SL93 - Genomes | Genetics S2 ’!Collinerity ... nfsg-052 PVGA-1677/1678 PVCAG-2569/2570...
16
L. Liu et al. 1 SI Figure S1 Detection of 49 bp deletion in trnLUAA intron in lowland and upland switchgrass. Alamo and Kanlow represented the southern and northern lowland ecotypes, respectively. While Dacotah represented a typical upland ecotype. “M” indicated the molecular weight standard with 1 kb DNA Ladder (Axygen Biosciences, Union City, CA) 700 bp 500 bp Kanlow Dacotah SL93 NL94 Alamo lowland upland 1000 bp 1500 bp 2000 bp M
Transcript of SL93 - Genomes | Genetics S2 ’!Collinerity ... nfsg-052 PVGA-1677/1678 PVCAG-2569/2570...
L. Liu et al. 1 SI
Figure S1 Detection of 49 bp deletion in trnL-‐UAA intron in lowland and upland switchgrass. Alamo and Kanlow represented the southern and northern lowland ecotypes, respectively. While Dacotah represented a typical upland ecotype. “M” indicated the molecular weight standard with 1 kb DNA Ladder (Axygen Biosciences, Union City, CA)
700 bp
500 bp
Kanlow Dacotah SL93 NL94 Alamo
lowland upland
1000 bp 1500 bp 2000 bp
M
L. Liu et al. 2 SI
Figure S2 Collinerity between the initial and final framework linkage maps. Here only linkage groups (LGs) 1a and 2a are shown as the representatives of all LGs. The LG number of initial framework map is indicated by a quote symbol. All loci mapped with the same markers across LGs are highlighted with matching colors
CP pop
sww-1667
PVCAG-2199/2200
PVAAG-3327/3328sww-112
nfsg-69PVGA-1253/1254nfsg-105PVGA-1589/1590
PVGA-1669/1670PVGA-2107/2108
PVAAG-3199/3200
sww-606
PVGA-2119/2120
nfsg-197PVGA-1573/1574
PVCAG-2379/2380
nfsg-26
6
PVCAG-2537/2538PVCAG-2439/2440
PVGA-1271/1272_300
PVCAG-2199/2200
sww-1667
PVAAG-3327/3328
sww-112
nfsg-69PVGA-1253/1254
nfsg-105PVGA-1589/1590
PVGA-1669/1670PVGA-2107/2108
PVAAG-3199/3200
sww-606
PVGA-2119/2120
nfsg-197PVGA-1573/1574
PVCAG-2379/2380
PVCA-411/412_290
nfsg-26
sww-1615
PVCAG-2373/2374
6
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1a’ 1a 2a’ 2a
CP pop
sww-5325211_B07PVGA-1105/1106PVCA-969/970PVAAG-3353/3354
sww-2525
sww-2455PVGA-1677/1678PVCAG-2569/2570nfsg-50sww-938nfsg-52Millet-MPGD25PVCA-765/766PVCAG-2623/2624
sww-217PVGA-1819/1820PVGA-1719/1720PVCA-555/556sww-2640sww-718_175PVCA-815/816sww-718_185PVAAG-2973/2974sww-2059PVAAG-2847/2848PVGA-1133/1134PVCA-317/318nfsg-130PVAAG-3245/3246nfsg-129_282PVCA-327/328_130
sww-1553
1
sww-223sww-108sww-704PVGA-1337/1338sww-5325211_B07PVGA-1105/1106PVCA-969/970PVAAG-3353/3354sww-2251sww-2525PVAAG-3311/3312PVGA-1251/1252sww-2455PVAAG-2787/2788PVAAG-3355/3356PVCAG-2569/2570PVGA-1677/1678nfsg-52sww-938Millet-MPGD25PVCA-765/766PVGA-1819/1820nfsg-50PVCAG-2623/2624PVGA-1719/1720sww-2640PVCA-555/556sww-217sww-718_175PVCA-815/816PVAAG-2973/2974sww-718_185sww-2059PVAAG-2847/2848PVGA-1133/1134PVCA-317/318nfsg-130PVAAG-3245/3246nfsg-129_282sww-360PVCA-327/328_130sww-668sww-393sww-1553
sww-687
sww-1805
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L. Liu et al. 3 SI
Figure S3
1b!!!!!!!!!!!!!!!!!Ib$f!!!!!!!!!!!!!!!!Ib$m!!sww-359sww-2405_160PVGA-1353/1354sww-660sww-177sww-2489sww-2034sww-775nfsg-031sww-333PVAAG-3351/3352sww-399PVCA-627/628PVAAG-3041/3042PVGA-1549/1550PVGA-1947/1948sww-196PVCA-179/180sww-2356sww-2196PVCA-491/492sww-2405_200sww-2320PVGA-1735/1736PVGA-1925/1926PVAAG-2987/2988sww-2115PVGA-1419/1420PVGA-1271/1272_345sww-2271PVGA-1401/1402sww-162sww-761PVGA-2143/2144PVCAG-2361/2362sww-2240sww-673nfsg-070
1b
sww-2489sww-2196sww-2405sww-333sww-1839nfsg-102sww-2115sww-2319sww-2659nfsg-026nfsg-154sww-2523nfsg-199sww-200sww-2290sww-2162nfsg-183nfsg-201nfsg-162sww-2098sww-2596sww-2151sww-2027sww-1948sww-2320sww-2956sww-2964sww-2271sww-2959
1b-f
sww-2489
sww-196sww-2405nfsg-102sww-2319sww-2659nfsg-199sww-273sww-2290sww-1736nfsg-201sww-2356sww-257nfsg-162sww-975sww-2970sww-1621sww-177sww-2596sww-2959sww-2964sww-1948sww-1598sww-2271
1b-m
05101520253035404550556065707580859095100105110115120125130135
1a$$!!!!!!!!!!!!!!!Ia$f!!!!!!!!!!!!!!!!Ia$m!!
