VI. MAIZE GENOME DATABASE (MaizeGDB)
Maps, Map Integration, and Community Curation
Notable new maps provided this year to MaizeGDB include two major maps prepared using the public, 94 individual intermated B73XMo17 (IBM) population available from the Stock Center. This population is a subset of the larger population used to create the IBM2 map that anchors the physical, BAC contig map maintained at Arizona <www.genome.arizona.edu/fpc/maize>.
IBM IDP + MMP bd (ver 4) maps from Pat Schnable.
1407 newly mapped insertion-deletions polymorphisms (IDP) <maize-mapping.plantgenomics.iastate.edu>. Some 655 IDP loci map to a statistically well-defended order. Probe details, including primer sequences and GenBank accessions have been made available to MaizeGDB.
IBM GNP 2004, from Falque, M. et al., Genetics 170:1957-1966, 2005.
954 newly mapped maize ESTs. Details about probes, both RFLP and PCR based, have been provided to MaizeGDB and are also included as supplemental material in the publication. Probes monomorphic on the IBM are mapped on a second population, and those maps are called LHRFGnp2004.
Also newly added are the maize recombination nodule (RN) maps <http://www.maizegdb.org/RNmaps.php> reported by Anderson, L.K. et al., Genetics 165:849-865, 2003. Since the publication of the RN distribution for all ten chromosomes in maize, Anderson and others (Genetics 166:1923-1933, 2004) demonstrated that the distribution of RNs along the maize pachytene chromosome structure could be used to accurately predict physical, cytological map locations for loci mapped genetically (Anderson, L.K. et al.). In an effort to automate that process, a new tool called the ‘Morgan2McClintock Translator’ has been created by Lawrence, C.J., Seigfried, T.E., Bass, H.W., and Anderson, L.K. (manuscript in preparation). The alpha version of this new tool is currently accessible through the RN map data page (see above).
The Genetic 2005 maps, provided by Ed Coe (see this Newsletter, pages 116-126). This re-working includes a total of 2465 loci: a frame of 400 well-ordered loci largely from the Genetic 1997 maps, and also 754 from the UMC 98 RFLP maps. Establishing a well-ordered framework integrated with one of the maps that can be projected onto the IBM2 map means that many loci, in particular, those with empirically determined and confirmed functions, can be incorporated into the IBM neighbors consensus maps. Genes and breakpoints added to the IBM2 neighbors by this resource include:
Chromosome 1. T1-2a(1), T1-2b(1), T1-2c(1), T1-3a(1), T1-3k(1), T1-4b(1), T1-5(6899)(1), T1-6b(1), T1-6c(1), T1-7a(1), T1-7c(1), T1-9(8389)(1), T1-9b(1), T1-9c(1), TB-1La(1), TB-1Sb(1), ad1, amp1, bm2, br1, br2, cp3, d8, dek1, dia2, f1, gs1, gsr1, hsp26, ij2, l16, les2, lw1, mmm1, mpl1, ms17, ms9, msv1, nec2, obf1, pgm1, ptd1, rd1, sr1, tb1, ts6, vg1, vp5, vp8, zb4, zb7.
Chromosome 2. T2-10a(2), T2-3(5304)(2), T2-3(6270)(2), T2-3a(2), T2-3c(2), T2-5a(2), T2-5g(2), T2-9b(2), agp1, akh2, al1, ba2, ch1, d5, emp2, fl1, gl11, gl14, gl2, gn1, ht1, les1, les10, les15, lg1, nec4, px1, rDNA5S, rf3, sk1, sks1, ts1, v24, v4, wlv1, ws3, wt1.
Chromosome 3. K3L, T1-3(5597)(3), T1-3(8995)(3), T3-9(8447)(3), TB-3La(3), TB-3Lc(3), TB-3Sb(3), a3, ba1, brn1, cg1, cl1, cr1, d1, et1, ga7, gl6, hex1, ig1, lxm1, mv1, na1, pm1, ra2, rf1, rp3, rt1, sdw2, spc1, te1, ts4, w19, wlu1, wrk1, wsm2, y10, ys3.
Chromosome 4. Dt6, T1-4b(4), T4-7(4698)(4), T4-9g(4), TB-4Sa(4), TB-4Sg(4), akh1, als1, cp2, dsc1, dzr1, gl3, gl4, gl5, gl7, la1, lw4, mdr1, ms41, ms44, ns2, o1, ra3, sos1, su1, tga1, tu1, v17, v8, zrp4.
