XI. COMMUNITY SURVEY RESULTS
Maize Genetics Executive Committee
(MGEC) Survey Results (172 responses)
Posted at MaizeGDB May 2006.
<http://www.maizegdb.org/mgec.php>
As follow-up to the open community forum held at the Maize Genetics Conference Asillomar 2005, a questionnaire was developed by the Maize Genetics Executive Committee (MGEC) and posted to cooperators from MaizeGDB. Results are summarized below.
A score of 1 was assigned for "highest priority�.
Question 1
Prioritizing General Community Needs
1. High quality maize genome sequence annotation. (avg: 5.72)
2. Improved maize reverse genetics resources that allow investigator to move from sequence to seed. (avg: 6.72)
3. An improved maize database that allows investigator to move seamlessly between multiple genomic datasets and expression analysis. (avg: 7.12)
4. Improved maize transformation that is inexpensive, fast, and possible in multiple backgrounds. (avg: 7.16)
5. Resources for rapid mapping of all maize mutants. (avg: 8.66)
6. Functional studies that focus on individual genes, gene families or networks. (avg: 9.06)
7. High density markers (MaizeHapMap): SNPs for all genes and a catalog of genes not in B73. (avg: 9.35)
8. Enhanced capacity at the Maize Stock Center including increased seed storage space. (avg: 9.45)
9. Improved tools for quantitative genetics. (avg: 10.1)
10. Gene replacement tools. (avg: 10.2)
11. Support of training workshops in maize genetics, genomics, and bioinformatics. (avg: 10.8)
12. Further development of a maize global transcript profiling service. (avg: 11.0)
13. Proteomic tools and data for maize. (avg: 11.6)
14. Continued development of cytogenetic methods including chromosome painting techniques. (avg: 12.9)
15. Funded support for community field space. (avg: 14.0)
16. Other; see individual responses (avg: 14.8)
Question 2
Future Sequencing Strategies
Which survey sequences would be
most valuable?
1. Full-length cDNAs (avg: 2.55)
2. ESTs (avg: 3.99)
3. Methylation filtered genomic sequences (avg: 4.20)
4. High-Cot genomic sequences (avg: 4.49)
5. Random shotgun genomic sequences (avg: 4.55)
6. Other; see individual responses (avg: 6.25)
Which lines would be most valuable
to sequence after B73?
1. Mo17 (avg: 2.25)
2. W22 (avg: 3.72)
3. Other Zea species; see individual responses (avg: 4.52)
4. Other inbred line; see individual responses (avg: 4.91)
5. Other grass; see individual responses (avg: 5.15)
When comparing overall sequencing strategies, 52.3% of those surveyed stated that they preferred near-complete sequencing of one line over survey sequencing of multiple lines.
Question 3
Database and Annotation Issues
What features do you want to see
in an improved community database?
1. Tools to navigate from maize sequence to map position and possible mutants or QTL (avg: 4.16)
2. Tools to navigate from gene to reverse genetics tools such as insertion sites (avg: 4.68)
3. Tools to navigate from maize sequence to homologous and syntenous sequence from other grasses (avg: 4.77)
4. Tools to navigate from maize sequence to a complete profile of expression studies (avg: 5.19)
5. Tools to navigate from maize sequence to homologous sequences in other species (avg: 5.62)
6. Increased interoperability between MaizeGDB and Gramene (avg: 6.14)
7. More tutorials on using existing database resources, both at MaizeGDB and at individual project sites (avg: 7.11)
8. Availability of a sequence browser such as Ensembl at/through MaizeGDB that supports and maintains user-contributed annotations in addition to automatic annotations (avg: 7.15)
9. Other; see individual responses (avg: 8.89)
For a community annotation
pipeline
47.0% of the respondents indicated that centralized annotation efforts by a single bioinformatics group was their preference
37.7% of the respondents indicated that decentralized annotation where individual groups contribute annotation to a curatorial site was their preference
15.1% of the respondents indicated an alternative solution was their preference (see individual responses)
Optional Individual Responses to
Question 1 - General Community Needs
(27 responses total)
Maize specific small molecule database (metabolomics)
Better support for computational biology
Improved software tools for maize curators
Studies of mechanisms of resistance of maize to pathogens
454 Sequence Multiple Diverse Maize Inbreds
Funding opportunity for pilot studies
Maize Activation Tagging resources for dominant phenotypes
Support for non-wet lab genetic analysis
Increased support for Gramene to provide end-user analytical tools for analysis of all cereal genomic sequences
Further development of off the shelf maize global transcript profiling platform
Improved affy chip, incorporation of quality checked data into MaizeGDB & PLEXdb
Agronomist trained in genomics to apply what we have learned to the field
Establishment of a metabolomics center and service (NMR and GC-MS and NIRS)
Better channels for communication & collaboration
Career development workshops for young scientists
Make important papers web-available when poorly accessible (e.g. Wilkes 1979)
More support for long-term public corn breeding programs
Affymetrix whole genome array
Richer BIOLOGICAL CONTENT in the maize database
Quantitative genetics
Complete maize genome sequence
Genetics of reproductive signs. Nuclear-cytoplasmic interaction.
