Bchromosomal Locations Were Assigned Using Aneuploid Stocks and the Genetic Map
Table S1. The primer sequences flanking a microsatellite sequence of select BAC-end sequences of Gossypium hirsutumAcala ‘Maxxa’ and placed into an SSR linkage map.
Primer Sequence (5'-3')Marker name / Forward / Reverse / Method
MUSB0073 / CTTCCAAAACCAACATGAAGC / GTGAGGGAGGAAGGGAACC / Primer3
MUSB0078 / CCCTCGAGACACCTAAGACC / GTGATGGTGGTAGTCATTTGG / Primer3
MUSB0087 / CAGGTTTCATTTGTTCTCATGC / CGATATTGATGCCCTCTATGC / Primer3
MUSB0100 / TTCTGTTCCCACATTTCAAGC / AAAGGGGTGCTGGTTTCG / Primer3
MUSB0139 / ATGCAGCATGCAAATGTCC / GGCGGAGAGAGTAGAGAACG / Primer3
MUSB0155 / TCACAAGGCCTAGATTGATGC / TGCATGTGACATAAACTGAAGG / Primer3
MUSB0175 / GGAACCAAGTGAAGTGATATGC / TTCGCCCCCATATTTTCTC / Primer3
MUSB0194 / CCCATTCAAGGGACATAATCC / TGAGCTTTGAAACCGAAAGG / Primer3
MUSB0224 / TATCACCCATCCCACTCACC / AGGGGAAGGAAGAGAAGAGG / Primer3
MUSB0255 / TACCGGAATTCGTTGTGTTG / CATGGAGGTTTGGTTGTTAGAG / Primer3
MUSB0303 / GGCCAAAAGATTGATGTTGG / TGGTCGAATGCTATTGTTTCTC / Primer3
MUSB0309 / CAACAGCTGGTTGACTTTCC / CGCAAGGAACATTGTTGAGC / Primer3
MUSB0312 / CCTCCATTATCTTCTCCTTTTCC / TCTTTCTTTTGTGCGTGTGG / Primer3
MUSB0319 / AACGTGCCTAACAGGCTTGA / CCTTCTCCTGCCCTTCTTTT / Primer3
MUSB0325 / TTTGAAACGTGTGGCACTTG / AGAAAGCATCAAAGAGCACCA / Primer3
MUSB0337 / CCAACACACACACACAAAAGC / ATTGTGGGGGCCACATATAA / Primer3
MUSB0338 / CGGAGGGATTGTATTGAACG / AAACGCAAGGCAAAGAAGC / Primer3
MUSB0369 / GACCGTCCACACCTACCATC / GGGAGAAAGAGGGAGAAGAGG / Primer3
MUSB0399 / GGATCGAACCAAGATTTTTCC / AGTTGTAACGCCCCAACAAT / Primer3
MUSB0404 / CCACAACCAACTGATCTAGGG / GGTCGATTCTGCTTCTCCAG / Primer3
MUSB0411 / GATCCACATCAAACCCAAGC / GAAAATTCGTTGGCAGTAGGG / Primer3
MUSB0422 / AGTTGGAGAGGAGGGGTTTG / TACATGAGGGCCAATGAGTG / Primer3
MUSB0440 / TGCAAACCATGCTAGTGACC / GATTTCCCCTCCAAATGAGC / Primer3
MUSB0442 / GAGCCGTACGAGGAGAAAAC / CGAGGTGGCAAGGAATCTAC / Primer3
MUSB0444 / TGATTTCATTGTGGGGACAC / ATTTACCGCCTCATGCAAAG / Primer3
MUSB0463 / CCAAGAGAAAAACGGCAAGG / CCTCGTACTCGAAATTGACG / Primer3
MUSB0497 / TGAAAGCGAAACTCGAGGTAA / CTTGGAGGCATCAACGAAAT / Primer3
MUSB0500 / TGGATGAACATTTGGTACGC / CATGGTCGAAACTGACTTGG / Primer3
