SSLP ecotype size survey

Allele sizes from 6 common ecotypes. This table shows the 
the simple tandem repeat sequences (from Columbia), and the expected 
sizes of PCR products amplified from 6 common ecotypes. This data
can be used to decide what kind of separation system (acrylamide
versus agarose) to use to score the polymorphisms, and gives some
measure of how polymorphic each locus is.

Locus           Repeat  Col-0  Ler  Ws-0  No-0  Nd-0  RLD   # alleles

AthCHIB         (AT)14  84     74   82    72    66    90       6
AthEAT1         (AT)11  172    162  162   164   164   162      3
AthACS          (A)36   259    256  262   259   259   259      3
AthGENEA        (A)39   209    205  211   221   213   217      6
ca72            (CA)18  124    110  110   106   106   106      3
ATHATPASE       (AG)18  85     69   69    69    69    77       3
AthCTR1         (AG)16  159    143  145   143   147   143      4
nga6            (GA)31  143    123  131   147   123   133      5
nga8            (GA)27  154    198  166   168   188   160      6
nga12           (GA)16  247    234  247   n.a.  232   n.a.     3
nga32           (GA)13  260    256  260   250   260   252      4
nga59           (CT)19  111    115  83    141   111   111      4
nga63           (GA)23  111    89   91    89    91    89       3
nga76           (GA)22  231   >250  199   n.a.  203   n.a.     4
nga106          (GA)26  157    123  123   131   123   123      3
nga111          (GA)16  128    162  146   140   128   130      5
nga112          (GA)16  197    189  189   189   n.a.  189      2
nga126          (AG)31  119    147  119   131   149   103      5
nga128          (AG)16  180    190  172   180   186   188      5
nga129          (GA)20  177    179  165   165   165   165      3
nga139          (AG)29  174    132  132   132   182   136      4
nga151          (CT)31  150    120  102   150   110   120      4
nga158          (GA)13  108    104  120   106   112   124      6
nga162          (GA)21  107     89   85    87    97    91      6
nga168          (GA)25  151    135  135   135   135   135      2
nga172          (GA)29  162    136  138   162   164   180      5
nga225          (CT)18  119    189  119   123   131   97       5
nga248          (CT)24  143    129  133   125   133   135/115  6
nga249          (TC)15  125    115  115   115   135   115      3
nga280          (AG)15  105    85   85    85    85    85       2

Col size products are derived from sequence information. Other sizes are estimated from agarose gels.

chromosome primers Col Ler Nd-O No-O RLD WS

I AthSRP54A 247 245 247 ? 247 249

I T27K12-Sp6 146 152 146 ? 146 152

I AthZFPG 143 139 143 ? 143 141

I AthSO392 142 156 156 156 156 142

I nga392 170 162 ? ? ? ?

I nga692 119 115 119 115 123 115

II nga1145 213 217 209 209 217 213

II AthGPa1 101 99 99 99 99 99

II nga1126 191 199 191 ? 191 191

II nga361 114 120 ? ? ? ?

II AthBIO2 141 209 180 200 ? 200

II AthUBIQUE 146 148 146 146 150 146

III AthGAPab 142 150 142 150 150 142

III AthCDC2BG 131 129 133 ? 133 129

III nga707 132 128 128 128 132 128

IV AthDET1 138 136 138 140 140 136

IV nga1111 148 154 148 146/150 148 150

IV nga1139 114 118 118 114 110 118

IV nga1107 150 140 140 140 140 140

V AthEMC 131 135 131 ? 135 131

V AthCDPK9 106 104 ? 108 104 104

V AthSO262 145 159 145 159 159 151

V AthPHYC 207 222 222 222 222 222

V AthSO191 148 156 148 148 162 162


chromosome	SSLPs	Col	Ler	C-24	No	Nd	WS	RLD
I	nF19G10	197 bp	~195 bp	~195 bp	~190	~190	~197	~197
I	nF19K23	200 bp	~185	~200	~195	~200	~195	~190
I	nF19P19	202 bp	~195 bp	~195 bp	~195 bp	~195 bp	~190 bp	~195 bp
I	nF20D22	201 bp	~190 bp	~185 bp	~200 bp	~190 bp	~205 bp	~205 bp
I	nF21B7	199 bp	~195 bp	~200 bp	?	?	~200 bp	~200 bp
I	nF21J9	189 bp	~175 bp	~175 bp	~175 bp	~175 bp	~175 bp	~180 bp
I	nF21M12	200 bp	~160 bp	~200 bp	~200 bp	~200 bp	~215 bp	~210 bp
I	nF22K20	206 bp	~215 bp	~200 bp	~195 bp	~220 bp	~200 bp	~200 bp
I	nF5I14	195 bp	~290 bp	~290 bp	~290 bp	~195 bp	~290 bp	~290 bp
I	nF7G19	197 bp	~190 bp	~190 bp	?	~190 bp	~195 bp	~195 bp
I	nF11P17	209 bp	~195 bp	~195 bp	~195 bp	~210 bp	~190 bp	~215 bp
I	nT1G11	206 bp	~180 bp	~190 bp	~185 bp	~185 bp	~180 bp	~180 bp
I	nT7I23	199 bp	~195 bp	~215 bp	~190 bp	~190 bp	~185 bp	~185 bp
I	nyUP8H12R	202 bp	~165 bp	~165 bp	~165 bp	~230 bp	~225 bp	~190 bp

ATGC June 22, 1999

E-Mail Address: atgc@atgenome.bio.upenn.edu

chromosome	primers	Col	Ler	Nd-O	No-O	RLD	WS
I	AthSRP54A	247	245	247	?	247	249
I	T27K12-Sp6	146	152	146	?	146	152
I	AthZFPG	143	139	143	?	143	141
I	AthSO392	142	156	156	156	156	142
I	nga392	170	162	?	?	?	?
I	nga692	119	115	119	115	123	115
II	nga1145	213	217	209	209	217	213
II	AthGPa1	101	99	99	99	99	99
II	nga1126	191	199	191	?	191	191
II	nga361	114	120	?	?	?	?
II	AthBIO2	141	209	180	200	?	200
II	AthUBIQUE	146	148	146	146	150	146
III	AthGAPab	142	150	142	150	150	142
III	AthCDC2BG	131	129	133	?	133	129
III	nga707	132	128	128	128	132	128
IV	AthDET1	138	136	138	140	140	136
IV	nga1111	148	154	148	146/150	148	150
IV	nga1139	114	118	118	114	110	118
IV	nga1107	150	140	140	140	140	140
V	AthEMC	131	135	131	?	135	131
V	AthCDPK9	106	104	?	108	104	104
V	AthSO262	145	159	145	159	159	151
V	AthPHYC	207	222	222	222	222	222
V	AthSO191	148	156	148	148	162	162