Page 55 Integrative placement and orientation of non-redundant SSR loci in cotton
Table A. Monosomic, monotelodisomic, and segmentally trisomic-monosomic (duplication-deficient) F1 interspecific chromosome substitution stocks of G. hirsutum from crosses with G. barbadense line 3-79 and G. tomentosum.
aCytogenetic conditions transmitted maternally from G. hirsutum: M = monosomic (primary), sh = monotelodisomic for short arm, , and Lo = monotelodisomic for long arm, where monosomics are deficient for an entire G. hirsutum chromosome, and monotelodisomics are deficient for all or part of arm opposite the telosome. H23 arose paternally from a cross involving G. barbadense 3-79 pollen (Ji et al. 1997), so the F1 lacks the 3-79 chromosome, and is monosomic for the G. hirsutum chromosome.
bThe segmental deficiencies listed here are translocation-derived segmental trisomic-monosomics, sometimes alluded to as "duplication-deficients". Dp11-Df13, for example, is trisomic for a segment of Chr-11 and monosomic for a segment of Chr-13, and thus hemizygous for this segment of G. barbadense Chr-13.
Chr. / G. barbadense / G. tomentosumMa / sha / Loa / M / sh / Lo / Segmental deficienciesb
1 / 200208051.06 / 9708030.05 / 200208054.07 / 200108072.07 / 200108077.01 / 200100323.12 / -
2 / 200208051.07 / 9200214.04 / 9708030.06 / 200108072.09 / 200108077.03 / 200100324.03 / -
3 / 200208051.08 / 200208054.10 / 200208054.08 / - / 200108077.09 / 200108077.05 / -
4 / 200208052.01 / 200208055.04 / 200208055.03 / 200108073.06 / 200100325.16 / 200108078.02 / -
5 / - / - / 9708031.04 / - / - / 200108078.06 / -
Table A. Cont.
Ma / sha / Loa / M / sh / Lo / Segmental deficienciesb
6 / 200208052.02 / 200208055.06 / 9708031.05 / 200108073.08 / 200108078.10 / 200108078.08 / -
7 / 200208052.03 / 200208055.08 / 200208055.07 / 200108073.09 / 200108079.02 / - / -
8 / - / - / 200208055.09 / - / - / 200100431.09 / -
9 / 200208052.06 / - / 200208055.10 / 200108074.08 / - / 200108079.04 / -
10 / 200208052.09 / 200208056.02 / 200208056.01 / 200108075.02 / 200108080.01 / 200100326.12 / -
11 / 200401612.17 / - / 200208056.03 / - / - / 200108080.04 / -
12 / 200208053.01 / - / 200208056.04 / 200201121.01 / - / 200108080.07 / -
13 / - / - / - / - / - / - / Dp11-Df13 (200100354.02)
Dp19-Df13 (200208074.08)
14 / - / - / 200208056.05 / - / - / 200108080.10 / -
15 / - / - / 200208056.06 / - / - / 200108081.03 / -
Table A. Cont.
Ma / sha / Loa / M / sh / Lo / Segmental deficienciesb
16 / 200208053.03 / 200208056.07 / 200008049.05 / 200108075.06 / - / 200108081.05 / -
17 / - / 200208056.08 / - / 200108075.10 / 200108081.07 / - / -
18 / 200208053.06 / 200208056.09 / 9908050.01 / 200108076.02 / 200108081.10 / 200108081.09 / -
19 / - / - / - / - / - / - / Dp13-Df19 (200100361.03)
20 / 200208053.08 / 200208057.02 / 200208056.10 / 200100283.01 / 200100334.09 / 200108082.03 / -
22 / - / 9908051.04 / 200208057.03 / - / 200108082.08 / 200108082.06 / -
23 / 200208053.10 / - / - / - / - / - / -
24 / - / - / - / - / - / - / -
25 / 200208054.03 / - / 200208057.07 / 200108076.09 / - / 200108083.01 / -
26 / - / 200208057.10 / - / - / 200108083.05 / - / -
Table B. Chromosome locations of cotton SSR loci as indicated by deficiency tests with Gossypium barbadense (CS-B) and Gossypium tomentosum (CS-T) hypoaneuploid series (monosomic and monotelodisomic plants), and comparisons to previously reported locations.
