NetNews Usenet Archive 1992 #31

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Path: sparky!uunet!biosci!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) Newsgroups: bionet.genome.arabidopsis Subject: Linkage Data Summary for Visible Markers Message-ID: <921230105336.20c030ac@Frodo.MGH.Harvard.EDU> Date: 30 Dec 92 15:53:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 461 [ Note: A printed copy of the following table, created by David Meinke, was included in the recent postal mailing from the ABRC at Ohio State. This table is now electronically available from the Arabidposis Research Companion Gopher in the "Arabidopsis Genetic Maps and Tables" folder. The information contained within this table has been incorporated into the AAtDB database available via gopher and wais. The next version of the Unix AAtDB database, release 1-4, will also contain this information. Special thanks go to David Meinke for volunteering to be the Genetics Curator for Arabidopsis. Mike Cherry AAtDB Project ] Linkage Data - Mutant Gene Markers of Arabidopsis thaliana Explanation of Attached Information David W. Meinke (12/15/92) The attached information summarizes existing linkage data for mutant genes of Arabidopsis thaliana. Information on molecular markers and cloned wild- type genes is not included. This table was constructed in response to the mapping survey recently distributed to the Arabidopsis community. The main purpose of this table is to summarize information on linked visible markers and approximate map locations for mutant genes. Over 260 genetic loci are included in this table. Contributors will be asked in the future to submit recombination data in a standardized format to facilitate construction of updated maps. Forms and additional information will be distributed to the Arabidopsis community in the near future. Please send additions and/or corrections to this linkage table to: David Meinke, curator: FAX 405-744-7673; phone 405-744-6549; email: btnydwm@osucc.bitnet; or to Mike Cherry (curator@frodo.mgh.harvard.edu). Additional information on each column of this table is presented below. Mutant Locus: This lists each mutant locus for which recombination data are available. I have added a space between the gene symbol and locus number to avoid confusion between the letter "l" and the number "1". Linkage Group: (Self-explanatory) Map: This reveals the current status of the locus with respect to mapping. M: The mutant locus is included on the attached visible marker map. R: The mutant locus should be ready to add to the visible marker map once recombination data are obtained in the appropriate format. X: The mutant locus is not ready to place on the map, often because recombination data are available for only a single linked marker. U: The precise status of this locus with respect to placement on the map is