PVCAG-2373/2374sww-1615
nfsg-026PVCA-411/412_290
PVCAG-2379/2380PVGA-1573/1574nfsg-197PVGA-2119/2120sww-606PVAAG-3199/3200PVGA-2107/2108PVGA-1669/1670PVGA-1589/1590nfsg-105PVGA-1253/1254nfsg-069sww-112PVAAG-3327/3328sww-1667PVCAG-2199/2200
PVGA-1271/1272_300
PVCAG-2439/2440PVCAG-2537/2538
1a
sww-2955sww-359nfsg-031sww-2405sww-1513nfsg-116sww-2962sww-1611sww-1615sww-2372sww-2659nfsg-026nfsg-070nfsg-006sww-2967sww-2957sww-2966sww-2568sww-2958nfsg-187nfsg-197sww-2356nfsg-105sww-2188sww-2558sww-2953nfsg-224sww-177sww-180nfsg-069sww-1955sww-2027nfsg-204nfsg-073sww-2362sww-1777sww-2954sww-472
Ia-f
sww-1513sww-333sww-2315sww-2307sww-2405nfsg-031sww-2971sww-2955sww-2967sww-1666nfsg-197nfsg-105sww-1591sww-2396sww-2558sww-2953sww-274sww-807sww-191nfsg-069nfsg-205sww-2027nfsg-204nfsg-073sww-1948sww-1777sww-2362sww-2954
Ia-m
05101520253035404550556065707580859095100105110
L. Liu et al. 4 SI
!!2a!!!!!!!!!!!!!!!!!!!!!!!IIa$f!!!!!!!!!!!!!!!!IIa$m!!
2b!!!!!!!!!!!!!!!!!!!!!!!IIb$f!!!!!!!!!!!!!!!!IIb$m!!
PVCA-911/912
sww-461
sww-523sww-1534PVCA-867/868sww-2545PVCA-269/270PVCA-65/66PVCA-225/226PVCA-861/862PVAAG-3205/3206PVAAG-2797/2798sww-2501sww-716PVCA-149/150PVGA-1889/1890sww-573PVCAG-2207/2208PVCAG-2647/2648PVCAG-2461/2462sww-2352PVCA-917/918nfsg-135sww-2399nfsg-125PVGA-2079/2080sww-83MPVCA-597/598sww-1581nfsg-009sww-1622nfsg-129_260sww-2231sww-389sww-583PVCA-173/174PVGA-2073/2074sww-2662PVCA-529/530PVCA-309/310sww-2605nfsg-285
2b
nfsg-232sww-234sww-1517nfsg-154nfsg-119nfsg-285nfsg-009sww-131sww-169sww-2352sww-83nfsg-050nfsg-125sww-108sww-716sww-371sww-1622sww-3024sww-1748sww-2165sww-2351
sww-897sww-2103
nfsg-100
sww-1878
2b-f
sww-1068
sww-1581
sww-2223
sww-2591sww-2017
nfsg-315sww-2051sww-393sww-2662nfsg-062
sww-1517
2b-m
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85
90
sww-1805sww-687sww-1553sww-393sww-668PVCA-327/328_130sww-360nfsg-129PVAAG-3245/3246nfsg-130PVCA-317/318PVGA-1133/1134PVAAG-2847/2848sww-2059sww-718_185PVAAG-2973/2974PVCA-815/816sww-718sww-217PVCA-555/556sww-2640PVGA-1719/1720PVCAG-2623/2624nfsg-050PVGA-1819/1820PVCA-765/766Millet-MPGD25sww-938nfsg-052PVGA-1677/1678PVCAG-2569/2570PVAAG-3355/3356PVAAG-2787/2788sww-2455PVGA-1251/1252PVAAG-3311/3312sww-2525sww-2251PVAAG-3353/3354PVCA-969/970PVGA-1105/11065211_B07sww-532PVGA-1337/1338sww-704sww-108sww-223
2a
nfsg-025nfsg-082sww-2226sww-2059sww-1086sww-2450nfsg-129sww-205sww-234nfsg-104nfsg-232sww-718sww-2640nfsg-125sww-371sww-148nfsg-052sww-1748sww-2604sww-32SWW-938
sww-114nfsg-074sww-532sww-2373
2a-f
SWW-393nfsg-025nfsg-082sww-2226sww-2059sww-1086sww-2450nfsg-129sww-205sww-234nfsg-104nfsg-232sww-718sww-2640nfsg-125sww-371sww-148nfsg-052sww-1748sww-2604sww-32
sww-114nfsg-074sww-532sww-2373
2a-m
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Figure!S3$Con$nued(
L. Liu et al. 5 SI
CP pop
PVGA-1859/1860
sww-593
PVCAG-2397/2398sww-25025054_F06_140PVCAG-2393/2394PVCA-535/536PVGA-1703/1704PVCA-893/894PVAAG-2721/27225054_F06_170PVCA-605/606PVGA-2105/2106PVCA-405/406PVGA-1957/1958PVCA-931/932PVAAG-3029/3030 PVGA-1197/1198sww-2481sww-1761PVAAG-3319/3320PVGA-1201/1202PVGA-1599/1600PVGA-1733/1734sww-2177sww-2099PVGA-1853/18545005_B08PVGA-1665/1666PVGA-1727/1728PVGA-1983/1984PVAAG-2869/2870PVGA-1187/1188PVCA-631/632sww-611sww-2116PVCA-151/152PVCA-349/350sww-2945PVGA-2059/2060PVAC-145/146sww-2070sww-2906sww-1643PVAAG-3119/3120sww-2922
7
sww-2024
nfsg-017
sww-1818sww-659sww-2526sww-1561sww-2585
sww-2322
sww-593
sww-2630 nfsg-091sww-178
sww-119
3b-f
sww-2502
sww-944
sww-323nfsg-284
sww-1963sww-2024sww-2130sww-2033sww-2116nfsg-017sww-1693 sww-615
sww-2420
sww-1917sww-2906sww-1818
sww-2526 sww-1761sww-1561sww-7sww-2585sww-2099sww-2083
sww-2322sww-2040sww-2423sww-1556 sww-162nfsg-091
sww-43sww-1857sww-2264
3b-m
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155
3b!!!!!!!!!!!!!!!!!!!!!!IIIb$f!!!!!!!!!!!!!!!!!!!IIIb$m!!