MUSB0537 / TCACCAAGCAGCAATTTAGC / CAAAGCTCCACAATTTCAGG / Primer3
MUSB0550 / ATGGCATGTATAGGGGCTTG / CACCATTACTTGCACCAACG / Primer3
MUSB0564 / TCCCCTCTCTTTTTCCATCA / AGCATTCCACACCAATTTCA / Primer3
MUSB0570 / TGATTTAACGTGCCACATCAG / ACCCAAACCCTCTCACTTTTC / Primer3
MUSB0590 / TTGGGGCCATTCTTTTTATC / GATTGGATGTTGGCAATGAC / Primer3
MUSB0592 / CCGGTATGGTTTGAAATAATGG / TTTCCCCAAAGTAAAGGTCAC / Primer3
MUSB0596 / GCCATGAAAGGTGGCTCATA / ACCCTCAAGCACTCACACAA / Primer3
MUSB0606 / TGCCATGGCTTATAAATGAGG / CCAAGAAAAGGGGACTAAATTG / Primer3
MUSB0611 / TCTATGTTTTGCATGCCTGGT / TCAAACGAACACACACACACA / Primer3
MUSB0625 / GGGTGGAAATTGTATATGTTGAGG / TTGAAGAAGAAGGGGAAGATGG / Primer3
MUSB0632 / CGTGTAACTCACCATTTCAAAGTC / AGCAGCACCGTGTAGCTATG / Primer3
MUSB0634 / ATAATCTGCAACGCCCTCAC / TCGGATTCGTAAGACACAGG / Primer3
MUSB0639 / CCATCTCCAAACTCTTACATGC / AATCCGAGGCAGAATGAGG / Primer3
MUSB0641 / GAGCTGGTCCAAAAGTGTGC / GGCAAGTCACGAGAAACTCC / Primer3
MUSB0662 / CTGTTGGAGGTGGTTCAAGG / TTGGTGGTGGGTAAGCTAGG / Primer3
MUSB0664 / GATGAAATTTGGGGAAGCTG / TGTCCCTTCAAGCTTTGTTG / Primer3
MUSB0685 / CCTTCTTCTCTTCTTCCTCGCTAT / CCCGTTCCTCTTCAGGTAAAC / Primer3
MUSB0749 / TTCAACGGGCATATTCAAGAC / TGGCGGTGTTCTTTATTTCAC / Primer3
MUSB0754 / TGTCTATTGCCGTCCACCTAC / GCTTTGTAACAGCCCGATTTAG / Primer3
MUSB0780 / TGCATTCATCAAAGGTAGCC / TCATGCGCCTTATTCGTTTC / Primer3
MUSB0799 / GTCACCAGAGTCAAGTTTGAGG / ACACAGGGGTCAGAGTAGTCG / Primer3
MUSB0808 / TGGCAGAATCAAAGCACCACTC / GTAGTTCCCTGCCTCCTTCC / FastPCR
MUSB0810 / TGCTCTTGACCCTTCCACC / CCGAGAAGCACCCGTGAC / FastPCR
MUSB0812 / GCTCACCGTACCTGCAGC / TGGTGGCACGACGACCTC / FastPCR
MUSB0818 / ACTCCGCGAACCACAGTG / GTCGCCAGGCCGTGTAAC / FastPCR
MUSB0823 / GCTACAAGCTATCTGCCAGAGC / TCCTGCCAATGACTCATCGGA / FastPCR
MUSB0827 / CGTGCGCCTGCATACACG / CCTGTTCTGAGGACGGTTTGG / FastPCR
MUSB0831 / GATCCTGCAGAAGAGGCTACC / TCCTGGTGTGCTTGGTTCC / FastPCR
MUSB0846 / CCGCACAAGCAGGACCTC / CCTTGTAGAACTCGGCAATGTCC / FastPCR
MUSB0847 / CGTGGCACATCCTCATCAGG / CGAGAGCCATGCTCCAGC / FastPCR
MUSB0849 / CGTGAGTCTTCAACAACCCAAGC / CCGAGACCAAGATCAGCTTCAG / FastPCR
MUSB0859 / GCGGAAGCATTAAGTAGGCATAAGC / GGACATGGCATCGGCCTAG / FastPCR
MUSB0876 / TGGAGCCTACAAGTTTGTGCTG / CGAGGACCAGTTCGAAACCAG / FastPCR
