TABLE 1.
Identification and selection of sorghum BACs
| Locus | Bin | RFLP size (bp) | Probe typea | Probe name | Sorghum FPC contigs | No. of BACs hit | Selected sorghum BACsb | FISH probe selected | cMc | Mean ± SEM (n)d | FISH locus (cMC)e | Cytolocus name |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| agrr118b | 9.00 | 500 | R | agrr118 | YN | 0.0 | ||||||
| bnl9.07a | 9.00 | 2400 | R | bnl9.07 | YN | 10.1 | ||||||
| umc109 (CBM 9.01)f | 9.01 | 800 | R | umc109 | 1220 | 7 | a0055A15, a0055B21, a0064C07, a0004M18, a0068L03, a0085L22, a0040A04 | a0004M18 | 15.5 | 9S.79 | spb-CBM9.01_S79 (umc109) | |
| umc148 | 9.01 | 520 | R | umc148 | 389 | 5 | a0030K10, a0038L23, a0038N20, a0094A07, a0013E22 | a0038L23 | 16.4 | FN | ||
| rz144a | 9.01 | 1500 | O | SOG1672 | 389 | 1 | a0030K10 | a0030K10 | 17.4 | 0.815 ± 0.004 (15) | 9S.82 | spb-9.01_S82 (rz144a) |
| rz144c | 9.01 | 1500 | O | SOG1672 | 389 | 1 | a0030K10 | a0030K10 | 21.4 | 0.745 ± 0.004 (12) | 9S.75 | spb-9.01_S75 (rz144c) |
| php10005 | 9.01 | 850 | R | php10005 | 389 | 5 | a0073F07, a0014C11, a0068G09, a0045A20, a0017D11 | a0045A20 | 24.8 | 0.730 ± 0.002 (31) | 9S.73 | spb-9.01_S73 (php10005) |
| csu95a | 9.01 | 1100 | O | SOG0620 | 130 | 1 | a0012H11 | a0012H11 | 27.7 | 0.678 ± 0.002 (10) | 9S.68 | spb-9.01_S68 (csu95a) |
| csu95a | 9.01 | 1100 | R | csu95 | 390 | 8 | a0018G19, a0094O05, a0095J06, a0095O12, a0060M11, a0096I01, a0095L23, a0042B21 | |||||
| umc248a | 9.01 | 600 | R | umc248 | YN | 27.7 | ||||||
| sh1 | 9.01 | 2500 | R | p246A | 392 | 7 | a0084C09, a0094F18, a0021O07, a0015M03, a0088L22, a0021O04, a0091L24 | a0015M03 | 36.4 | 0.661 ± 0.001 (18) | 9S.66 | spb-9.01_S66 (sh1) |
| bz1 (CBM 9.02)f | 9.02 | 1500 | R | pBZ | 1308 | 2 | a0028C12, a0020G06 | a0020G06 | 39.3 | 9S.65 | spb-CBM9.02_S65 (bz1) | |
| csu471 | 9.02 | 850 | R | csu471 | 393 | 11 | a0005O05, a0034A09, a0043E13, a0044I06, a0057D08, a0063M03, a0061M22, a0068O17, a0075C01, a0016H09, a0015L15 | a0075C01 | 42.8 | 0.636 ± 0.002 (55) | 9S.64 | spb-9.02_S64 (csu471) |
| umc256a | 9.02 | 700 | R | umc256 | 805 | 7 | SN | 43.2 | ||||
| csu486a | 9.02 | 1350 | R | csu486 | 394 | 8 | a0064N21, a0086K22, a0014H21, a0053H23, a0005O15, a0086N18, a0007E04, a0024L14 | a0086K22 | 45.5 | 0.385 ± 0.003 (34) | 9S.39 | spb-9.02_S39 (csu486) |
| prc1 | 9.02 | 1080 | R | 5C02A05 | 394 | 9 | a0064N21, a0086K22, a0014H21, a0053H23, a0005O15, a0086N18, a0007E04, a0024L14, a0076L04 | a0076L04 | 50.2 | 0.373 ± 0.002 (42) | 9S.37 | spb-9.02_S37 (prc1) |
| umc105a | 9.02 | 610 | R | umc105 | 396 | 3 | a0016B24, a0084H21, a0054A13 | a0054A13 | 54.7 | 0.276 ± 0.003 (17) | 9S.28 | spb-9.02_S28 (umc105) |