3a$!!!!!!!!!!!!!!!!!!!!!!!!!IIIa$f!!!!!!!!!!!!!!!!!!!IIIa$m!!
sww-323
nfsg-035
sww-530sww-1747PVCA-687/688PVCA-255/256PVGA-1165/1166PVCA-243/244PVAAG-2959/2960sww-2503Millet-b255PVAAG-2857/2858nfsg-025nfsg-075PVCA-55/56PVGA-2125/2126PVCAG-2297/2298sww-1673PVGA-1499/1500PVCAG-2473/2474PVGA-1907/1908PVGA-1387/1388sww-447PVCAG-2239/2240PVGA-1555/1556PVAAG-3095/3096PVAAG-3315/3316sww-1993
3a
nfsg-214
sww-1947nfsg-225
sww-1828sww-530sww-2503nfsg-264sww-1841sww-875sww-2538sww-1673sww-82sww-2142sww-2134sww-1556sww-1953sww-579sww-2457
3a-f
sww-1882nfsg-035nfsg-214sww-519sww-323sww-1947nfsg-225sww-2054sww-1866
sww-530sww-1828sww-2503nfsg-075sww-2444sww-2099nfsg-264sww-1841sww-875sww-1673sww-82sww-1803sww-2134sww-2142sww-1987sww-141sww-579
3a-m
05101520253035404550556065707580859095100105110115120125130135140145150
Figure!S3$Con$nued(
L. Liu et al. 6 SI
Figure!S3$Con$nued(
4a$$$$$$$$$$$$IVa$f!!!!!!!!!IVa$m!
4b!!!!!!!!!!!!IVb$f!!!!!!!!!IVb$m!
nfsg-036PVGA-1135/1136PVCA-411/412_345PVCAG-2211/2212PVCA-219/220PVGA-1637/1638PVCA-793/794PVCAG-2209/2210PVAAG-3167/3168nfsg-054_175PVGA-1759/1760sww-697_165PVCA-1045/1046nfsg-223sww-1918_165sww-1813
4b
sww-1695
nfsg-189
sww-1967
sww-1858sww-1959nfsg-036sww-1918
nfsg-054
sww-705nfsg-255
4a-f
sww-9nfsg-304
nfsg-189
sww-2497
sww-1967sww-1414
sww-2271
sww-389sww-1918nfsg-036sww-2457
sww-117
nfsg-054sww-586sww-909sww-203nfsg-223nfsg-255sww-705
4a-m
05101520253035404550556065707580859095100
PVCAG-2269/2270
sww-2249
PVAAG-2979/2980
sww-1795PVGA-1955/1956
nfsg-054
PVGA-1553/1554sww-322PVGA-1955/1956PVAAG-2937/2938PVCAG-2527/2528PVCAG-2289/2290PVGA-1311/1312PVCAG-2211/2212PVGA-1723/1724PVCA-615/616PVCA-949/950sww-1918
4b
nfsg-255sww-705nfsg-054nfsg-254sww-236sww-107sww-117sww-99sww-244sww-1918nfsg-036nfsg-250nfsg-130nfsg-058nfsg-018sww-1670sww-1959sww-1858sww-383sww-1795sww-1967sww-2110sww-1830nfsg-189sww-1695nfsg-118sww-1174
4b-f
sww-705
nfsg-255nfsg-223sww-438sww-1576sww-1045nfsg-231nfsg-134nfsg-254sww-107sww-117
sww-99
sww-1959nfsg-250sww-2079nfsg-130nfsg-058sww-152sww-1414sww-1967sww-383
sww-1696
sww-1830sww-1695
4b-m
0
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L. Liu et al. 7 SI
sww-2235sww-2578
sww-2581PVGA-1989/1990PVCA-599/600PVCA-327/328_145sww-358sww-2402sww-1539PVGA-1773/1774PVGA-2123/2124nfsg-288sww-556PVAAG-3163/3164PVAAG-3139/3140PVGA-1963/1964PVGA-1243/1244PVGA-1431/1432nfsg-65Millet-MPGD19sww-489sww-2250sww-695PVCA-11/12sww-603PVCAG-2153/2154PVCA-963/964nfsg-246sww-2376PVCAG-2545/2546PVCAG-2535/2536PVAAG-2895/2896 PVAAG-3149/3150PVAAG-3365/3366 PVAAG-3343/3344PVAAG-3297/3298_320PVAAG-3297/3298_260
PVGA-1485/1486PVGA-1729/1730PVCA-1037/1038PVCAG-2599/2600
PVGA-2197/2198
PVCAG-2471/2472
