A set of microsatellite markers of general utility in maize

A set of microsatellite markers of general utility in maize --Register, JC, III*, Sullivan, HR, Yun, Y, Cook, D, Vaske, DA
* To whom correspondence should be addressed. Over the past several years microsatellites (often referred to as simple sequence repeats [SSRs] or short tandem repeats [STRs]) have become the most commonly used class of molecular marker for high-throughput genotyping of many higher eukaryotes including maize. During this time we (and others at Pioneer Hi-Bred Int'l Inc.) have, in collaboration with public researchers, made well over 100 SSR markers available for public use (Chin ECL, Senior ML, Shu H, Smith JSC [1996] Genome 39, 866-873; Senior ML, Chin ECL, Lee M, Smith JSC, Stuber CW [1996] Crop Sci 36, 1676-1683; Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J [1997] Theor Appl Genet 95, 163-173; also see Maize Genome Database - http://mnl.maizegdb.org ). As is always the case for this kind of resource, broad application of these markers has demonstrated that, for various reasons, some are more useful (i.e. robust, informative, easily scorable, etc.) than are others. We report here on the subset of those markers that we have found to be most useful for our applications.

All PCR primers were designed to work under a single set of conditions in 10 ml reactions. Genomic DNA (10 ng) was amplified in 1.5 mM MgCl2, 50 mM KCl, 10 mM Tris-Cl (pH 8.3) using 0.3U AmpliTaq Gold DNA polymerase (PE Corporation), oligonucleotide primer pairs at 0.17 mM and 0.2 mM dNTPs. This mixture was incubated at 95 C for 10 min (hot start), then amplified by 45 cycles of: denaturation, 95 C for 50 sec; annealing, 60 C for 50 sec; extension, 72 C for 85 sec, followed by a final 10 min 72 C incubation. A water bath thermocycler manufactured at Pioneer Hi-Bred Int'l Inc. was used. PCR products were prepared for analysis using ABI377 Automated DNA Sequencers (PE Corporation) by diluting 3 ml of each product to a total of 27 ml using a combination of other PCR products (multiplexing) and/or dH2O. 1.5 ml of this mixture was then diluted to 5 ml with gel loading dye and analyzed using ABI hardware and software according to manufacturer�s specifications.

The Table below lists approximately 80 markers and relevant associated information. For some markers, PCR primers have been redesigned since their initial publication for optimal performance under the conditions described above. The Table also notes the fluorescent dyes with which each marker is labeled. Minimum and maximum allele sizes were obtained by rounding down or up to the nearest basepair respectively. These sizes and PIC values (Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J [1997] Theor Appl Genet 95, 163-173) were obtained from an analysis of over 500 Pioneer Hi-Bred Int'l Inc. proprietary maize genotypes. Even though the PIC and allele range values were obtained working with proprietary Pioneer Hi-Bred Int'l Inc. germplasm, we do know that the values presented here are largely representative of North American dent germplasm in general.

MARKER CHROM DISTANCE BIN REPEAT PRIMER SEQUENCE (F / R) MIN/MAX ALLELE* PIC NEARBY LOCI**

phi109275 1 0 1.00 AGCT 6FAMCGGTTCATGCTAGCTCTGC 122 / 140 0.77 umc274, umc275

GTTGTGGCTGTGGTGGTG

phi056 1 9 1.01 CCG NEDACTTGCTTGCCTGCCGTTAC 239 / 259 0.67 rgpc654, bnlg149

CGCACACCACTTCCCAGAA

phi427913 1 26.71 1.01 ACG NEDCAAAAGCTAGTCGGGGTCA 123 / 131 0.23 bnlg1112, bnlg1458

ATTGTTCGATGACACACTACGC

phi339017 1 72 1.01 AGG HEXACTGCTGTTGGGGTAGGG 147 / 157 0.34 csu745d, bnlg2180

GCAGCTTGAGCAGGAAGC

phi002 1 173.9 1.08 AACG HEXCATGCAATCAATAACGATGGCGAGT 71 / 80 0.51 csu580a, bnl17.06

TTAGCGTAACCCTTCTCCAGTCAGC

phi423298 1 174 1.08 CCG NEDGGGCTGCTACTTTGACAAGGAC 128 / 135 0.43 bnl17.06, umc83a

CCTCCATCATCCGCTGGTA

phi323065 1 179 1.08 AGC HEXGATCGATCGACGACCAGC 327 / 334 0.53 csu531, cdo680a

CTTCTGCGTGGGCAAAGA

phi335539 1 181.37 1.08 CCG HEXGAGTCCGCTGAAATTTTGGT 90 / 93 0.17 csu1174, csu745e