MUSB0888 / ACTTACTTGCCGTACTCGGAGG / TGGTTCCACACCTGCAGAG / FastPCR
MUSB0894 / CCCAAGAGGTAACGTTCCTCC / CCAATGCGAAAACCCACAAAGG / FastPCR
MUSB0904 / ACAAATTGATGCCAACGTCCCA / TCGAATAGTCGTTCCGATCCGTC / FastPCR
MUSB0907 / TCACCCACCTTATTGATGGAACGA / CATGACATCACATGGGTGCCA / FastPCR
MUSB0915 / AGCTGAGGATTCTGGGCTTTG / GCCTGGTCTTGTGGTTCCA / FastPCR
MUSB0919 / ACGACCTGAAACCGAACGTC / GGGCATCTTCTGATTGCTTGC / FastPCR
MUSB0930 / GGGACTCACTGGGCAATTCA / CGTGTTGACCCGTGACACAG / FastPCR
MUSB0953 / ACACCCTGATTTCGGCACATTC / TCATGTGTCCAAACCGTGTGTC / FastPCR
MUSB0955 / GTAACGATGCTCCTTGACGATCC / TGGCATTGTACGAGCTATGTGC / FastPCR
MUSB0958 / CGAAACCACTTCCCGACTAGG / GGTTGCATTCGGCAACTTGC / FastPCR
MUSB0969 / GCACAGTCTGTTACGGGGTG / GGCTTCGGCCCAGTAACC / FastPCR
MUSB0971 / TGCTCTACCTTGGTGACCCA / ACCTAAGACCCAGCGAACCA / FastPCR
MUSB0972 / TCAGGTTAGCTCGGCATTGG / ACCCTGTGTTGGCGTAGG / FastPCR
MUSB0973 / GGCTTGCCTTCGTCTAGGTG / CCACATGCAACATTAGCAACTTGCA / FastPCR
MUSB0977 / CAGGCATGCAAGCTTTCGAAC / TGCCAGCAATCTTGCTGACTG / FastPCR
MUSB0984 / ACAAACTATCATTTGCGTCCCATGC / CCTCCGAGAAGTGCCAACAA / FastPCR
MUSB0995 / AGCTGTCGCATTATTCGATCACAC / ACACCTCATCATTCATTCACCAAGC / FastPCR
MUSB1000 / TCTGCCAAAGAGCCAACTCAG / TGACAACCGGTGCGATAAGC / FastPCR
MUSB1001 / ACATCAACCATGCCATGCCA / GCTCACATGTTGAAGCCGATGC / FastPCR
MUSB1015 / TGTGAGCTCGGGGATTGC / ACCATAGCTAACACATGCCAAAAGC / FastPCR
MUSB1017 / CTCTCTTGGACTCAAACCTGAGC / ACATTCCAACTCTGGGTCTGC / FastPCR
MUSB1018 / CCTAGGCCGAAATTCAACCCTCA / TCATCCTTACTTCTCCATTGCCGA / FastPCR
MUSB1035 / TCATGATAGCAACGAGTGGTGC / GTCGAGTTGTATTAGTGTGCCCG / FastPCR
MUSB1040 / AAAAGCGGTATTGCACCGAATCA / GCAGAAACCTTGGAGCCTAACC / FastPCR
MUSB1043 / TCACTGTCGTTTGGCATGCA / TGGGAGCTTAGGAATAGCCTAAACC / FastPCR
MUSB1050 / ATCTTTGAAAGGTAGGTCCGAGTGT / TGCTGACAAATTCAGAAGCTTGCT / FastPCR
MUSB1051 / ACTTGGCTATTACCACAAACATGCC / TCGGGAATCGTCAGAGACCTC / FastPCR
MUSB1056 / TTTCCGAGGCTGAGCTCC / GGCGATTAGGAAACCTACGTGC / FastPCR
MUSB1064 / GCGGTAGCGATTGAAGGCTC / ACTTCGGCAACGGTCTCG / FastPCR
MUSB1076 / GGTTGGACTTGTGTAGCAATCTCC / AGGATCAGTCTGTTAAGCTTTGGGT / FastPCR
MUSB1079 / GGAAGGCAAGTGAACCTGAGAGA / CAAAACATTGCCATTTGCCAATGC / FastPCR
MUSB1081 / ACATTGCACCAAGCCCTACATG / AGTTTCTCGTGACTTGGCAACTC / FastPCR