3
sww-2106sww-920
sww-1406sww-2402sww-1892sww-61sww-535sww-1539nfsg-128nfsg-028 nfsg-065nfsg-183 sww-2581nfsg-243
sww-2250
sww-1896nfsg-246 sww-2376sww-256sww-189
sww-2132sww-2212
5b-f
sww-2106
sww-511
sww-2581sww-2402
sww-898
sww-1539sww-1824
sww-1923sww-556nfsg-231nfsg-065 nfsg-267nfsg-128nfsg-028nfsg-288nfsg-243
sww-2250
sww-2088sww-1896nfsg-246 sww-2376
sww-1575sww-189
sww-2132
sww-332
5b-m
0
5
10
15
2025
30
3540
45
5055
60
6570
75
8085
90
95100
105
110115
120
125130
135
140145
150
155160
165
5b!!!!!!!!!!!!!!!!!Vb$f!!!!!!!!!!!!!!!!Vb$m!!
CP pop
nfsg-171
PVCAG-2279/2280sww-2338
nfsg-48_175
PVGA-1143/1144
PVCA-797/798
PVGA-2067/2068
PVAAG-2861/2862
sww-598
PVGA-1357/1358
PVAAG-3331/3332
PVGA-1813/1814
PVGA-1649/1650
sww-2404PVGA-1971/1972
PVAAG-2939/2940
sww-2368
sww-2387
4
sww-2106
nfsg-048sww-2402
sww-1892sww-2648sww-2338
sww-88sww-2271
sww-918 nfsg-065nfsg-287 sww-2791
sww-1674
nfsg-126
nfsg-195
sww-2078
sww-2344sww-240nfsg-291
nfsg-256
sww-2517nfsg-246
sww-2589sww-352
5a-f
sww-194
nfsg-171nfsg-048nfsg-027sww-2402sww-3016sww-1892sww-2648sww-2338
sww-88
sww-2271
nfsg-065sww-2437sww-389
sww-1674
nfsg-126nfsg-195
sww-240nfsg-291
nfsg-256nfsg-246sww-2517
sww-115
sww-2132 nfsg-165
sww-824
sww-2306 sww-2428sww-352sww-35
5a-m
0
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5a!!!!!!!!!!!!!!!!!Va$f!!!!!!!!!!!!!!!!Va$m!!
Figure!S3$Con$nued(
L. Liu et al. 8 SI
6b$!!!!!!!!!!!!!!!!!!!!VIb$f!!!!!!!!!!!!!!!!VIb$m!!
!!!!!!!6a!!!!!!!!!!!!!!!!!!!VIa$f!!!!!!!!!!!!!!!!VIa$m!!
PVCA-1023/1024
PVCAG-2147/2148PVCA-477/478
PVAAG-3053/3054_180d
sww-1969
sww-1889PVGA-1115/1116PVAAG-3017/3018PVCA-347/348PVGA-2081/2082nfsg-079nfsg-051PVCA-929/930nfsg-057
PVCAG-2437/2438sww-1749
6b
sww-1889sww-2580sww-2284sww-3039sww-3033 sww-381sww-2180 sww-3046sww-3043nfsg-057sww-1549sww-1573sww-1926sww-47sww-3026
6b-f
sww-545sww-2580sww-456sww-971sww-3039sww-3033 sww-381sww-3046sww-2159 nfsg-057nfsg-079nfsg-209nfsg-051nfsg-090sww-49sww-3047sww-2272sww-47sww-3026sww-3035sww-2796sww-3027
6b-m
05101520253035404550556065707580859095100105110115120125130135140145150155160
sww-209
sww-1754
PVCA-341/342
sww-1573
PVCA-415/416sww-568sww-685
sww-2557nfsg-164PVGA-1209/1210PVAAG-3053/3054_175
nfsg-145
nfsg-239
6a
sww-209
sww-3034sww-2342sww-1729sww-1649sww-65sww-3025nfsg-007sww-3041
sww-3035
nfsg-145
6a-f
sww-2180sww-3034sww-1729sww-2342nfsg-203nfsg-265sww-1914sww-3043sww-1813sww-842
sww-2072
sww-3035
nfsg-145nfsg-239
6a-m
05101520253035404550556065707580859095100105110115120125130135
Figure!S3$Con$nued(
L. Liu et al. 9 SI
7a$!!!!!!!!!!!!!!!VIIa$f!!!!!!!!!!!!!!VIIa$m!!
VIIb$
VIIa!
Circos!image!was!taken!from!Okada!et(al.!2010!!Gene@cs.!Doi:10.1534/[email protected]!!!
