TABLE 3.
Performance comparison between SSRMMD and other two software programs for developing candidate polymorphic SSRs.
| Organism | Rice (∼0.39 Gb) |
Cotton (∼2.29 Gb) |
Wheat (∼14.23 Gb) |
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| Software | SSRMMD | GMATA | CandiSSRc | SSRMMD | GMATA | CandiSSR | SSRMMD | GMATA | CandiSSRd |
| Total number of SSRa | 111,960 | 111,905 | 111,905 | 384,488 | 384,400 | 384,400 | 1,345,128 | 1,343,831 | 1,331,146 |
| Number of candidate marker | 68,242 | 34,667 | 8,230 | 292,307 | 166,813 | 16,315 | 572,023 | 477,531 | 129,461 |
| Candidate marker rate (%) | 60.95 | 30.98 | 7.35 | 76.02 | 43.40 | 4.24 | 42.53 | 35.54 | 9.73 |
| Number of monomorphic SSR | 50,895 | 22,865 | 0 | 259,972 | 135,821 | 0 | 364,279 | 225,287 | 0 |
| Number of polymorphic SSR | 17,347 | 11,802 | 8,230 | 32,335 | 30,992 | 16,315 | 207,744 | 252,244 | 129,461 |
| Polymorphic rate (%) | 15.49 | 10.55 | 7.35 | 8.41 | 8.06 | 4.24 | 15.44 | 18.77 | 9.73 |
| Time (min:s)b | 6:08 | 16:15 | 8,117:37 | 30:30 | 119:06 | 1,746:23 | 184:55 | 6,363:45 | 118,953:53 |
Note. SSRMMD, Simple Sequence Repeat Molecular Marker Developer; SSR, simple sequence repeat. aTotal number of SSR referred to Zhenshan97 (rice), TM1 (cotton), and CS (wheat). bBecause GMATA could not simultaneously mine different types of motifs in one task, it was multiply performed to identify SSRs, and then the time was added. cBecause CandiSSR could not normally calculate chromosome 8 of rice (the program stopped at the BLAST stage), the results of CandiSSR did not include chromosome 8. dBecause CandiSSR spent numerous time to mine polymorphic SSRs of wheat, we only selected chromosome 5D (closest to the total SSR density of wheat) to estimate the number of polymorphic SSRs.