currently unresolved. Closest Marker Tested: This shows the most closely-linked visible marker (already on the map) for which recombination data with the mutant locus in question are available. Other visible markers may be more closely linked, but recombination data with those markers have not been reported. In some cases, no recombinants were found among relatively small populations of F2 plants. Recombination estimates (0.00) for these markers were frequently misleading and inconsistent with data for other closely-linked markers. Information on additional linked markers has therefore been included for these mutants. Molecular markers are included in this column only if recombination data for linked visible markers are not available. r: This shows the recombination estimate (%) between the mutant locus in column #1 and the most closely-linked marker tested in column #4. A/B: This summarizes what is known about the relative orientation of the mutant locus and linked marker. A: The mutant locus in column 1 has been definitively shown to be Above the marker on the genetic map. This fixed order has also been given to JOINMAP. B: The mutant locus in column 1 has been definitively shown to be Below the marker on the genetic map. This fixed order has also been given to JOINMAP. *: The fixed order noted above is not reflected on the current map because it is somewhat inconsistent with other 2-point data and was consequently rejected by JOINMAP. Efforts are underway to resolve the inconsistencies associated with these fixed orders. a: If the mutant locus is on the map, then JOINMAP has placed this locus above the closest tested marker shown in column 4, though this location has not been confirmed. In the remaining cases, other data indicate that the mutant locus is above the marker. b: Same as described above for "a", but in this case, the mutant locus is below the tested marker. LOD: This calculation performed by JOINMAP illustrates the certainty of tight linkage between the mutant locus and tested marker. A high LOD score indicates a high degree of certainty of tight linkage between the two genes. High LOD scores result from large F2 populations, small standard errors, and small recombination estimates. Current Location: This shows the current estimated map location of the mutant locus on the attached visible marker map constructed by JOINMAP with visible marker data only. Reference Laboratory: This lists the laboratory that contributed the recombination data for the mutant locus and most closely-linked visible marker. Other laboratories may have initially placed the mutant locus on the map or contributed additional recombination data. This column has been left blank if the source of the corresponding recombination data has not yet been identified. Suggested Protocol for the Future: Place greater emphasis on mapping