MUSB1093 / ACATTGTGGATTGGTGGGTTCC / AGCACTTCCAATCAGACCACC / FastPCR
MUSB1101 / TTCCACCGATTTCACCTAAGTGC / ACAAGCTGATACAATCTTGCCTCGA / FastPCR
MUSB1112 / AGTCGGAGCTGGTGTTGC / TCCAACACTGACACGAAACCC / FastPCR
MUSB1117 / AGAAGCTTGTCATACGTTGCTTGG / CATCTAAGCCAGCCAAGTCTGG / FastPCR
MUSB1121 / GCAAGGCAGTTGACCTCTGAC / TGCGGAATTGTGCCGTTAGAC / FastPCR
MUSB1127 / GGTCCCTCTTGGTGCTGTG / TTTTGGGCTAAGGGTTTTGGGT / FastPCR
MUSB1135 / CCGCCGTCATTTCCATCACC / TGGTACGGATCATGGGAATCCT / FastPCR
MUSB1155 / GCCCTTGTACTTAGTCAATGCCG / ACACACAAGCTGACGGTTGG / FastPCR
MUSB1163 / ATGTGCCCGGCGGAATCC / GAAGCCTCTCGAACAGTGACC / FastPCR
MUSB1164 / ACGTCGGATTTGGCCATAACG / CGAAATGCACTGGCTGAGCT / FastPCR
MUSB1166 / AGACGTGGAACTTATGACACCCA / GCTTGATGGGTGAAAACACTGCA / FastPCR
MUSB1168 / TGTTCTATGGGCAATGCAATTGGT / TCCAACAATGTTCCAATCGACAGC / FastPCR
MUSB1178 / TGTACCACTCACCGCATGG / AGACCTGTTTGCGACACCG / FastPCR
MUSB1181 / TGCACAATGCTGACCCTACAC / TCATCAGGAGTTCGCAGTTGC / FastPCR
MUSB1188 / AGCACAGATGGCACAACCTC / CACAAACCACCCACCAACC / FastPCR
MUSB1189 / TGCCAACACATGTATGGTCAACAC / GGAGGTTAGGCAAGGTGAACAC / FastPCR
MUSB1197 / ACTGCCGTCACTTAGCAGC / GGCAAGATAGAGATGCATGTGACG / FastPCR
MUSB1220 / AGCTTATGCTACAAGGGTCCCA / TGGCTGGACATGGAGCCTTA / FastPCR
MUSB1230 / ACACGCTTTCGCTAGTCCAG / ATTCTTGGAAGACACCAAGTCAGC / FastPCR
MUSB1242 / CGATCATTGGCGCAACCTACG / TTCCCGTAAGGGTTTCCACG / FastPCR
MUSB1248 / GGGTCCTTGCACAACTTGC / CCTCAGCCTCTGATCCCAG / FastPCR
MUSB1251 / GGGTCCTTGCGACACTTGC / CGGTTCAGTACAAACTGCTACTGTG / FastPCR
MUSB1252 / TGCCGAATGCCCTAAGCTC / GTAGGGAGGGCAAGGGAG / FastPCR
MUSB1263 / GGTTAGACAAAGGCATACTCTGGCA / GCGAACCTCCATTTATTGGGACATG / FastPCR
MUSB1267 / TCATGGTGACACATGGCAGTC / CATGAACATAGCACTGACGGCT / FastPCR
MUSB1278 / GCTTTAACCCATAGCATGGCCG / CGAAACCACTATTCCGATTAGGCC / FastPCR
MUSB1304 / AGTGGTCTGATGTTGCTCCGA / GCTACTCGGTCTCGGGTG / FastPCR
MUSB1307 / CGGGCAAGCCTCCGAAAC / GGCACATAGTGTGAGAAACGCTG / FastPCR
MUSB1316 / GCCTCAGACTTGACCATTCAGG / CCCGAAAACTTTGCCCAAACC / FastPCR
Table S2. Protein homology from GenBank (BLASTX) to BAC-end sequences of Gossypium hirsutum L. Acala Maxxa from which MUSB markers were assigned to chromosomes using hypoaneuploid cytogenetic stocks and placed in the cotton genetic map.
