready physical/genetic map with high coverage and accuracy has been constructed. About 91% of the genome is assembled into contigs; about 78% is anchored to the genetic map. Repetitive sequences (60% of the genome) and duplications have not prevented assembling. Maize FPC was first released on 7/26/01. High-information-content fingerprinting and rice synteny have been incorporated. There is approximately 17x depth-of-coverage in BAC clones. See Dr. Coe’s report for more details. There are now 2,002 loci detected by SSR probes available for crop improvement applications. There are 3,882 mapped RFLP loci, most of which have sequence information, and 388 mapped SNP/INDEL loci. GenBank contains over 438,000 EST’s representing over 58,000 unique sequences. At least 944 of these have been mapped genetically; over 13,000 have been mapped physically to contigs. There are over 81,000 sequence-tagged sites, and over 1,885,000 genomic sequences in GenBank.Diversity Data:
Mary Polacco reported that Marilyn Warburton (CIMMYT) has determined SSR alleles for 66 public SSRs, and various populations from CIMMYT and Zimbabwe. Data were partly curated at CIMMYT using nomenclature and schema representation from MaizeGDB.Maize Mapping Project; Maize Evolution Project; Maize Diversity Project. SNP and INDELs.
Mary reported that several hundred genes with low copy number (1-2) overgo probes on BAC contigs are being sequenced for some two dozen corn belt, tropical and wild maize relatives. Early data provided by Mike McMullen has been incorporated into MaizeGDB. Bioinformatics for data from the Maize Diversity Project is being handled by Gramene, as is SNP representation for rice and wheat.Map integration to enhance genetic scaffold for anchoring BAC contigs has resulted in a simple strategy to merge map sets, retain relative order of all markers and assign approximate IBM map coordinates. The output is called IBM neighbors. The intermediate steps in the process have resulted in maps useful in their own right, which are provided in Maize GDB. To date, only genetically mapped loci are included; in the future, all potential genetic markers (unigenes; SSR) that have been ordered on anchored BAC contigs will be included on the IBM neighbors.
Traits for Comparative Studies:
Mary reported that MaizeGDB is supplying 1502 QTL positions to Gramene using a controlled vocabulary for traits (harmonized with GRIN and with Gramene), and positions as coordinate range on the IBM maps, based on assigned bin values. This project involves Grainegenes also.