the chromosomal location of your favorite mutant gene prior to publication. Perform complementation tests between your mutant and other closely-linked mutants with related phenotypes. Report preliminary linkage information for your mutant gene as soon as possible by contacting David Meinke at 405-744-6549 (phone), 405-744-7673 (FAX), or btnydwm@osucc.bitnet (email). Initial linkage assignments may be reported even before the precise map location has been determined. Direct submission of mapping data to existing databases is planned for the future. Summary of Current Linkage Data Mutant Gene Markers - Arabidopsis thaliana Updated December 15, 1992; David W. Meinke See Attached Page for Explanations of Columns ______________________________________________________________________________ Closest Mutant Linkage Marker Current Reference Locus Group Map Tested r A/B LOD Location Laboratory ______________________________________________________________________________ aba 5 M min 6.8 b 13.6 97.1 Koornneef abi1 4 M cer2 3.0 b 31.4 50.4 Koornneef abi2 5 R tz - - - - Finkelstein abi3 3 M gl1 10.2 a 113.6 37.9 Koornneef aca1 5 X - - - - - Lehle acd1 3 R gl1 20.7 b - - Ausubel acd2 4 X ap2 - - - - Ausubel act1 1 M an 30.1 B 2.8 35.3 Somerville adh 1 R clv1 5.5 a - - Meyerowitz ag 4 M ch42 2.8 a 20.6 38.1 Koornneef alb1 1 M ga4 0.0 A 5.6 12.1 Koornneef dis1 10.4 a 145.0 - Koornneef alb2 5 M co 1.2 b 50.5 15.8 Koornneef amt1 5 X ASA-1 <1.0 - - - Town an 1 M emb76 0.4 B* 165.1 1.0 Meinke ap1 1 M cer6 2.3 b 3.9 100.8 Koornneef ap2 4 M cer4 0.0 b 5.7 64.0 Koornneef fad4 0.0 a 5.1 - Somerville fd 1.2 b 103.9 - Koornneef ap3 3 M tt5 0.0 b 60.2 84.6 Koornneef gl1 35.6 B 5.3 - Koornneef ara1 4 M fca 0.2 b - 32.5 Cobbett as 2 M re 0.0 b 5.1 58.2 Koornneef emb18 0.6 A* 106.3 - Meinke aux 2 M hy1 14.7 a 7.8 23.9 Koornneef axr1 1 R dis1 6.6 a - - Estelle axr2 3 M gl1 12.5 a 22.2 33.8 Estelle axr3 1 R axr1 1.0 a - - Estelle bio1 5 M tz 3.7 a 102.2 74.5 Meinke bp 4 M emb178 2.0 a 79.2 8.6 Meinke cad1 5 U tt3 - - - - Cobbett cer1 1 M an 0.7 b 71.5 1.7 Koornneef cer2 4 M emb140 0.0 - 100.3 48.1 Meinke fad6 0.0 a 6.7 - Somerville ga5 1.1 a 245.6 - Koornneef cer3 5 M lfy 0.0 a 11.2 82.3 __________ tz 5.1 b 276.7 - Koornneef cer4 4 M ap2 0.0 a 5.7 57.0 Koornneef ga5 0.0 b 2.4 - Koornneef cp3 14.5 a 9.4 - Koornneef cer5 1 M ch1 0.0 b 5.2 71.2 Koornneef clv2 16.2 a 3.8 - Koornneef cer6 1 M ap1 2.3 a 3.9 97.2 Koornneef cer7 3 M emb78 0.4 b 165.1 90.9 Meinke cer8 2 M emb39 0.3 a 97.1 70.0 Meinke cer9 4 M ap2 8.6 b 8.1 72.4 Koornneef ch1 1 M cer5 0.0 a 5.2 59.5 Koornneef emb22 3.9 a 134.4 - Meinke ch5 5 M th2 0.0 a 5.8 43.6 Koornneef tt2 1.6 a 34.5 - Koornneef ch6 3 M tt5 2.9 b 107.4 87.3 Koornneef ch42 4 M ag 2.8 b 20.6 39.7 Koornneef chl1 1 M dis1 2.6 a 108.3 14.6 Koornneef chl2 2 M er 11.6 a 75.6 31.0 Koornneef chl3 1 M ch1 6.2 a 51.7 55.9 Koornneef