History of Maize cooperators, contact with maize cooperators
Understanding cellular localization of maize gene products
MaizeGDB: capture the empirical data; a strong professional curation staff for maize and cereal genome peer-reviewed literature to capture the empirically confirmed information.
Maize genome evolution
Reverse genetics in rice
Optional Individual Responses to
Question 2(a) � which survey sequences would be most valuable?
(28 total responses)
Selected BAC clones of gene rich regions (6 responses)
MPSS developmental profiles (3)
454 sequencing (3)
Finish B73 to completion (2)
Selected gene amplicons for diversity resequencing & transposon flanking sequences (2)
Organelle genomes from many inbreds and relatives (shotgun) (2)
Ab10 in addition to chromosome 10 from B73 and Mo17
BAC/EST/GSS contigs from multiple inbreds anchored to a genetic map
ESTs from Normalized cDNA libraries
PCR amplicons corresponding to maize genes
Repetitive sequences
Affy-style arrays to discover SNPs across diverse germplasm or RIL pop. members
Gene enriched sequences (methyl & Cot are equivalent)
Set of BAC ends optimizing genome coverage
Optional Individual Responses to
Question 2(b) - Suggested Inbred Lines For Sequencing
(47 responses)
A188, tissue culture and transformation ability (7)
Gaspe flint - short flowering time inbreds will enable comparative adaptive studies (3)
The diverse germplasm lines being studied by Buckler/Doebley group. (2)
F7: european counterpart to B73 (2)
Oh43; another commonly used inbred line and a third heterotic group (2)
A619, mutants behave very differently in this inbred (2)
Mp313E (aflatoxin resistant inbred),
Iodent line (an expired PVP),
H99 (phenotypic penetrance has been altered)
NC89 and K55 (4x intermated population of 500 lines is being developed),
W23 (distinct from W22 and used by many on the west coast),
Michoac�n 21 (best inbred for tropical lines),
CML247 (CIMMYT line with high market value but low (a)biotic stress tolerance -- commonly used in crop improvement programs for developing countries), Parthenogenetic maize lines-haploinductors,
M20W (good suppresser of many mutations),
Mo20W (drought and stress tolerance),
CML103 (a tropical source that is relatively early in the Midwest and results in reliable seed set),
PH207, recently public elite inbred line that is important progenitor to many current commercial hybrids
F2 (using INRA reference stock) as a representative of flint material, which represents an high divergence with dent material and has been used for genomic studies in France
27 linkage founders from NAM
The 16 progenitors of the Iowa Stiff Stalk Synthetic (BSSS). This would be a step toward understanding how genes respond to selection in populations. BSSS is the most economically important. pop
An inbred equidistant (by genetic distance) from B73 and Mo17
Other inbreds mentioned are P 165, KYS, KY21, popcorn, B37, W64A, Tzi8, CML69, P39, 4 Co63
Optional Individual Responses to
Question 2(b) - Suggested Zea
Species For Sequencing
(68 total responses. most just suggested �teosinte�).
17 supported sequencing Z. parviglumis.
5 supported sequencing Z. diploperennis.
3 supported sequencing Z. luxurians.
Optional Individual Responses to
Question 2(b) - Suggested Grass Species For Sequencing
(43 responses)
12 suggested sequencing Sorghum bicolor (Important economically and phylogenetically, small genome, relative with desirable traits, closest relative that is a crop, sufficiently different from maize for numerous traits).
9 suggested sequencing Tripsacum. T. andersonii and T. dactyloides were suggested. (Closest genera to Zea to compare genome evolution with Zea)
4 suggested wheat (major polyploid grass species; Pooideae for comparative purposes)
2 suggested barley (major true diploid crop species, access to genes not tractable in maize)
2 suggested Brachypodium; it's a promising model
Switch grass- perennial, may have important agronomic properties
sugar cane( because of its economic importance).
foxtail millet, small genome, outgroup for maize and sorghum, rapid cycling, potential model
Streptochaeta from base of grasses for comparisons with rice and maize
Eleusine indica; fills gap grass taxonomy, is diploid, and has small genome
Joinvillia sp.-- outgroup to the pre-grass tetraploidy.
Coix; a close relative of Zea
Optional Individual Responses to
Question 3(a) What features do you want to see in an improved community
database?
(23 responses)
Some 15% of respondents listed other, but lower ranked priorities. Notably, many focused on enhancing content of biological information, in particular phenotypic, both mutant and QTL. This aligns with the top navigation tool priority. Many indicated a need for a single unified genome browser, easier to use than gbrowse should be the navigation tool target. Others indicated a need for better access to machine-readable formats; deposit of all project data into the community database; more flexible BLAST; archival/historical information; interoperability with other databases (e.g. TIGR; GO; TAIR).
Optional Individual Responses to
Question 3(b) Community annotation pipeline
(26 responses)
Virtually all of the 15% �write-in� respondents indicated a preference for an initial annotation by a single group, with support provided for updates by others in the community, with or without curation.