PVCAG-2167/2168 0.0
PVCAG-2491/2492 1.4
PVCAG-2163/2164 1.9
PVCAG-2389/2390 3.8
7b7b$
CP pop
sww-2896
PVCAG-2503/2504
PVAAG-3051/3052
PVAAG-3253/3254PVAAG-2881/2882sww-2532
PVGA-1869/1870
sww-1394
sww-2167
sww-2876
PVGA-2139/2140
Millet-MPGD17
sww-1742
17
sww-2480sww-1718 nfsg-241sww-2864 sww-3017sww-2883sww-2887sww-2167sww-2803sww-2876sww-3013sww-1589 sww-2899sww-2819 sww-2934sww-3005sww-2947sww-2851 sww-2859sww-2865 sww-2880sww-2890 sww-348sww-2922sww-2830 sww-2893sww-2938 sww-3018sww-566sww-2312sww-1656 sww-2891sww-1176 sww-2832sww-2908 sww-3021nfsg-075sww-2426sww-2931nfsg-109sww-2068nfsg-008 sww-2722sww-2833 sww-3011sww-1741 sww-2777nfsg-081sww-2670 sww-2677sww-433
7a-f
sww-2449sww-1718 sww-2480nfsg-241 sww-2818sww-2112 sww-386sww-2896sww-2149sww-124sww-2951sww-2864 sww-3017sww-2869sww-2887sww-1394 sww-2167sww-2803sww-2883sww-2876sww-3013sww-2881 sww-3023sww-2789 sww-2853sww-2934sww-2819sww-3005sww-2947sww-2779sww-348sww-2859sww-2865sww-2851sww-2880sww-3018sww-1656sww-2312sww-1176sww-2845 sww-2848sww-2874sww-2908sww-2927
7a-m
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
Figure!S3$Con$nued(
L. Liu et al. 10 SI
8b!!!!!!!!!!!!!!!!!VIIIb$f!!!!!!!!!!!!!VIIIb$m!!
8a!!!!!!!!!!!!!VIIIa$f!!!!!!!!!!!VIIIa$m!!
PVAAG-2961/2962
PVCAG-2187/2188Millet-b159PVCAG-2651/2652
PVCA-541/542
nfsg-112
PVGA-1149/1150PVGA-1275/1276PVGA-2005/2006PVGA-1627/1628nfsg-219PVGA-1291/1292
nfsg-034
sww-2631sww-1862
8b
sww-2308sww-2656nfsg-034
sww-271
sww-539sww-2135
nfsg-066
sww-2980sww-2985
8b-f
sww-579
sww-2335
nfsg-112sww-2998sww-2140sww-1750sww-2281sww-1982sww-416nfsg-102sww-37sww-2984nfsg-215nfsg-219sww-2308sww-2656nfsg-034sww-271
nfsg-066
sww-2980sww-2985
8b-m
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
nfsg-190
5048_B06_180
PVAAG-2955/2956
sww-2443
nfsg-179
PVCA-979/980
PVAAG-3181/3182
PVCA-285/286
sww-123
8a
nfsg-164
sww-2225
nfsg-190sww-2496nfsg-231sww-416nfsg-277
nfsg-179sww-873nfsg-124sww-2135
8a-f
nfsg-190sww-2443sww-2656nfsg-179nfsg-215nfsg-277sww-2308sww-416sww-2135
sww-572sww-123
8a-m
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
Figure!S3$Con$nued(
L. Liu et al. 11 SI
Figure S3 Collinerity between this and published linkage map (Okada et al. 2010). The names of linkage groups (LGs) in this study are indicated with Arabic numbers in bold, and the designation of LGs and two subgenomes (‘a’ and ‘b’) is consistent with the reference map (Okada et al. 2010). The letter ‘f’ and ‘m’ at the end of reference LGs (Roman number) denotes female and male parent maps, respectively. To compare the two maps, the duplicated loci amplified from same markers in reference map and the band sizes were removed. All loci mapped with the same markers across LGs are highlighted with matching colors.
9a!!!!!!!!!!!!!!!!!!IXa$f!!!!!!!!!!!!!!IXa$m!!
