TABLE 2.
Tagging information in chromosomes of EST–SSRs from different genomes
| Genome (no. of primer pairs designed)
|
||||
|---|---|---|---|---|
| Chromosomea | Ab (1379) | ADc (1250) | Dd (1554) | Total (4453) |
| No. loci tagged | ||||
| A1 (Chr. 1) | 2 | 11 | 17 | 30 |
| A2 (Chr. 2) | 4 | 6 | 11 | 21 |
| A3 (Chr. 3) | 12 | 9 | 17 | 38 |
| A4 (Chr. 4) | 5 | 8 | 15 | 28 |
| A5 (Chr. 5) | 14 | 25 | 35 | 74 |
| A6 (Chr. 6) | 6 | 13 | 18 | 37 |
| A7 (Chr. 7) | 7 | 13 | 16 | 36 |
| A8 (Chr. 8) | 10 | 10 | 25 | 45 |
| A9 (Chr. 9) | 9 | 9 | 18 | 36 |
| A10 (Chr. 10) | 6 | 9 | 13 | 28 |
| A11 (Chr. 11) | 8 | 15 | 32 | 55 |
| A12 (Chr. 12) | 6 | 13 | 24 | 43 |
| A13 (Chr. 13) | 6 | 9 | 16 | 31 |
| Total in A-subgenome | 95 | 150 | 257 | 502 |
| D1(Chr. 15) | 5 | 10 | 27 | 42 |
| D2 (Chr. 14) | 4 | 15 | 34 | 53 |
| D3 (Chr. 17) | 3 | 10 | 24 | 37 |
| D4 (Chr. 22) | 1 | 12 | 24 | 37 |
| D5 (Chr. 19) | 6 | 24 | 53 | 83 |
| D6 (Chr. 25) | 6 | 7 | 23 | 36 |
| D7 (Chr. 16) | 2 | 12 | 34 | 48 |
| D8 (Chr. 24) | 12 | 12 | 36 | 60 |
| D9 (Chr. 23) | 4 | 6 | 22 | 32 |
| D10 (Chr. 20) | 7 | 10 | 25 | 42 |
| D11 (Chr. 21) | 4 | 12 | 31 | 47 |
| D12 (Chr. 26) | 10 | 13 | 40 | 63 |
| D13 (Chr. 18) | 0 | 10 | 30 | 40 |
| Total in D-subgenome | 64 | 153 | 403 | 620 |
| At:Dt | 1.5:1 | 1:1 | 1:1.6 | |
The chromosome designation is the same as in Table1.
The ESTs used to develop 1379 EST–SSR primer pairs were from fiber EST databases in a 7- to 10-dpa fiber cDNA library in Gossypium arboreum cv. AKA8401. Of these primer pairs, 544 were developed by Han et al. (2004), 219 by Wilkins (http://cfg.ucdavis.edu), and 616 by Park et al. (2005).
The ESTs used to develop 1250 EST–SSR primer pairs were from fiber EST databases in six cDNA libraries of Gossypium hirsutum. Of these primer pairs, 489 were developed by Han et al. (2004) from 3 cDNA libraries of 5- to 25-dpa of germplasm “7235,” -0 to 5-dpa ovules, and 3- to 22-dpa fibers from G. hirsutum cv. Xuzhou 142 (Gou and Chen); 454 from cDNA library of −3- to 3-dpa ovules from G. hirsutum cv. TM-1 (Yang and Chen); 97 from cotton boll abscission zone cDNA library (Wan and Wing); 210 from 5- to 10-dpa fibers from G. hirsutum cv. Xuzhou 142 (Zhu et al.).
The ESTs used to develop 1554 EST–SSR primer pairs were from G. raimondii ESTs, with 747 from the first true leaf library and 807 from ovules from −3- to 3-dpa cDNA library (Udall et al.). All ESTs were released in GenBank (http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html).