TAGAAGCCGCCGTGCCTAT

phi011 1 209 1.09 AGC HEXTGTTGCTCGGTCACCATACC 212 / 232 0.44 npi282b, uat4a

GCACACACACAGGACGACAGT

phi308707 1 220 1.09 AGC HEXGCAACAAGATCCAGCCGAT 118 / 125 0.39 umc161a, csu63a

GTCGCCCTCATATGACCTTC

phi265454 1 224.63 1.10 AGG 6FAMCAAGCACCTCAACCTCTTCG 220 / 238 0.61 npi238, csu868

TCCACGCTGCTCACCTTC

phi064 1 231 1.11 ATCC 6FAMCCGAATTGAAATAGCTGCGAGAACCT 73 / 110 0.83 csu33b, csu755

ACAATGAACGGTGGTTATCAACACGC

phi227562 1 266 1.11 ACC 6FAMTGATAAAGCTCAGCCACAAGG 309 / 325 0.78 csu1114, csu1193

ATCTCGGCTACGGCCAGA

phi109642 2 0 2.00 ACGG 6FAMCTCTCTTTCCTTCCGACTTTCC 133 / 145 0.58 csu1192, dup1383

GAGCGAGCGAGAGAGATCG

phi402893 2 0 2.00 AGC HEXGCCAAGCTCAGGGTCAAG 209 / 237 0.73 csu1192, dup1383

CACGAGCGTTATTCGCTGT

phi96100 2 6.04 2.00 ACCT 6FAMAGGAGGACCCCAACTCCTG 268 / 297 0.76 rz569b, csu29b

TTGCACGAGCCATCGTAT

phi083 2 86 2.04 AGCT NEDCAAACATCAGCCAGAGACAAGGAC 125 / 139 0.76 bnlg1831, umc184b

ATTCATCGACGCGTCACAGTCTACT

phi328189 2 145 2.08 CCG HEXACGCTCGAAGCAAATCCT 118 / 125 0.64 csu1103, uaz241b

TCGCGCTTGGTAGACGTA

phi251315 2 147.34 2.08 CCG 6FAMCCAGTCCAATGGAGAGGG 126 / 132 0.47 umc88(P450), umc36b

GAGATTCCCCTGCAGGACT

phi127 2 149.79 2.08 AGAC NEDATATGCATTGCCTGGAACTGGAAGGA 110 / 129 0.7 umc4a, bcd808c

AATTCAAACACGCCTCCCGAGTGT

phi435417 2 161 2.08 ACC NEDCTGACGCCACTGTTGCTTG 215 / 220 0.6 uaz239b, bnl8.44b

AAAAGTAGCCAATCTGCCACG

phi090 2 174 2.09 ATATC 6FAMCTACCTATCCAAGCGATGGGGA 139 / 150 0.44 bnlg1520, csu304a

CGTGCAAATAATTCCCCGTGGGA

phi427434 2 186.05 2.08 ACC NEDCAACTGACGCTGATGGATG 123 / 139 0.7 csu200a, csu109a

TTGCGGTGTTAAGCAATTCTCC

phi101049 2 194 2.08 AGAT 6FAMCCGGGAACTTGTTCATCG 229 / 249 0.8 csu665a, csu810a

CCACGTCCATGATCACACC

phi453121 3 0 3.00 ACC NEDACCTTGCCTGTCCTTCTTTCT 213 / 225 0.74 bnl(tas4l), umc32a

CAAGCAAGACTTTTGATCAGCC

phi104127 3 6.88 3.00 ACCG 6FAMCTTTGCTGCTGCTTCCTACG 156 / 166 0.58 php20905, csu628

AACCAGTGACGTACACAAAGCA

phi243966 3 46.8 3.02 AGC 6FAMCGACCGAAACGAATCAAAA 210 / 228 0.63 bnlg1647, umc154

TACTAGGCTGACACGCACG

phi374118 3 52 3.02 ACC HEXTACCCGGACATGGTTGAGC 216 / 230 0.72 umc92a, bnlg2136

TGAAGGGTGTCCTTCCGAT

phi193225 3 55 3.02 AAC 6FAMGCTCTTGGCGTGCTTCTT 133 / 141 0.72 umc92a, bnlg2136

GCGGGGAGGTGAAGAGCTA

phi053 3 67.9 3.05 ATAC 6FAMCTGCCTCTCAGATTCAGAGATTGAC 168 / 195 0.71 cdo459, cdo419a

AACCCAACGTACTCCGGCAG

phi029 3 91 3.04 AG/AGCG*** NEDTTGTCTTTCTTCCTCCACAAGCAGCGAA 142 / 161 0.71 bnlg1796, npi201a

ATTTCCAGTTGCCACCGACGAAGAACTT

phi102228 3 97.05 3.04 AAGC 6FAMATTCCGACGCAATCAACA 122 / 131 0.67 npi328b, bnlg1022