chl5 2 X - - - - - Crawford chl6 (cnx) 5 R - - - - - Crawford chm 3 M gl1 15.0 a 149.8 31.0 Koornneef chp7 5 M co 5.6 a 37.9 9.1 Koornneef chs1 1 M an 28.6 b 9.3 33.5 Somerville ckr1 5 U - - - - - Howell clv1 1 M emb36 3.7 a 68.4 111.4 Meinke clv2 1 M ft 0.0 b 6.3 90.7 Koornneef emb158 2.3 b 70.3 - Meinke cn 4 X cer2 20 a - - Relichova cnx 5 R - - - - - Koornneef co (fg) 5 M alb2 1.2 a 50.4 14.4 Koornneef cop1 2 M as 3.1 A 72.4 54.3 Meinke cp1 4 M ag 13.1 a 191.7 24.2 Koornneef cp2 2 M hy1 0.0 a 6.5 32.6 Koornneef hy3 0.0 b 5.7 - Koornneef fve 5.8 b 30.6 - Koornneef cp3 4 M ap2 11.2 b 6.2 73.9 Koornneef crc 1 R ap1 - - - - Smyth csi 4 X bp - - - - Sussman csr 3 M tt5 9.0 a 24.1 74.6 Koornneef ctr1 5 R tt4 10.8 a - - Ecker det1 4 R bp 5 b - - Chory det2 2 R er - b - - Chory dis1 1 M emb30 2.2 A* 239.1 18.6 Meinke dis2 1 M gi 0.0 b 7.0 44.7 Koornneef emb88 1.8 b 72.3 - Meinke dw1 (dwf) 1 M gai 0.3 b 218.5 22.9 Koornneef dwf1 3 U - - - - - _________ ein1 1 R ap1 7 a - - Ecker ein2 5 R m217 2.7 a - - Ecker eir1 5 R tt3 12.4 b - - Ecker elf 2 U hy1 - - - - Meeks-Wagner emb9 5 M tt3 1.6 b 85.3 60.0 Meinke emb14 1 X clv2 24.4 - - - Meinke emb15 5 M yi 0.3 a 97.1 86.2 Meinke emb16 5 M yi 4.4 b 115.6 91.1 Meinke emb18 2 M as 0.6 B* 106.3 56.4 Meinke emb20 4 M cer2 1.4 B 237.9 50.4 Meinke emb22 1 M ch1 3.9 b 134.4 63.0 Meinke emb24 5 M lu 8.2 a 52.3 2.4 Meinke emb25 1 M clv1 6.2 a 40.3 101.3 Meinke emb28 4 M cer2 5.2 b 163.5 54.4 Meinke emb29 3 M hy2 10.7 b 45.2 23.6 Meinke emb30 (gn) 1 M dis1 2.2 B* 239.1 15.0 Meinke emb33 1 M clv1 5.4 b 47.6 115.9 Meinke emb34 2 M sti 2.3 a 70.3 0.0 Meinke emb35 4 M cer2 4.2 b 141.7 52.4 Meinke emb36 1 M gl2 3.3 a 76.0 115.9 Meinke emb39 2 M cer8 <0.3 b 97.1 71.3 Meinke emb43 1 M dis2 16.0 a 25.7 26.7 Meinke emb49 2 X er 14.9 - - - Meinke emb51 3 X gl1 26.3 a - - Meinke emb52 3 M hy2 9.3 a 43.4 2.8 Meinke emb53 2 X er 8.8 - - - Meinke emb55 2 X er 32.5 - - - Meinke emb56 4 X cer2 5.0 - - - Meinke emb57 2 X er 23.1 - - - Meinke emb58 2 X er 24.2 - - - Meinke emb59 5 X tt3 19.6 - - - Meinke emb62 2 X er 39.2 - - - Meinke emb64 5 M tt3 12.9 b 31.1 72.2 Meinke emb65 3 X gl1 14.3 - - - Meinke emb66 2 X er 13.7 - - - Meinke emb67 5 R yi 5.3 a - - Meinke emb69 3 R tt5 8.1 - - - Meinke emb70 4 X cer2 5.4 - - - Meinke emb71 1 M clv2 5.4 a 63.4 85.3 Meinke emb76 1 M an 0.4 A* 165.1 3.7 Meinke emb78 3 M cer7 0.4 a 165.1 90.2 Meinke emb86 5 M ttg 4.3 a 113.8 25.2 Meinke emb87 5 M yi 0.3 a 97.1 86.1 Meinke emb88 1 M dis2 1.8 a 72.3 42.3 Meinke emb93 2 M sti 2.0 b 79.2 6.3 Meinke emb95 3 M hy2 9.0 b 42.3 23.7 Meinke emb101 2 M as 1.6 b 149.4 59.3 Meinke emb104 4 M cer2 14.8 B 26.0 63.4 Meinke emb106 4 X cer2 1.4 - - - Meinke emb107 4 X cer2 7.4 b - - Meinke emb108 5 X tt3 30.5 - - - Meinke emb109 4 M cer2 14.3 a 28.5 34.5 Meinke emb110 1 X ch1 13.1 - - - Meinke emb111 2 M as 3.4 B 64.2 62.6 Meinke