Loci are organized by genomes, A genome (chromosomes 1-13) and D genome (chromosomes 14-26). aAllele size (bp) of the TM-1 allele that was absent from the respective hypoaneuploid F1 interspecific chromosome substitution stock, except chromosome 23. For the latter, the hypoaneuploid was monosomic for G. barbadense chromosome 23, so the 3-79 allele was absent. bDuplicated loci for which allele fragment sizes differed and each locus was polymorphic relative to G. tomentosum and/or G. barbadense. Amplicons from the duplicate loci were absent from different hypoaneuploid F1 interspecific chromosome substitution stocks, indicating non-allelism. Duplicated loci are denoted by a numerical suffix (-1, -2, or -3) that also denotes relative (increasing) G. hirsutum allele fragment size. cDuplicated loci with amplicons of equivalent size (bp). The loci, however, were polymorphic relative to G. tomentosum and (or) G. barbadense, and localized by the hypoaneuploid screening to different chromosomes. dReferences 1Liu et al. 2000a,b; 2Zhang et al. 2002; 3Lacape et al. 2003; 4Han et al. 2004; 5Mei et al. 2004; 6Rong et al. 2004; 7Nguyen et al. 2004; 8Lacape et al. 2005; 9Lin et al. 2005; 10Shen et al. 2005; 11Song et al. 2005; 12Park et al . 2005;13Cantrell, R. Unpublished; 14Frelichowski et al. 2006, 15Lacape et al. 2007, 16He et al. 2007, 17Guo et al. 2007. eRedundant Loci
Table B. Cont.
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL1667 / 164a / 174 / 171-176 / 01Lo / 01Lo / 1, 2, 14, 15 / 2, 3, 6, 11, 12, 14, 16, 17
BNL2664 / 122a /
122
/ 120 / - / 01Lo / 15 / 16BNL2921 / 158a /
162
/ 166 / 01Lo / 01Lo / 1, 24 (D03) / 2, 3, 6, 9, 11, 15, 16, 17BNL3085 / 93, 108a /
91, 100
/ 93, 100 / 01Lo / 01Lo / - / -BNL3090 / 211, 238a /
222
/ 214, 246 / 01Lo / 01Lo / 1, 15, 16 / 2, 3, 6, 11, 15, 16, 17BNL3580 / 211a /
205, 211
/ 201 / - / 01Lo / 1, 15 / 2, 3, 7, 8, 11, 14, 15, 16, 17BNL3778 / 122a /
122
/ 113 / - / 01Lo / 1 / 2, 15BNL3848 / 204, 225a /
204, 246
/ 204, 221 / 01Lo / 01Lo / 15 / 14Table B. Cont.
SSR locus / Allele size / Chromosome or arm location (CS-B series) / Chromosome or arm location (CS-T series) / Previously reported location / ReferencedTM-1
bp / 3-79
bp / G. tomentosum
bp
BNL3878 / 195, 203a /
195, 203
/ 195, 199 / - / 01Lo / - / -BNL3888 / 182a /
195
/ 180 / 01Lo / 01Lo / 1, 14 / 2, 3, 5, 6, 11, 15, 16, 17BNL4095 / 196a, 213 /
204, 215
/ 196, 215 / 01Lo / - / - / -BNL1693 / 239a /
239, 241
/ 241, 243 / - / 01sh / 1, 15, 21 (D02) / 3, 11, 16BNL2440-1b / 177a /
183
/ 177 / 01sh / - / 1, 5, 10, 15 / 2, 3, 6, 9, 11, 15, 16BNL3655 / 127a /
108
/ 108 / 01sh / 01sh / 25 / 16BNL1434 / 247a /
263
/ 239 / 02Lo / 02Lo / 2, 9 / 1b, 3BNL1897 / 143a /
137
/ 135 / 02Lo / 02Lo / 2, 14, / 3, 4, 11, 15, 16, 17Table B. Cont.