TTCATCTCCTCCAGGAGCCTT

phi073 3 120 3.05 AGC 6FAMGTGCGAGAGGCTTGACCAA 176 / 195 0.65 bnlg1108, umc226a

AAGGGTTGAGGGCGAGGAA

phi072 4 12 4.00 AAAC HEXACCGTGCATGATTAATTTCTCCAGCCTT 141 / 164 0.63 bnlg1241, uaz60

GACAGCGCGCAAATGGATTGAACT

phi295450 4 17.3 4.01 AGG/AAG*** 6FAMCCTTTTCATGTTGCTTTCCC 187 / 199 0.77 cyp5, zp11a

GCCCAATCCTTCCTTCCT

phi213984 4 24.1 4.01 ACC 6FAMGTGACCTAAACTTGGCAGACCC 286 / 304 0.52 umc277, uaz67

CAAGAGGTACCTGCATGGC

phi308090 4 53.03 4.04 AGC 6FAMCAGTCTGCCACGAAGCAA 210 / 223 0.49 csu855, bnlg292b

CTGTCGGTTTCGGTCTTCTT

phi096 4 4.04 AGGTG NEDTCCACCATTTGACACTTAGGCA 232 / 241 0.48 fl2

GCGTAGGACGACCGTTGAA

phi079 4 64 4.05 AGATG 6FAMTGGTGCTCGTTGCCAAATCTACGA 179 / 196 0.73 uaz69b, bnlg1621a

GCAGTGGTGGTTTCGAACAGACAA

phi438301 4 102 4.05 ACC NEDCCTTCATTGTTCGGCTGG 210 / 215 0.68 umc66a, rz446a

ACGAAGCTGATGATCTAACGCT

phi093 4 141 4.08 AGCT HEXAGTGCGTCAGCTTCATCGCCTACAAG 283 / 295 0.62 npi449b, rz476a

AGGCCATGCATGCTTGCAACAATGGATACA

phi076 4 178 4.11 AGCGGG HEXTTCTTCCGCGGCTTCAATTTGACC 160 / 174 0.65 csu315b

GCATCAGGACCCGCAGAGTC

phi109188 5 0 5.00 AAAG 6FAMAAGCTCAGAAGCCGGAGC 162 / 170 0.61 cdo484, csh13

GGTCATCAAGCTCTCTGATCG

phi396160 5 73 5.02 AGGCG NEDGGAGCCTCCTCAACCCTT 300 / 304 0.6 ucr1b, umc1

GCTCGAGGTCCATGAGCA

phi331888 5 88 5.02 AAG HEXTTGCGCAAGTTTGTAGCTG 129 / 136 0.67 php06012, bnlg653

ACTGAACCGCATGCCAAC

phi330507 5 91.32 5.02 CCG HEXGTAAAGTACGATGCGCCTCCC 134 / 143 0.21 tum3, bnlg386

CGGGGTAGAGGAGAGTTGTG

phi333597 5 93.55 5.02 AAG HEXAGCTCGAGTACCTGCCGAG 213 / 259 0.71 cent5, rz476b

TGCATCTCTGAGACCATCACC

phi085 5 130 5.07 AACGC HEXAGCAGAACGGCAAGGGCTACT 236 / 266 0.79 bnlg1885, csu1164

TTTGGCACACCACGACGA

phi423796 6 31 6.01 AGATG NEDCACTACTCGATCTGAACCACCA 131 / 139 0.45 csu1196, uaz23a

CGCTCTGTGAATTTGCTAGCTC

phi389203 6 81.33 6.03 AGC NEDGACGAAAAGGTGGCTCGT 301 / 310 0.23 tug6, tda51

TGCAGTCCTAGATCAGTTCCAA

phi452693 6 95 6.04 AGCC NEDCAAGTGCTCCGAGATCTTCCA 124 / 142 0.61 bcd221a, npi330

CGCGAACATATTCAGAAGTTTG

phi445613 6 106.7 6.05 ACG NEDTGACCACACACGAGCGAG 99 / 103 0.6 npi608, php10016

GCTCACAATATGTGGCAGAGG

phi070 6 114 6.07 AGCTG NEDGCTGAGCGATCAGTTCATCCAG 76 / 90 0.76 cdo89, bnl8.08c

CCATGGCAGGGTCTCTCAAG

phi364545 6 125.4 6.07 AGC HEXTAAGCAAAGCAAGGCAACC 127 / 138 0.64 php20904, npi280

TCGCCTCACTCTCACACTCC

phi299852 6 129 6.07 AGC 6FAMGATGTGGGTGCTACGAGCC 99 / 132 0.76 uaz251d, umc266c

AGATCTCGGAGCTCGGCTA

phi034 7 33 7.02 CCT 6FAMTAGCGACAGGATGGCCTCTTCT 118 / 145 0.57 bnlg2160, uaz20b

GGGGAGCACGCCTTCGTTCT

phi328175 7 102.12 7.04 AGG HEXGGGAAGTGCTCCTTGCAG 101 / 130 0.71 bnlg1161, bnl8.39