emb115 4 X cer2 28.0 - - - Meinke emb116 5 X ttg 23.5 - - - Meinke emb117 3 M tt5 4.2 a 63.0 80.1 Meinke emb118 1 M ch1 9.0 b 42.9 70.6 Meinke emb120 1 X ch1 38.8 - - - Meinke emb125 3 M gl1 10.0 a 44.4 37.1 Meinke emb127 1 M dis1 10.2 b 36.2 28.7 Meinke emb128 1 M clv2 14.7 a 28.4 77.9 Meinke emb130 4 M cer2 6.7 a 100.4 42.3 Meinke emb131 1 R dis1 9.6 - - - Meinke emb132 4 X cer2 22.7 - - - Meinke emb133 3 X gl1 35.1 - - - Meinke emb134 5 X gl3 11.3 - - - Meinke emb135 2 X er 23.9 - - - Meinke emb140 4 M cer2 <0.3 - 100.3 48.1 Meinke emb141 5 R tt3 1.1 - - - Meinke emb142 1 M dis1 3.5 b 55.2 21.9 Meinke emb144 3 X gl1 24.4 - - - Meinke emb145 3 M hy2 11.5 a 66.1 0.0 Meinke emb146 2 X er 35.6 - - - Meinke emb148 4 M bp 12.2 b 34.0 21.6 Meinke emb149 3 M tt5 4.5 a 66.1 78.3 Meinke emb152 2 M er 3.9 B 134.4 45.7 Meinke emb154 3 M tt5 6.4 a 52.7 78.0 Meinke emb155 4 X cer2 4.5 - - - Meinke emb158 1 M clv2 2.3 a 70.3 88.3 Meinke emb163 5 M ttg 20.1 a 17.0 8.0 Meinke emb173 1 M an 1.8 b 94.5 5.9 Meinke emb175 5 M ttg 22.3 a 12.7 7.5 Meinke emb176 1 M dis1 6.5 b 53.1 24.8 Meinke emb177 1 M gl2 1.6 a 85.3 117.4 Meinke emb178 4 M bp 2.0 b 79.2 10.9 Meinke emb179 1 X clv2 13.8 - - - Meinke emb181 4 M cer2 7.6 b 50.5 55.8 Meinke emb224 3 X gl1 11.5 - - - Meinke er 2 M hy1 2.0 b 116.5 42.3 Koornneef eto 5 R yi 2.2 - - - Ecker etr 1 R clv2 4 b - - Bleecker fad2 3 R g2488-9 2.0 b - - Somerville fad3 2 R ASA2 0.4 a - - Somerville fad4 (A) 4 M ap2 0.0 b 5.1 65.2 Somerville cer2 16.8 b 6.9 - Somerville fad5 (B) 3 M hy2 0.0 b 3.6 15.4 Somerville gl1 25.7 a 6.1 - Somerville fad6 (C) 4 M cer2 0.0 b 6.7 49.2 Somerville ap2 12.8 a 5.0 - Somerville fad7 (D) 3 M hy2 2.6 a 43.7 8.0 Somerville fas1 1 U gl2 29 a - - Furner fas2 5 U yi 33 a - - Furner fca 4 M th3 5.2 a 19.1 28.4 Koornneef fd 4 M ga5 0.0 b 5.4 59.9 Koornneef ap2 1.2 a 103.9 - Koornneef fe 1 M gl2 0.0 b 4.9 123.4 Koornneef ap1 21.9 b 19.3 - Koornneef fha 1 M ga4 10.8 A 10.0 11.7 Koornneef fk 3 R tt5 4 a - - Jurgens fl 1 X an 41 b - - Relichova flo10 (sup) 3 R axr2 0.7 - - - Haughn fpa 2 M cer8 16.9 b 5.2 81.6 Koornneef fri 4 X 3843 6.2 - - - Dean fs 5 U ttg 5 - - - Jurgens ft 1 M clv2 0.0 a 6.3 89.7 Koornneef ap1 11.7 a 71.9 - Koornneef fus2 4 R bp 5 b - - Jurgens fus3 3 X gl1 5.0 a - - Muller fus7 4 U bp 20 b - - Jurgens fus9 3 R hy2 10 b - - Jurgens fus12 2 R py 5 a - - Jurgens fve 2 M hy3 4.4 a 19.4 26.0 Koornneef fwa 4 M ga5 2.1 B 65.2 50.9 Koornneef fy 5 M ttg 20.0 a 5.2 0.4 Koornneef ga1 4 M bp 10.2 a 30.0 0.0 Koornneef ga2 1 M gl2 0.0 b 9.4 120.5 Koornneef clv1 9.0 b 177.3 - Koornneef ga3 5 M ttg 4.0 b 367.1 33.7 Koornneef ga4 1 M alb1 0.0 b 5.6 22.5 Koornneef gai 0.1 a 297.3 - Koornneef ga5 4 M cer4 0.0 a 2.4 48.6 Koornneef fd 0.0 a 5.4 - Koornneef cer2 1.1 B 245.6 - Koornneef gai 1 M ga4 0.1 b 297.3 22.6 Koornneef gf 2 U - - - - - Redei gi (fb) 1 M dis2 0.0 a 7.0 