SSR locus / Allele size / Chromosome or arm location (CS-B series) / Chromosome or arm location (CS-T series) / Previously reported location / ReferencedTM-1
bp / 3-79
bp / G. tomentosum
bp
BNL2877 / 114a / 120, 123 / 108, 114 / 02Lo / - / - / -
BNL3413 / 176a / 224 / 179 / 02Lo / 02Lo / 17 / 16
BNL3512e / 84, 99a / 84, 91 / 105, 110 / 02Lo / 02Lo / 2 / 14
BNL3545-2b / 187a / 214 / 211 / 02Lo / 02Lo / 15 / 16
BNL3547e / 85, 99a / 85, 91 / 85, 105, 111 / 02Lo / 02Lo / - / -
BNL3590-1b / 180a / 174 / 172 / 02Lo / 02Lo / 2 / 3, 4, 7, 8, 10, 11, 16, 17
BNL3971 / 140a / 116 / 140 / 02Lo / - / 2, 17 / 1b, 2, 3, 4, 11, 12, 14, 15, 16, 17
BNL3972 / 240a /
238
/ 227 / 02Lo / 02Lo / - / -BNL4060 / 84, 99a /
84, 91
/ 84, 105, 111 / 02Lo / 02Lo / - / -BNL834-1b / 120a /
-
/ 120 / 02sh / - / - / -Table B. Cont
SSR locus / Allele size / Chromosome or arm location (CS-B series) / Chromosome or arm location (CS-T series) / Previously reported location / ReferencedTM-1
bp / 3-79
bp / G. tomentosum
bp
BNL3292 / 110, 113a /
110, 122
/ 110 / 02sh / 02sh / - / -BNL3424-1b / 148a /
152
/ 148 / 02sh / - / 2 / 14BNL226 / 225, 229a /
213, 233
/ 233, 237 / 03Lo / 03Lo / 3, 14 / 2, 3, 4, 6, 9, 11, 12, 14, 16, 17BNL1059 / 205a, 213 /
207, 224
/ 209 / 03Lo / 03Lo / 3, 14 / 3, 4, 6, 9, 11, 15, 16, 17BNL3259 / 201, 207a /
216, 236
/ 207 / 03Lo / - / 3, 14 / 3, 4, 11, 15, 16, 17BNL3398 / 194a /
177
/ 189 / 03Lo / 03Lo / 3 / 11, 15BNL3463-1c / 230a /
270
/ 234 / 03Lo / 03Lo / 3 / 2, 11
Table B. Cont
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL3566 / 217, 224, 230, 235, 248a, 311, 335 /
217, 224, 228, 230, 234, 237, 308, 335
/ 217, 222, 224, 228, 234, 308, 311, 335 / 03Lo / 03Lo / - / -BNL3989 / 190a, 227 /
227
/ 176, 227 / 03Lo / 03Lo / 3 / 2, 7, 11, 16BNL4017 / 220, 232a /
225
/ 225 / 03Lo / 03Lo / - / -BNL4034 / 78, 88a /
78, 84
/ 78, 81 / 03Lo / 03Lo / - / -CM106 / 79, 93a /
79, 86
/ 73, 79, 86 / 03Lo / 03Lo / - / -CM129A / 59a /
63
/ 67 / 03Lo / 03Lo / - / -BNL3408-1b / 128a /
133
/ 128 / 03sh / - / 3 / 1b, 3, 6, 12, 14, 15, 16
Table B. Cont
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL3441 / 210a / 202 / 204 / 03sh / 03sh / 3 / 1b, 3, 4, 11, 12, 14, 15, 17
BNL3443-1b / 120a / 122 / 120 / 03sh / - / 3 / 16
BNL530 / 139a / 139 / 135 / - / 04Lo / 4, 26 / 2, 3, 4, 10, 11, 14, 17
BNL2572 / 248a, 250a / 234 / 240, 254, 256 / 04Lo / 04Lo / 4 / 3, 4, 6, 7, 8, 9, 11, 15, 16, 17
BNL3433 / 78, 231a / 78, 143, 295 / 78, 143, 295 / 04Lo / 04Lo / 4 / 2, 6
BNL3988 / 138a / 117 / 112 / 04Lo / 04Lo / - / -
BNL4049-2b / 156a / 157 / 159 / 04Lo / 04Lo / 4 / 3, 4, 7, 11, 17
BNL3089 / 128a / 124 / 128 / 04sh / - / 4, 9, 24 (D03) / 2, 11, 13, 17
Table B. Cont
SSR locus / Allele size / Chromosome or arm location (CS-B series) / Chromosome or arm location (CS-T series) / Previously reported location / ReferencedTM-1
bp / 3-79
bp / G. tomentosum
bp
BNL4047-2b / 155a / 161 / 161 / 04sh / 04sh / 4, 9 / 2, 5, 7, 11, 15, 16, 17
BNL1666 / 119, 124, 140a / 119, 124 130, 136 / 119, 124, 128, 140 / 05sh / - / 7, 15 / 11, 12, 14, 16