CGGTAGGTGAACGCGGTA

phi069 7 120.3 7.05 GAC NEDAGACACCGCCGTGGTCGTC 187 / 207 0.66 bnl16.06, csu920b

AGTCCGGCTCCACCTCCTTC

phi260485 7 134 7.05 AGC 6FAMTCATTCGACAGAGGCAAAAG 288 / 321 0.75 csu814a, phi051

CATGGGAACTAACACTGGATGC

phi116 7 145.82 7.06 ACTG/ACG*** 6FAMGCATACGGCCATGGATGGGA 151 / 174 0.68 php20728, umc35a

TCCCTGCCGGGACTCCTG

phi420701 8 18 8.00 CCG NEDGATGTTTCAAAACCACCCAGA 291 / 300 0.73 rnp2, bnlg2235

ATGGCACGAATAGCAACAGG

phi233376 8 56.32 8.03 CCG 6FAMCCGGCAGTCGATTACTCC 138 / 155 0.69 cdo1160a, php20727

CGAGACCAAGAGAACCCTCA

phi121 8 77.13 8.04 CCG HEXAGGAAAATGGAGCCGGTGAACCA 96 / 102 0.59 cdo1395e, csu254d

TTGGTCTGGACCAAGCACATACAC

phi115 8 84.71 8.03 AT/ATAC*** HEXGCTCCGTGTTTCGCCTGAA 291 / 312 0.56 rz206c, umc12a

ACCATCACCTGAATCCATCACA

phi100175 8 116.8 8.04 AAGC 6FAMTATCTGACGAATCCCATTCCC 132 / 142 0.81 bcd134c, umc117

GTACGTAACGGACGGACGG

phi015 8 159 8.08 AAAC 6FAMGCAACGTACCGTACCTTTCCGA 80 / 106 0.7 csu223a, rz444a

ACGCTGCATTCAATTACCGGGAAG

phi033 9 41 9.01 AAG NEDATCGAAATGCAGGCGATGGTTCTC 236 / 264 0.24 bz1, csu665b

ATCGAGATGTTCTACGCCCTGAAGT

phi032 9 90 9.04 AAAG NEDCTCCAGCAAGTGATGCGTGAC 223 / 243 0.52 uaz119c, cdo938b

GACACCCGGATCAATGATGGAAC

phi448880 9 108.73 9.04 AAG NEDCGATCCGGAGGAGTTCCTTA 178 / 188 0.72 npi425d, bnlg1270

CCATGAACATGCCAATGC

phi236654 9 124 9.05 CCG 6FAMGCTTGTTTCCCTTGGTCG 120 / 127 0.59 std2a, csu870

GGACTCGCGAATAAGGTCTGG

phi108411 9 126.15 9.05 AGCT 6FAMCGTCCCTTGGATTTCGAC 116 / 123 0.66 bnlg1191, bnlg1156

CGTACGGGACCTGTCAACAA

phi041 10 7 10.00 AGCC NEDTTGGCTCCCAGCGCCGCAAA 196 / 218 0.67 php20626, bnl3.04

GATCCAGAGCGATTTGACGGCA

phi059 10 52 10.02 ACC 6FAMAAGCTAATTAAGGCCGGTCATCCC 146 / 146 0.39 csu625, npi417b

TCCGTGTACTCGGCGGACTC

phi96342 10 53.16 10.02 ATCC 6FAMGTAATCCCACGTCCTATCAGCC 240 / 250 0.59 csu625, npi417b

TCCAACTTGAACGAACTCCTC

phi050 10 63 10.03 AAGC NEDTAACATGCCAGACACATACGGACAG 76 / 87 0.57 umc155, bnlg1526

ATGGCTCTAGCGAAGCGTAGAG

phi301654 10 85.8 10.04 CCG 6FAMGAATGCATGCTTTTCAAGGAC 132 / 138 0.31 npi563, npi269b

CGCACAGAGAGCAGAACG

phi062 10 96 10.04 ACG NEDCCAACCCGCTAGGCTACTTCAA 159 / 165 0.63 bcd386b, umc44a

ATGCCATGCGTTCGCTCTGTATC

phi323152 10 119.2 10.07 CCG HEXTCAGGGAGCTCACCTACTACGG 137 / 147 0.68 bnlg1450, npi254b

CACGACTGCACCGATTAGC

* Min and max allele values were obtained by rounding the former down and the latter up to the next integer

** Nearby public loci/markers in Maizedb; not obtained directly from mapping data. NM = not mapped with sufficient resolution

*** Compound repeat motifs

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

Return to the MNL 75 On-Line Index
Return to the Maize Newsletter Index
Return to the MaizeGDB Homepage