33.9 Koornneef ga4 11.1 b 76.7 - Koornneef gl1 3 M sup 8.5 b 20.0 46.5 Koornneef gl2 1 M fe 0.0 a 4.9 119.6 Koornneef ga2 0.0 a 9.4 - Koornneef emb177 1.6 b 85.3 - Meinke gl3 5 M tt2 0.0 b 5.8 54.4 Koornneef tt3 0.0 a 4.6 - Koornneef ga3 18.9 b 43.4 - Koornneef gr 5 U gl3 17 b - - Relichova grl 2 X as - - - - Jurgens hls1 4 U cer2 9.3 b - - Ecker hls2 4 U cer2 13.4 a - - Ecker hy1 2 M cp2 0.0 b 6.5 41.4 Koornneef er 2.0 a 116.5 - Koornneef hy2 3 M fad5 0.0 a 3.6 10.9 Somerville fad7 2.6 b 43.7 - Somerville hy3 2 M cp2 0.0 a 5.7 28.9 Koornneef fve 4.4 b 19.4 - Koornneef hy4 4 M fca 17.9 a 3.5 5.6 Koornneef hy5 5 M ms1 15.4 a 96.8 8.8 Koornneef hy6 2 U det2 11.7 a - - Chory im 4 M cer2 3.5 a 47.0 44.5 Koornneef keu 1 R dis1 5 a - - Jurgens klk 5 X ttg - b - - Jurgens kn 1 U dis1 10 a - - Jurgens le 1 M ch1 7.9 b 834.8 67.4 Koornneef lec 1 M dis1 8.8 b 42.5 28.5 Meinke lfy 5 M cer3 0.0 b 11.2 82.9 Haughn tz 9.0 b 20.6 - Haughn lu 5 M tt4 1.5 a 13.7 11.6 Koornneef min 5 M aba 6.8 a 13.6 89.9 Koornneef mp 1 U an 36 b - - Jurgens ms1 5 M tt7 0.0 b 5.0 23.8 Koornneef ttg 5.9 a 913.3 - Koornneef nia1 1 R gl2 3.0 - - - Crawford pgm 5 M yi 22.1 a 16.9 64.5 Koornneef pho1 3 R g4708 3.1 b - - Somerville pi 5 M ttg 9.7 a 46.9 21.5 Koornneef pid 2 R as - - - - Smyth py 2 M hy1 5.0 b 60.4 47.7 Koornneef rac1 1 R m299/m33 - - - - Benyon re 2 M as 0.0 a 5.1 57.2 Koornneef er 18.6 b 12.1 - Koornneef rgn (chl4) 1 M an 0.6 a 188.9 0.0 Koornneef rhd1 1 X ap1 - - - - Schiefelbein rhd2 5 X tt3 - - - - Schiefelbein rhd3 3 X gl1 - - - - Schiefelbein rhd4 3 X gl1 - - - - Schiefelbein rpm1 3 R - - - - - _________ rpp1 3 R gl1 - - - - Benyon rpp2 4 R m600/m55 - - - - Benyon sex1 1 M an 12.2 b 5.0 13.5 Caspar spt 4 R ap2 - - - - Smyth sti 2 M emb93 2.0 a 79.2 3.4 Meinke su 5 M ttg 7.2 b 87.5 36.1 Koornneef sul 2 M as 9.6 b 222.0 68.1 Koornneef sup (flo10) 3 M gl1 8.5 a 20.0 34.5 __________ tfl 5 M tt4 14.7 a 26.1 0.0 __________ th1 1 M gi 0.0 - - 33.9 Koornneef th2 5 M ch5 0.0 b 5.8 47.6 Koornneef tt2 0.6 b 44.7 - Koornneef th3 4 M fca 5.2 b 19.9 30.1 Koornneef trp1 5 U tt4 - - - - Last trp2 5 U - - - - - Last tt1 1 M ch1 4.4 A 14.4 55.6 Koornneef tt2 5 M gl3 0.0 a 5.8 45.2 Koornneef th2 0.6 a 44.7 - Koornneef tt3 5 M gl3 0.0 b 4.6 58.1 Koornneef emb9 1.6 a 85.3 - Meinke tt4 5 M lu 1.5 b 13.7 14.1 Koornneef tt5 3 M ap3 0.0 a 60.2 84.1 Koornneef ch6 2.9 a 107.4 - Koornneef tt6 3 M gl1 38.0 b 2.1 96.7 Koornneef tt7 5 M ms1 0.0 a 5.0 7.1 Koornneef alb2 10.4 a 40.3 - Koornneef ttg 5 M ga3 4.0 a 367.1 29.5 Koornneef tz 5 M bio1 3.7 b 102.2 77.2 Meinke uvh1 3 X g2778 - a - - Mount uvh3 3 X gl1 0.1 a - - Mount var1 5 U cer3 18.2 a - - Martinez-Zapater var2 2 U er 22.6 b - - Martinez-Zapater vr2 2 U - - - - - Redei xv 1 U - - - - - Redei yi 5 M emb15 0.3 b 97.1 86.5 Meinke ______________________________________________________________________________