BNL2609 / 126, 136a, 151 / 122, 126, 136 / 124, 126 / - / 05sh / 5 / 16
BNL2732 / 192, 208a / 192, 212 / 195 / 05sh / 05sh / - / -
BNL3241 / 119a / 117 / 123 / 05sh / 05sh / - / -
BNL3601 / 166a, 176 / 174 / 164, 174 / 05sh / 05sh / 17 / 16
BNL3945 / 167a / 165 / 167 / 05sh / - / - / -
BNL3995 / 195a / 185 / 177 / 05sh / 05sh / 5 / 1ab, 2, 3, 4, 9, 11, 14, 15, 16, 17
Table B. Cont
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL2884 / 163a / 171 / 172 / 06Lo / 06Lo / 6 / 3, 4, 9, 11, 16, 17
BNL3594-1b / 180a / 178 / 180 / 06Lo / - / 6 / 3, 15, 17
BNL3650 / 352a / 338 / 338 / 06Lo / 06Lo / 6 / 3, 4, 11, 12, 14, 17
BNL3914 / 153, 155, 158, 180a, 185 / 152, 155, 157, 182, 187, 195 / 152, 156, 158, 190, 194 / 06Lo / 06Lo / - / -
BNL3987 / 211a / 215 / 218, 220 / 06Lo / 06Lo / 6 / 16
BNL4001-1b / 134a / 134 / 132 / - / 06Lo / - / -
BNL4016-1b / 165a / 166 / 165 / 06Lo / - / - / -
BNL1047-1b / 149a / 149 / 160 / - / 06sh / - / -
Table B. Cont
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL1064 / 140a / 148 / 157 / 06sh / 06sh / 6, 26 / 1b, 3, 4, 5, 6, 11, 14, 15,16, 17
BNL1440-2b / 256a / 266 / 256 / 06sh / - / 5, 6, 8 (A02) / 1b, 3, 4, 5, 6, 11, 12, 14, 16, 17
BNL2569 / 169a / 173 / 175 / 06sh / 06sh / 6, 25 / 2, 3, 5, 11, 16, 17
BNL3359 / 206a / 210 / 204 / 06sh / 06sh / 6, 25 / 2, 3, 4, 11, 16, 17
BNL4004 / 121a / 119 / 119 / 06sh / 06sh / - / -
BNL580-1b / 198, 204a / 202 / 198, 204 / 07Lo / - / 10, 16 / 16
BNL1122-2b / 172a / 168 / 174 / 07Lo / 07Lo / 7, 12 16 / 2, 4, 10, 11, 16
BNL1531-1b / 118a, 124 / 118 / 124 / - / 07Lo / - / -
BNL1597 / 210a / 215 / 227 / 07Lo / 07Lo / 7 / 1b, 3, 6, 15, 16
Table B. Cont
SSR locus / Allele size / Chromosome or arm location (CS-B series) / Chromosome or arm location (CS-T series) / Previously reported location / ReferencedTM-1
bp / 3-79
bp / G. tomentosum
bp
BNL1694 / 221, 237a / 221, 225, 233, 237 / 241 / 07Lo / 07Lo / 7, 16 / 2, 3, 4, 6, 9, 10, 16, 17
BNL2634 / 195a / 194 / 191 / 07Lo / 07Lo / - / -
BNL3415 / 233a / 240 / 235, 237 / 07Lo / 07Lo / - / -
BNL3793 / 155a / 157 / 159 / 07Lo / 07Lo / - / -
BNL3871 / 130, 139a / 130, 136 / 130, 139 / 07Lo / - / 7 / 16
CM66-1b / 127a / 122 / 127 / 07Lo / - / - / -
BNL1041-1b / 136, 138a / 136 / 138 / 07sh / - / - / -
BNL1604-1b / 101a / 110 / 122 / 07sh / 07sh / 7 / 3, 9, 16, 17
BNL387 / 210a / 220 / 199 / 08sh / 08sh / 8 (A02) / 9, 16
BNL2772 / 179a / 188 / 177 / 08sh / 08sh / - / -
Table B. Cont
TM-1
bp / 3-79
bp / G. tomentosum
bp
BNL3255-1c / 227a / 206 / 227 / 08sh / - / 4, 8 (A02) 10, 15 / 1b, 2, 3, 4, 6, 11, 17
BNL3257 / 207a / 190 / 189 / 08sh / 08sh / 8 (A02), 26 / 2, 3, 4, 6, 11, 15, 16, 17
BNL3556 / 133a / 129 / 120, 143, 145 / 08sh / 08sh / 5, 8 (A02) / 1b, 3, 6
BNL4037 / 247a / 247 / 245 / - / 08sh / - / -
BNL597-2b / 192a / - / 194 / 09Lo / 09Lo / 9 / 11, 12, 14
BNL686-2b / 184a / 188 / 190 / 09Lo / 09Lo / 9 / 1b, 3, 11, 16, 17
BNL1030-1b / 93, 232a / 93, 224 / 93, 233 / 09Lo / 09Lo / 9 / 2, 3, 4, 6, 10, 11, 15, 17
BNL1317-1b / 181a / 173 / 175 / 09Lo / 09Lo / 9 / 2, 3, 4, 10, 11, 12, 14, 17
Table B. Cont