9b!!!!!!!!!!!!!!!!!!IXb$f!!!!!!!!!!!!!!IXb$m!!sww-564
nfsg-055Sorghum-Xtxp46PVCA-425/426nfsg-137sww-170PVAAG-3091/3092sww-651PVAAG-3027/3028PVGA-1513/1514PVGA-1405/1406sww-2285sww-2561sww-463nfsg-133nfsg-270sww-2364PVCA-17/18PVGA-1605/1606_160PVCA-17/18_210sww-2097_205PVCA-863/864PVGA-1091/1092sww-2292PVGA-1611/1612PVCAG-2517/2518sww-125nfsg-039
9a
sww-2260sww-2654sww-125sww-391nfsg-133nfsg-055nfsg-273sww-389sww-2173sww-50sww-124sww-2285sww-2113sww-225nfsg-302sww-1123sww-242sww-170nfsg-137nfsg-290nfsg-107sww-342nfsg-211sww-1789sww-2201sww-2194sww-1794
9a-f
sww-2260sww-2654sww-2262nfsg-055sww-2524sww-2022sww-50nfsg-211sww-737nfsg-302sww-1123sww-170sww-2175sww-1523sww-2606sww-968sww-2221sww-2331nfsg-101sww-2295sww-554sww-2168nfsg-059nfsg-096nfsg-021sww-2369sww-2647nfsg-154sww-2292nfsg-270sww-2391sww-466sww-2274sww-127
9a-m
05101520253035404550556065707580859095100105110115120125130135140145150155
sww-2234PVGA-1605/1606_315nfsg-139PVGA-1941/1942nfsg-002PVGA-1843/1844sww-2527PVGA-1605/1606_210Millet-b171PVGA-1663/1664PVGA-1225/1226_168PVGA-1769/1770sww-387nfsg-262sww-2031PVGA-1301/1302PVGA-1225/1226_190PVGA-2083/2084PVGA-1559/1560PVAAG-2901/2902sww-466nfsg-202nfsg-299sww-2446PVGA-1153/11545008_B05nfsg-045sww-166sww-2381sww-166_100sww-1678_130dPVCA-811/812sww-2221nfsg-200sww-2097sww-2377PVCA-37/38sww-2113PVCA-7/8nfsg-132PVCAG-2487/2488Millet-p44PVCA-19/20PVGA-1351/1352sww-1678nfsg-021PVCA-717/718nfsg-010PVCAG-2615/2616PVCA-17/18_340sww-585sww-364sww-1812
9b
sww-341
sww-2144nfsg-005sww-620nfsg-139nfsg-002sww-2527nfsg-237sww-391sww-2524sww-2403sww-2446nfsg-039nfsg-262nfsg-294sww-166nfsg-290sww-59nfsg-200sww-2221sww-2377nfsg-132nfsg-021sww-2528
sww-2391nfsg-230
sww-2274
9b-f
sww-341sww-516sww-2144nfsg-005nfsg-006sww-620sww-1924nfsg-061nfsg-139sww-2244nfsg-002sww-2527nfsg-237sww-1746nfsg-283sww-369sww-147nfsg-262sww-251nfsg-294nfsg-202sww-166nfsg-290sww-59nfsg-045nfsg-154sww-1678sww-2097nfsg-200sww-276sww-2221sww-376nfsg-132sww-833sww-2528sww-453sww-2391sww-748sww-2091sww-346nfsg-010sww-2044nfsg-164
9b-m
05101520253035404550556065707580859095100105110115120125130135140145150155160165170
Figure!S3$Con$nued(
L. Liu et al. 12 SI
File S1
Raw Genotyping Data
File S1 is available for download at http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.111.001503/-‐/DC1.
L. Liu et al. 13 SI
Table S1 Expected progeny phenotypes and segregation ratios for disomic and tetrasomic inheritance in a selfed
population of a tetraploid switchgrass plant
Inheritance mode
Marker scoring types
Genotypes of two bands
observed a
Theoretical genotypes of selfed progeny b Expected selfed progeny band pattern
Expected progeny ratio
Disomic
co-‐dominant
AB 1AA, 2AB, 1BB a:ab:b 1:2:1
Tetrasomic ABBB (1AABB,2ABBB),1BBBB ab:b 3:1
AABB 1AAAA,(8AAAB,18AABB,8ABBB),1BBBB a:ab:b 1:34:1
AAAB 1AAAA,(2AAAB,1AABB) a:ab 1:3
Disomic
dominant
A_ (1AA, 2A_ ), 1_ _ presence:absence 3:1
Tetrasomic A_ _ _ (1AA_ _ ,2A_ _ _ ),1_ _ _ _ presence:absence 3:1
AA_ _ (1AAAA,8AAA_ ,18AA_ _ ,8A_ _ _ ),1_ _ _ _ presence:absence 35:1
AAA_ (1AAAA,2AAA_ ,1AA_ _ ) presence:absence all presence a Italicized capital letters represent genotypes. b The genotypes in parenthesis produce the same gel banding phenotypes.