| csu228(pfk) | 9.02 | 1190 | R | csu228 | 397 | 6 | a0038I11, a0043G06, a0025D24, a0044C12, a0039P12, a0095E12 | a0043G06 | 59.7 | 0.269 ± 0.003 (24) | 9S.27 | spb-9.02_S27 [csu228(pfk)] |
| wx1 (CBM 9.03) | 9.03 | 2300 | G | umc25 | 131L1 (Bennetzen, UGA) | 131L1 | 63.7 | 0133 ± 0.005 (16) | 9S.13 | sbb-CBM9.03_S13 (wx1) | ||
| wx1 (CBM 9.03) | 9.03 | 2300 | R | umc25 | YN | |||||||
| tda66d | 9.03 | 300 | R | tda66 | 89 | 3 | a0074N08, a0054I24, a0064A03 | a0054I24 | 63.7 | 0.031 ± 0.001 (25) | 9S.03 | spb-9.03_S03 (tda66d) |
| cdo17 | 9.03 | 900 | O | SOG0101 | 874 | 5 | a0011N04, a0047J04, a0060M19, a0082G20, a0093K24 | a0047J04 | 67.7 | 0.027 ± 0.003 (15) | 9L.03 | spb-9.03_L03 (cdo17) |
| rf2 | 9.03 | 1200 | R | rf2a | 383 | 3 | a0060G13, a0070K10, a0090D12 | a0090D12 | 67.7 | FN | ||
| csu680d | 9.03 | 1550 | R | csu680 | 202 | 6 | a0047C15, a0005O02, a0060L03, a0058B07, a0064I11, a0051F17 | a0058B07 | 67.7 | FN | ||
| csu680d | 9.03 | 1550 | O | SOG1356 | 202 | 3 | a0058B07, a0064I11, a0051F17 | a0051F17 | ||||
| bnl7.24a | 9.03 | 2100 | R | bnl7.24 | 1 | 3 | SN | 68.7 | ||||
| bnl5.33c | 9.03 | 2100 | R | bnl5.33 | 53 | 5 | a0067P21, a0026E11, a0093B10, a0020L09, a0032H22 | a0020L09 | 68.7 | 0.043 ± 0.002 (64) | 9L.04 | spb-9.03_L04 (bnl5.33c) |
| csu321 | 9.03 | 750 | R | csu321 | 1361 | 5 | a0082L07, a0081N24, a0020F10, a0024F19, a0041D08 | a0020F10 | 69.1 | 0.035 ± 0.002 (40) | 9L.04 | spb-9.03_L04 (csu321) |
| rgpr3235a | 9.03 | ND | O | SOG1297 | 327 | 1 | a0040B08 | a0040B08 | 69.1 | 0.049 ± 0.003 (25) | 9L.05 | spb-9.03_L05 (rgpr3235a) |
| umc81 | 9.03 | 820 | R | umc81 | 14 | 5 | SN | 69.6 | ||||
| csu193 | 9.03 | 1270 | R | csu193 | 797 | 5 | a0014C14, a0025K08, a0060B09, a0057H24, a0095I20 | a0014C14 | 70.6 | FN | ||
| std6a(dba) | 9.03 | 1200 | R | pAS8 | 797 | 6 | SN | 70.6 | ||||
| gl15 | 9.03 | 1150 | R | HS1100.43 | 376 | 4 | a0073J07, a0075D13, a0084N16, a0009B14 | a0075D13 | 70.6 | 0.063 ± 0.002 (48) | 9L.06 | spb-9.03_L06 (gl15) |
| gl15 | 9.03 | 1150 | O | SOG0488 | 376 | 3 | a0073J07, a0075D13, a0084N16 | |||||
| csu147 (CBM 9.04) | 9.04 | 800 | O | SOG1865 | 69 | 4 | a0022A12, a0049N08, a0054F07, a0068M13 | a0049N08 | 72.8 | 0.073 ± 0.003 (21) | 9L.07 | spb-CBM9.04_L07 (csu147) |
| csu147 (CBM 9.04) | 9.04 | 800 | R | csu147 | YN | |||||||
| csu183b(cdc48) | 9.04 | 850 | R | csu183 | 401 | 3 | SN | 78.0 | ||||
| csu43 | 9.04 | 600 | R | csu43 | 550 | 4 | SN | 83.1 | ||||
| sus1 | 9.04 | 6000 | R | p21.2 | YN | 83.1 | ||||||
| csu694a(uce) | 9.04 | 950 | O | SOG0872 | 1336 | 1 | a0093O18 | a0093O18 | 84.5 | 0.355 ± 0.003 (14) | 9L.36 | spb-9.04_L36 [csu694a(uce)] |
| csu694a(uce) | 9.04 | 950 | R | csu694 | 179 | 6 | a0053I22, a0086B07, a0076H16, a0023A07, a0073A14, a0094G22 | |||||