Chromosome 5. T1-5(8041)(5), T1-5b(5), T5-6b(5), T5-9(4817)(5), TB-5La(5), TB-5Lb(5), TB-5Ld(5), TB-5Sc(5),ae1, als2, am1, anl1, bm1, bv1, d9, dap1, dek33, ga2, gl17, got3, gpc4, hsf1, lu1, lw2, lw3, na2, nec3, nec6, nl2, pr1, ps1, ren1, sh4, td1, v12, v3, vp2.
Chromosome 6. Dt2, NOR, T4-6(6623)(6), T4-6(8428)(6), T6-9(043-1)(6), T6-9(6019)(6), T6-9e(6), TB-6Lc(6), TB-6Ld(6), TB-6Sa(6), adk1, l10, l11, l12, l15, ln1, mdm1, mn3, ms1, pg11, po1, rgd1, rhm1, sm1, su2, tan1, w1, w14, w15, wi1, wsm1.
Chromosome 7. TB-7Lb(7), TB-7Sc(7), les9, lhcb2, mn2, nbp1, o15, o5, pep4, px3, ra1, ren2, rs4, sl1, sod2, tp1, v5, va1, vp9, w16, w17, y8.
Chromosome 8. TB-8Lc(8), clt1, emp3, fl3, ht2, htn1, j1, lg4, ms8, pdc2, pro1, rf4, rgh1.
Chromosome 9. Dt1, T8-9a(9), T9-10b(9), TB-9La(9), TB-9Lc(9), TB-9Sb(9), TB-9Sd(9), ar1, baf1, bf1, bk2, bm4, eno1, g6, l7, les8, lo2, ms2, obf2, pg12, pyd1, rld1, trn1, v1, v30, v31, w11, wc1, wd1, yg2, zb8.
Chromosome 10. TB-10L14(10), TB-10L15(10), TB-10L16(10), TB-10L18(10), TB-10L19(10), TB-10L2(10), TB-10L20(10), TB-10L21(10), TB-10L22(10), TB-10L23(10), TB-10L26(10), TB-10L32(10), TB-10L36(10), TB-10L6(10), TB-10L7(10), TB-10La(10), TB-10Lb(10), TB-10Sc(10), bf2, cx1, du1, g1, isr1, l1, l13, lc1, li1, mac1, ms10, ms11, mst1, nl1, o7, og1, oy1, rp1, rp5, rp6, rps11, sn1, sr2, tp2, w2, wsm3, y9, zn1.
IBM2 2005 Neighbors, provided by MaizeGDB. These maps are computed by a reiterative projection algorithm (Polacco M. et al., MNL 77:137-179, 2003). IBM2 neighbors relies on the IBM2 framework of 1552 statistically well-defended ordered and maps curated in MaizeGDB which share some commonality with IBM2. The 2005 version adds new genetically mapped loci described above; and over 20,000 loci identified by SSR and Overgo probing of BACs and whose genetic map order is defined by their positions on anchored BAC contigs (www.genome.arizona.edu/fpc/maize).
New ‘Community Curation Tools’
Small datasets can be added directly to the database using a new set of Web-accessible Java-based Community Curation Tools that are currently available for general use. Datatypes accessible through these tools include: Clone Library, Gel Pattern, Gene Product, Linkage Group, Locus, Map, Map Scores, Panel Of Stocks, Person, Phenotype, Primer/Enzyme, Probe, Recombination Data, Reference, Species, Stock, Term, and Variation. A QTL data entry tool is under development and is expected to be available for use in the near future. As always, large datasets can be made available through MaizeGDB by special arrangement. Use the feedback form at the bottom of any page at MaizeGDB to request information on Community Curation or to enquire about how to get a large dataset into the database directly.
Other information about MaizeGDB may be found in 2 recent publications, accessible as full text through MaizeGDB:
Lawrence, CJ, Seigfried, TE, and Brendel, V., 2005. The Maize Genetics and Genomics Database. The community resource for access to diverse maize data. Plant Physiology 138:55-58.
Lawrence, CJ, Dong, Q, Polacco, ML, Seigfried, TE, and Brendel, V., 2004. MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Research 32:D393-D397.
Submitted by Mary Schaeffer and Carolyn Lawrence