L. Liu et al. 14 SI
Table S2 Detection of redundancy among published primers (Tobias et al. 2006, 2008; Wang et al. 2011) using
bl2seq basic local alignment search tool (BLAST) (NCBI, Bethesda, MD)
Marker ID of Wang et al. (2011)
Marker ID of Okada et al. (2010)
SSR type % Read (similarity)
Read length (bp)
E value Bit score b
PVGA-‐1225/1226 NFSG005 gSSR 100 21 9.00E-‐08 39.9
PVGA-‐1901/1902 NFSG006 gSSR 100 22 6.00E-‐08 41.7
PVGA-‐1643/1644 NFSG066 gSSR 100 21 4.00E-‐09 39.9
PVGA-‐1419/1420 NFSG102 gSSR 100 20 2.00E-‐10 38.1
PVGA2-‐1329/1330 NFSG136 gSSR 100 20 7.00E-‐09 38.1
NFSG249 gSSR 100 20 5.00E-‐08 39.9
PVGA-‐1669/1670 NFSG187 gSSR 100 21 4.00E-‐08 39.9
PVGA-‐1627/1628 NFSG215 gSSR 100 21 2.00E-‐09 38.9
PVGA-‐1657/1658 NFSG243 gSSR 100 21 1.00E-‐08 30.7
PVGA-‐1867/1868 SWW2864 eSSR 100 20 2.30E-‐08 39.9
PVGA-‐2035/2036 SWW2881 eSSR 100 21 4.00E-‐08 39.9
PVGA-‐1295/1296 SWW2954 eSSR 100 21 7.00E-‐09 38.8
PVCAG-‐2245/2246 SWW3033 eSSR 100 21 2.10E-‐09 30.7
PVGA6-‐1793/1794 SWW2839 eSSR 76 16 4.00E-‐06 38.8
PVGA5-‐1697/1698 sww2845 eSSR 100 21 1.41E-‐09 38.8
PVCA-‐ 985/986 SWW3043 eSSR 100 18 8.10E-‐07 38.1
sww1 a 4821_A04 eSSR 100 20 2.00E-‐09 38.1
sww842 4934_H04 eSSR 100 20 1.00E-‐09 38.1
SWW35 No reverse sequence hit in GenBank eSSR
NFSG028 Redundant with NFSG027 gSSR
a The last four primer pairs are the comparison of primer pairs from same research group (Tobias et al. 2006, 2008; Okada et al. 2010) b Note the bit score represents the normalized value that can be used to compare alignment scores from different searches
L. Liu et al. 15 SI
Table S3 Presentation of identical bridge markers in the linkage groups (LGs) of this map and a previous
study (Okada et al. 2010)
LGs in this study
Corresponding LGs and subgenome designation of Okada et al. 2010
No. of bridge markers
LGs and alternate subgenome
designation of Okada et al. 2010
No. of bridge markers
1a Ia 5 Ib 0
1b Ib 10 Ia 5
2a IIa 8 IIb 2
2b IIb 8 IIa 1
3a IIIa 6 IIIb 1
3b IIIb 7 IIIa 0
4aa IVa 4 IVb 1
4b IVb 3 IVa 2
5a Va 3 Vb 0
5b Vb 8 Va 2
6a VIa 3 VIb 1
6b VIb 4 Via 0
7a VIIa 4 VIIb 0
7b VIIb 0 VIIa 0
8a VIIIa 4 VIIIb 0
8b VIIIb 3 VIIIa 0
9a IXa 8 IXb 1
9b IXb 16 Ixa 2
Total 102 15
a Two bridge markers (nfsg-‐054 and sww-‐1918) were shared by both LG 4a and 4b.
L. Liu et al. 16 SI
Table S4 A list of switchgrass markers and their corresponding nine chromosomes of foxtail millet by BlastN
analysis in Phytozome v7.0
Chr. of foxtail millet
Switchgrass markers Total
I nfsg-‐026,nfsg-‐105,nfsg-‐197,PVAAG-‐2987/2988,PVAAG-‐3327/3328,PVAAG-‐3351/3352,PVCA-‐179/180,PVCA-‐411/412,PVCA-‐627/628,PVCAG-‐2199/2200,PVCAG-‐2379/2380,PVCAG-‐2439/2440,PVCAG-‐2537/2538,PVGA-‐1253/1254,PVGA-‐1271/1272,PVGA-‐1353/1354,PVGA-‐1573/1574,PVGA-‐1669/1670,PVGA-‐1735/1736,PVGA-‐1925/1926,PVGA-‐1947/1948,PVGA-‐2119/2120,sww-‐112,sww-‐1615,sww-‐162,sww-‐1667,sww-‐177,sww-‐196,sww-‐2115,sww-‐2196,sww-‐2240,sww-‐2271,sww-‐2320,sww-‐2405,sww-‐2489,sww-‐333,sww-‐359,sww-‐606,sww-‐660,sww-‐673
40