| umc95 (CBM 9.05) | 9.05 | 660 | R | umc95 | 182 | 7 | a0015A13, a0041F23, a0043K19, a0063J06, a0069D12, a0075C14, a0094N21 | a0063J06 | 86.1 | 0.377 ± 0.002 (34) | 9L.38 | spb-CBM9.05_L38 (umc95) |
| csu392a | 9.05 | 1000 | O | SOG0184 | 539 | 11 | a0010M15, a0012B01, a0016C21, a0030A02, a0031D14, a0038B08, a0043J23, a0044E15, a0059K01, a0073M05, a0080L20 | a0010M15 | 97.0 | 0.413 ± 0.005 (20) | 9L.41 | spb-9.05_L41 (csu392a) |
| csu392a | 9.05 | 1000 | O | SOG0184 | 188 | 5 | a0004C15, a0010J13, a0026E03, a0041K24, a0079J11 | |||||
| csu392a | 9.05 | 1000 | R | csu392 | 188 | 6 | a0076K14, a0074B22, a0067J12, a0004C15, a0026E03, a0072C14 | |||||
| csu710e(apx) | 9.05 | 700 | O | SOG0484 | 211 | 5 | a0019J05, a0030K14, a0044G10, a0064D18, a0067N15 | a0019J05 | 101.1 | 0.456 ± 0.003 (25) | 9L.46 | spb-9.05_L46 [csu710e(apx)] |
| csu710e(apx) | 9.05 | 700 | R | csu710 | 188 | 5 | a0047M11, a0066O15, a0066B02, a0058C12, a0093L24 | |||||
| csu219(tgd) | 9.05 | 500 | R | csu219 | 189 | 3 | a0059O14, a0071H18, a0067I12 | a0059O14 | 102.3 | 0.506 ± 0.006 (43) | 9L.51 | spb-9.05_L51 [csu219(tgd)] |
| csu219(tgd) | 9.05 | 500 | O | SOG0074 | 189 | 2 | a0059O14, a0067I12 | |||||
| csu61a (CBM 9.06) | 9.06 | 500 | R | csu61 | 403 | 6 | a0018G11, a0019H12, a0018J02, a0041I20, a0063F18, a0090O20 | a0018G11 | 104.4 | FN | ||
| csu61a (CBM 9.06) | 9.06 | 500 | O | SOG1475 | 403 | 4 | a0018G11, a0019H12, a0018J02, a0041I20 | |||||
| csu59a | 9.06 | 500 | O | SOG0619 | 270 | 3 | a0019C22, a0074G20, a0084M22 | a0074G20 | 104.4 | 0.523 ± 0.002 (24) | 9L.52 | spb-9.06_L52 (csu59a) |
| csu59a | 9.06 | 500 | R | csu59 | 189 | 3 | a0059O14, a0071H18, a0067I12 | a0071H18 | ||||
| ibp1 | 9.06 | 1150 | R | pOD3g | YN | 104.4 | ||||||
| csu145a(pck) | 9.06 | 700 | R | csu145 | 191 | 8 | a0043G12, a0041H16, a0046O17, a0052M07, a0067L02, a0068L14, a0079N13, a0093D20 | a0093D20 | 105.4 | 0.534 ± 0.003 (26) | 9L.53 | spb-9.06_L53 [csu145a(pck)] |
| csu145a(pck) | 9.06 | 700 | O | SOG0076 | 191 | 11 | a0043G12, a0041H16, a0046O17, a0052M07, a0067L02, a0068L14, a0079N13, a0093D20, a0006K22, a0011D09, a0087G20 | |||||
| csu145a(pck) | 9.06 | 700 | O | SOG0076 | 538 | 10 | a0035K11, a0055A21, a0065B16, a0069H02, a0071B24, a0081E07, a0084G14, a0088L04, a0089F23, a0095K18 | a0055A21 | 0.527 ± 0.003 (13) | 9L.53 | spb-9.06_L53 [csu145a(pck)] | |
| dba4 | 9.06 | 900 | R | pAS14 | YN | 109.8 | ||||||
| csu28a(rpS22) | 9.06 | 700 | R | csu28 | 191 | 5 | a0010A04, a0032K15, a0076F19, a0087A24, a0093D21 | a0093D21 | 109.8 | 0.537 ± 0.003 (50) | 9L.54 | spb-9.06_L54 [csu28a(rpS22)] |
