View Full Table | Close Full ViewTable 1.

Comparison of the results of different microsatellite (simple sequence repeat [SSR]) search software programs showing motif type and class for the perfect microsatellites and number of compound SSRs found with Automated Microsatellite Marker Development (AMMD), SSRLocator (SSRL), and Tandem Repeats Finder (TRF).

 
AMMD
SSRL
TRF
Perfect
Perfect
Perfect
Motif Class I Class II C Class I Class II C Class I Class II
Di-nt 105 (91.3%) 1270 (29.7%) 771 (93.3%) 1674 (13.8%) 805 (71.8%)
Tri-nt 10 (8.7%) 1212 (28.3%) 55 (6.7%) 4012 (33.2%) 236 (21.1%) 42 (9.0%)
Tetra-nt 1219 (28.5%) 4337 (35.9%) 9 (0.8%) 23 (4.9%)
Penta-nt 262 (6.1%) 1009 (8.3%) 15 (1.3%) 31 (6.6%)
Hexa-nt 313 (7.3%) 1055 (8.7%) 56 (5.0%) 372 (79.5%)
Subtotals 115 4,276 336 826 12,086 1,844 1,121 468
Total 4,727 14,756 1,589
Percentages indicate amount of microsatellite loci in that category of motif and class for perfect microsatellites compared to the total number of SSRs identified with the software program in a given class.
Class I microsatellite loci defined as those SSRs with 10 or more repeats and class II microsatellite loci are defined as those SSRs with less than 10 repeats according to Shultz et al. (2007).
§Total number of identified SSRs, including SSRs with and without primer design.
C = compound SSRs were not detected by TRF.
#nt, nucleotide.



View Full Table | Close Full ViewTable 2.

Characteristics of the integrated map showing number of simple sequence repeat (SSR) loci based on two microsatellite (SSR) search software programs as well as number of contigs and clones integrated per linkage group (LG) and bacterial artificial clone (BAC). Contig length and genetic versus physical distances and lengths are calculated for each LG.

 
LG or chromosome No. BMb markers (BP3) No. BMb markers (AMMD) Total BMb markers Total SSR markers No. linked BAC contigs No. linked BAC clones BAC contig length (Mbp) Genetic length (cM) Genetic distance between markers (cM) Physical length (Mbp) Kbp:cM ratio
b01h 8 13 21 29 21 1535 13.0 195.2 6.7 58.1 297.6
b02d 11 10 21 43 20 659 7.5 212.0 4.9 57.1 269.3
b03c 9 8 17 27 17 552 6.5 151.3 5.6 60.1 397.2
b04b 7 6 13 26 13 617 5.6 155.1 6.0 55.9 360.4
b05e 5 4 9 17 9 497 4.2 125.0 7.3 51.4 411.2
b06g 5 6 11 18 11 332 3.4 84.1 4.7 46.2 549.3
b07a 9 6 15 24 15 785 8.6 116.0 4.8 61.2 527.6
b08f 14 9 23 29 22 802 7.3 145.8 5.0 63.6 436.2
b09k 6 3 9 20 9 189 2.3 142.2 7.1 60.4 424.8
b10i 10 6 16 22 15 1467 2.3 139.9 6.3 65.0 464.6
b11j 7 4 11 25 10 797 6.9 108.3 4.3 58.3 538.3
8.3 6.8 15.1 25.5 14.7 748.4 6.1 143.2 5.7 57.9 425.1
TOTAL 91 75 166 280 162 8232 78.2 1575 637.3
BP3, BatchPrimer3.
AMMD, Automated Microsatellite Marker Development software.
§Estimated physical length in Mbp for each linkage group (LG) or chromosome from Fonsêca et al. (2010).
Kbp:cM ratio was calculated using the estimated chromosome length reported by Fonsêca et al. (2010) and the genetic distances of the present integrated genetic map.