II PVCA-‐529/530,5211_B07,Millet-‐MPGD25,nfsg-‐050,nfsg-‐052,nfsg-‐125,nfsg-‐129,nfsg-‐130,nfsg-‐285,PVAAG-‐2787/2788,PVAAG-‐2797/2798,PVAAG-‐2847/2848,PVAAG-‐3205/3206,PVAAG-‐3245/3246,PVAAG-‐3311/3312,PVAAG-‐3353/3354,PVAAG-‐3355/3356,PVCA-‐173/174,PVCA-‐269/270,PVCA-‐309/310,PVCA-‐317/318,PVCA-‐327/328,PVCA-‐555/556,PVCA-‐597/598,PVCA-‐765/766,PVCA-‐815/816,PVCA-‐861/862,PVCA-‐867/868,PVCA-‐911/912,PVCA-‐917/918,PVCA-‐969/970,PVCAG-‐2207/2208,PVCAG-‐2461/2462,PVCAG-‐2569/2570,PVCAG-‐2623/2624,PVGA-‐1105/1106,PVGA-‐1133/1134,PVGA-‐1337/1338,PVGA-‐1677/1678,PVGA-‐1719/1720,PVGA-‐1819/1820,PVGA-‐2079/2080,sww-‐108,sww-‐1553,sww-‐1581,sww-‐1622,sww-‐1805,sww-‐217,sww-‐223,sww-‐2231,sww-‐2251,sww-‐2352,sww-‐2455,sww-‐2501,sww-‐2525,sww-‐2545,sww-‐2640,sww-‐2662,sww-‐360,sww-‐389,sww-‐393,sww-‐461,sww-‐523,sww-‐532,sww-‐573,sww-‐583,sww-‐668,sww-‐704,sww-‐716,sww-‐718,sww-‐938
71
III 5005_B08,5054_F06,Millet-‐b255,nfsg-‐025,nfsg-‐035,nfsg-‐075,PVAAG-‐2721/2722,PVAAG-‐2869/2870,PVAAG-‐2959/2960,PVAAG-‐3095/3096,PVAAG-‐3119/3120,PVAAG-‐3315/3316,PVAAG-‐3319/3320,PVCA-‐151/152,PVCA-‐405/406,PVCA-‐55/56,PVCA-‐631/632,PVCA-‐687/688,PVCA-‐893/894,PVCA-‐931/932,PVCAG-‐2239/2240,PVCAG-‐2297/2298,PVCAG-‐2393/2394,PVCAG-‐2473/2474,PVGA-‐1115/1116,PVGA-‐1187/1188,PVGA-‐1197/1198,PVGA-‐1201/1202,PVGA-‐1665/1666,PVGA-‐1703/1704,PVGA-‐1727/1728,PVGA-‐1957/1958,PVGA-‐1983/1984,PVGA-‐2059/2060,PVGA-‐2105/2106,PVGA-‐2125/2126,sww-‐1643,sww-‐1673,sww-‐1761,sww-‐1993,sww-‐2070,sww-‐2177,sww-‐2481,sww-‐2502,sww-‐2503,sww-‐2906,sww-‐2922,sww-‐2945,sww-‐323,sww-‐447,sww-‐530,sww-‐593,sww-‐611
53
IV PVCA-‐1045/1046,nfsg-‐036,nfsg-‐054,PVAAG-‐3167/3168,PVCA-‐219/220,PVCA-‐615/616,PVCA-‐793/794,PVCA-‐949/950,PVCAG-‐2269/2270,PVCAG-‐2527/2528,PVGA-‐1311/1312,PVGA-‐1553/1554,PVGA-‐1637/1638,PVGA-‐1723/1724,PVGA-‐1759/1760,PVGA-‐1955/1956,sww-‐1795,sww-‐697
18
V PVCA-‐1037/1038,Millet-‐MPGD19,nfsg-‐048,nfsg-‐065,nfsg-‐246,PVAAG-‐2861/2862,PVAAG-‐2895/2896,PVAAG-‐2939/2940,PVAAG-‐3139/3140,PVAAG-‐3149/3150,PVAAG-‐3331/3332,PVCA-‐11/12,PVCA-‐797/798,PVCAG-‐2153/2154,PVCAG-‐2197/2198,PVCAG-‐2279/2280,PVCAG-‐2471/2472,PVCAG-‐2535/2536,PVCAG-‐2545/2546,PVGA-‐1143/1144,PVGA-‐1243/1244,PVGA-‐1963/1964,PVGA-‐1989/1990,PVGA-‐2123/2124,sww-‐1539,sww-‐2235,sww-‐2338,sww-‐2368,sww-‐2376,sww-‐2387,sww-‐2402,sww-‐2404,sww-‐2578,sww-‐2581,sww-‐358,sww-‐598,sww-‐603
37
VI PVCA-‐1023/1024,nfsg-‐145,nfsg-‐164,nfsg-‐239,PVAAG-‐3017/3018,PVAAG-‐3053/3054,PVCA-‐341/342,PVGA-‐1209/1210,sww-‐1754,sww-‐1889,sww-‐1969,sww-‐209,sww-‐2557,sww-‐568,sww-‐685 16
VII Millet-‐MPGD17,PVCAG-‐2163/2164,PVCAG-‐2389/2390,PVCAG-‐2503/2504,PVGA-‐1869/1870,sww-‐1394,sww-‐1742,sww-‐2532 8
VIII 5048_B06,nfsg-‐034,nfsg-‐112,nfsg-‐219,PVAAG-‐2961/2962,PVAAG-‐3181/3182,PVCA-‐541/542,PVCAG-‐2187/2188,PVGA-‐1149/1150,PVGA-‐1275/1276,PVGA-‐1627/1628,sww-‐123,sww-‐1862,sww-‐2443 14
IX
Grand
5008_B05,Millet-‐b171,Millet-‐p44,nfsg-‐010,nfsg-‐039,nfsg-‐055,nfsg-‐132,nfsg-‐133,nfsg-‐200,nfsg-‐202,nfsg-‐262,nfsg-‐270,PVAAG-‐2901/2902,PVAAG-‐3027/3028,PVAAG-‐3091/3092,PVCA-‐17/18,PVCA-‐19/20,PVCA-‐37/38,PVCA-‐425/426,PVCA-‐7/8,PVCA-‐811/812,PVCA-‐863/864,PVCAG-‐2517/2518,PVCAG-‐2615/2616,PVGA-‐1091/1092,PVGA-‐1135/1136,PVGA-‐1153/1154,PVGA-‐1301/1302,PVGA-‐1351/1352,PVGA-‐1405/1406,PVGA-‐1513/1514,PVGA-‐1605/1606,PVGA-‐1611/1612,PVGA-‐1663/1664,PVGA-‐1843/1844,PVGA-‐1941/1942,PVGA-‐2083/2084,Sorghum-‐Xtxp46,sww-‐125,sww-‐166,sww-‐1678,sww-‐170,sww-‐1812,sww-‐2031,sww-‐2097,sww-‐2113,sww-‐2221,sww-‐2234,sww-‐2285,sww-‐2292,sww-‐2364,sww-‐2377,sww-‐2381,sww-‐2446,sww-‐2561,sww-‐364,sww-‐387,sww-‐463,sww-‐466,sww-‐564,sww-‐585,sww-‐651
62
total 319