| asg44 | 9.06 | 500 | R | asg44 | 191 | 7 | a0047G04, a0081A19, a0033A22, a0091J11, a0064A12, a0038E07, a0032I20 | a0033A22 | 110.9 | 0.624 ± 0.002 (28) | 9L.62 | spb-9.06_L62 (asg44) |
| cdo1387(emp70) | 9.06 | nd | O | SOG0100 | 56 | 4 | a0007F13, a0012H21, a0036J08, a0087E20 | a0036J08 | 113.5 | 0.717 ± 0.002 (50) | 9L.72 | spb-9.06_L72 [cdo1387(emp70)] |
| cdo1387(emp70) | 9.06 | nd | O | SOG0100 | 191 | 4 | a0016I16, a0036F07, a0036L01, a0093N18 | a0036F07 | 0.722 ± 0.002 (38) | 9L.72 | spb-9.06_L72 [cdo1387(emp70)] | |
| csu1004 | 9.06 | 1800 | R | csu1004 | 1048 | 5 | a0027H23, a0046F16, a0046P22, a0054L18, a0067H10 | a0046P22 | 119.9 | 0.766 ± 0.001 (18) | 9L.77 | spb-9.06_L77 (csu1004) |
| asg12 (CBM 9.07) | 9.07 | 700 | R | asg12 | 386 | 3 | a0007D16, a0064E21, a0094P12 | a0064E21 | 121.2 | 0.779 ± 0.003 (35) | 9L.78 | spb-CBM9.07_L78 (asg12) |
| R | asg12 | 194 | 3 | a0036L10, a0074H17, a0076L16 | ||||||||
| std2a(dba) | 9.07 | 600 | R | pAS9 | YN | 122.7 | ||||||
| csu1118 | 9.07 | 700 | R | csu1118 | 197 | 1 | a0078D03 | a0078D03 | 124.3 | 0.828 ± 0.003 (25) | 9L.83 | spb-9.07_L83 (csu1118) |
| asg59b | 9.07 | 750 | R | asg59 | 890 | 5 | SN | 132.8 | ||||
| csu285(his2B) | 9.07 | 800 | R | csu285 | 9 | 8 | a0049P09, a0078L14, a0064J04, a0026P15, a0020P12, a0066J18, a0032B18, a0062J05 | a0026P15 | 147.4 | 0.939 ± 0.003 (27) | 9L.94 | spb-9.07_L94 [csu285(his2B)] |
| csu54b (CBM 9.08)g | 9.08 | 1400 | R | csu54 | 203 | 5 | a0021O07, a0061D07, a0074A03, a0080B23, a0076H02 | a0074A03 | 150.4 | 9L.95 | spb-CBM9.08_L95 (csu54b) | |
| csu804a(dnp) | 9.08 | 500 | R | csu804 | 203 | 3 | a0021O17, a0061D07, a0074A03 | a0061D07 | 150.4 | FN | ||
| Xtxa325 | G | sbb18256/191b4 (P. E. Klein, TAMU) | sbb18256 | 0.262 ± 0.009 (9) | 9L.26 | sbb_9.04-L26 (Xtxa325) | ||||||
| Xtxp32 | G | sbb16685/174g5 (P. E. Klein, TAMU) | sbb16685 | 0.530 ± 0.006 (8) | 9L.53 | sbb_9.06-L53 (Xtxp32) |
CBM, core bin marker; TAMU, Texas A&M University.
a
Probe type: R, RFLP; O, overgo probe; G, gift (source is indicated).
b
YN, YRL negative (failure to detect hybridization of RFLP probe on BAC-grid filter arrays); SN, Southern blot negative (failure to detect hybridization of RFLP probe on BAC validation Southern blot).
c
Centimorgan) value from the UMC 98 9 linkage map.
d
Numbers represent the mean of the fractional distance of the above-background peak (see materials and methods) FISH signals on the chromosome arm. SEM, standard error of measurement at 95% confidence level; (n) is the number of FISH signals used to calculate the mean.
e
FN, FISH negative, failed to detect FISH signals suitable for mapping on two to three slides.
f
Locus previously mapped by Koumbaris and Bass (2003).
g
IBP2 cDNA (from pOD3, H. W. Bass, unpublished data).