Marker namea / Consensus BAC / Chromosomal locationb / Repeat Motif / GenBank accession; / Score / E-valueAccession ID / Aneuploid / Linkage map / Putative gene function
MUSB0087 / MBb0006J13r / Chr.9 / Chr. 9 / (CAT)9 / AAN17417; / 92.0 / 9e-18
mRNA capping enzyme-like protein [Arabidopsis thaliana]
MUSB0194 / MbB0011O01f / Chr. 2 / Chr. 2 / (TA)10 / BAC87430 / 45.8 / 0.001
Unnamed protein product [Homo sapiens]
MUSB0309 / MBb0018B03f / Chr. 15sh / Chr. 15 / (ATCA)3 / AAX92771 / 48.9 / 3e-04
Putative transposable element protein [Oryza sativa]
MUSB0338 / MbB0018F17r / Chr. 20Lo / Chr. 20 / (CGC)5 / AAN41301 / 111 / 6e-23
Unknown protein [Arabidopsis thaliana]
MUSB0404 / MBb0018O18f / Chr. 11/A03 / (TA)9 / AAM64527 / 73.2 / 1e-11
Putative lipase/acylhydrolase [Arabidopsis thaliana]
MUSB0440 / MBb0019E19r / Chr. 15 / (ATA)4 / BAD88164 / 55.8 / 2e-06
Unknown protein [Oryza sativa]
MUSB0497 / MBb0019L10f / Chr. 12 / (AT)5 / AAQ82037 / 191 / 5e-47
Gag/pol polyprotein [Pisum sativum]
MUSB0537 / MBb0020B13f / Chr. 15 / (CA)7 / AAV59279 / 77.0 / 1e-12
At5g02010 [Arabidopsis thaliana]
MUSB0639 / MBb0024D18r / Chr. 3 / (AT)6 / AAO63379 / 50.1 / 1e-04
At1g70210 [Arabidopsis thaliana]
MUSB0662 / MBb0024G16r / Chr. 8 / (ATC)4 / CAA08755 / 215 / 2e-54
Dof zinc finger protein [Nicotiana tabacum]
MUSB0780 / MBb0025L16r / Chr. 8 / (AAG)5 / CAB78094 / 78.2 / 4e-13
RNA-directed DNA polymerase like protein [Arabidopsis thaliana]
MUSB0823 / MBb0032H19r / Chr. 11/A03 / (TCA)4 / AAQ57226 / 129 / 9e-29
DREB2 [Glycine max]
MUSB0827 / MBb0033K23r / Chr. 11/A03 / (TTATT)5 / AAT38744 / 83.2 / 9e-15
Putative gag-pol polyprotein [Solanum demissum]
MUSB0831 / MBb0034D22r / Chr. 10 / (CAT)10 / NP_197433 / 186 / 7e-46
RAN GTPase activating protein [Arabidopsis thaliana]
MUSB0846 / MBb0037C16r / Chr. 12 / (CATA)14 / NP_172460 / 82.4 / 7e-15
Expressed protein [Arabidopsis thaliana]
MUSB0849 / MBb0037I19f / Chr. 11/A03 / (ACAT)3 / AAM91378 / 214 / 4e-54
At1g29900/F1N18_6 [Arabidopsis thaliana]
MUSB0894 / MBb0021C21f / Chr. 6 / (TTC)5 / CAA56791 / 60.1 / 8e-08
Integrase [Nicotiana tabacum]
MUSB0919 / MBb0022G17f / Chr. 6 / (TTAG)3 / NP_178019 / 85.5 / 1e-15
Leucine-rich repeat transmembrane protein kinase, putative [Arabidopsis thaliana]
MUSB0973 / MBb0027C22f / Chr. 23 / (TG)5 / AAM61487 / 64.3 / 4e-09
Unknown [Arabidopsis thaliana]
MUSB0977 / MBb0027F20r / Chr. 5 / (AATA)3 / NP_177004 / 69.3 / 1e-10
Gravity-responsive protein/altered response to gravity protein [Arabidopsis thaliana]
MUSB1040 / MBb0030D21f / Chr. 23 / (AT)10 / AAU87885 / 130 / 7e-29
s-locus lectin protein kinase [Carica papaya]
MUSB1056 / MBb0030M07f / Chr. 5 / (AT)8 / XP_463438 / 47.4 / 6e-04
P0512C01.10 [Oryza sativa]
MUSB1076 / MBb0031K15r / Chr. 11/A03 / (TAAA)8 / AAQ82037 / 57.0 / 8e-07
Gag-pol polyprotein [Pisum sativum]
MUSB1112a-e / MBb0033E09r / LG_1 / (TA)9 / XP_470614 / 132 / 2e-29
Putative squalene monooxygenase [Oryza sativa]
MUSB1117 / MBb0033F18f / Chr. 12 / (TA)5 / AAM66949 / 65.9 / 2e-09
Ribosomal protein S25 [Arabidopsis thaliana]
MUSB1163 / MBb0034K01f / Chr. 11/A03 / (TCT)4 / AAL33610 / 78.6 / 2e-13
SGT1 [Hordeum vulgare]
MUSB1242 / MBb0038A08f / Chr. 12 / (AAAAT)3 / AAQ20041 / 96.3 / 8e-19
Isoflavone 3’-hydroxylase [Medicago truncatula]
MUSB1251 / MBb0039C16f / Chr. 17 / Chr. 17 / (TA)8 / AAF26097 / 48.9 / 2e-04
Germin-like protein [Arabidopsis thaliana]
aDuplicated loci of the marker are indicated by lower case letters. The primer sequences of the markers are provided in supplementary Table 1.
bChromosomal locations were assigned using aneuploid stocks and the genetic map.