Determination of Raspberry Cultivar Authenticity Based on Multiplexed Microsatellite Fingerprinting

Figures & data

Table 1. The list of 12 selected SSR primers used in the study, their sequences, repeat motifs, allele sizes, optimized annealing temperatures (T_a), and numbers of cycles

Primer	Primer sequences (5ʹ-3ʹ)	Repeat motif	Reported allele sizes (bp)	Obtained allele sizes (bp)	Ta (°C)^a	No. of cycles
Rim15	F: CGACACCGATCAGAGCTAATTC R: ATAGTTGCATTGGCAGGCTTAT	(ATC)5	349–361	352–364	59	30
Rim17	F: GAAACAGGTGGAAAGAAACCTG R: CATTGTGCTTATGATGGTTTCG	(TG)6	185–205	193–199	59	25
Rim19	F: ATTCAAGAGCTTAACTGTGGGC R: CAATATGCCATCCACAGAGAAA	(AG)12	167–219	165–181	55	30
Rim36	F: AGCAACCACCACCTCAACTAAT R: CTAGCAGAATCACCTGAGGCTT	(TG)7	202–339	296–310	55	30
Rub25a	F: GCCAAACACACCGTTATCTT R: CATTACCACACGCTTGATGC	(GT)8	144–150	144–154	59	30
Rub108a	F: CCCTACACATCGATCGCTTAC R: AACACTCCAAATGCCCAATC	(CT)9 (AT)	149–174	151–157	59	30
Rub262	F: TGCATGAAGGCGATATAAAGG R: TCCGCAAGGGTTGTATCCTA	(AG)15	217–225	201–221	59	30
Rub277	F: GCCCCATCCTGTACAAAGAA R: TTGCAACAAAGGTACGTAATGG	(A)11(AG)8	234–250	235–243	59	25
Rhm3	F: CCATCTCCAATTCAGTTCTTCC R: AGCAGAATCGGTTCTTACAAGC	(TG)10	191–216	195–207	55	30
Rhm11	F: AAAGACAAGGCGTCCACAAC R: GGTTATGCTTTGATTAGGCTGG	(TC)18	270–319	284–294	55	30
Rhm21	F: CAGTCCCTTATAGGATCCAACG R: GAACTCCACCATCTCCTCGTAG	(TC)6	278–294	287–307	55	30
Rhm43	F: GGACACGGTTCTAACTATGGCT R: ATTGTCGCTCCAACGAAGATT	(AC)6	344–380	359–373	55	30

^aT_a – annealing temperature

Figure 1. Multiplex of three microsatellite locus: Rim001, Rub228, Rim277

Table 2. Fragment sizes (bp) of the six genotypes, at 12 microsatellite loci. Specific sizes are in bold

Cultivar	Rim15	Rim17	Rim 19	Rim 36	Rub 25a	Rub 108a	Rub 262	Rub 277	Rhm 3	Rhm 21	Rhm 11	Rhm 43
‘Glen Ample’	354	195	177	310	144 154	151 157	217	235 243	195 199	284	287 291	371 373
‘Polka’	356	193	179 181	296 310	144	157	207 209	235	195	284	291 293	371 373
‘Meeker’	352 364	195	165 177	310	144 154	151 153	217 221	235	199 207	284	287	377
‘Rose de Côte d’Or’	352	195 197	167 173	310	144 152	153	201 211	235	203	284	301 307	359 367
Sicoly	352 356	195 197	175 181	310	144	151 157	213	235	195 199	284 294	291 293	367 371
Dieffenbach	352 356	199	179 181	310	144 154	157	221	235	195	284	287 291	357 367

Table 3. SSR loci analyzed and parameters of genetic variability calculated for different microsatellite loci of the six Rubus genotypes: number of alleles (n), observed (H_o) and expected (H_e) heterozygosity, and polymorphic information content (PIC)

Locus	n	Ho	He	PIC
Rim15	4	0.500	0.742	0.622
Rim17	4	0.333	0.727	0.620
Rim19	7	0.833	0.894	0.796
Rim36	2	0.167	0.167	0.141
Rub25a	3	0.667	0.530	0.424
Rub108a	3	0.500	0.682	0.555
Rub262	7	0.500	0.894	0.796
Rub277	2	0.167	0.167	0.141
Rhm3	4	0.500	0.712	0.599
Rhm11	5	0.833	0.833	0.692
Rhm21	2	0.167	0.167	0.141
Rhm43	6	1.000	0.879	0.777
Average	4.083	0.514	0.617	0.526

Figure 2. Electrotraces for identification of the cultivar ‘Glen Ample’ based on combination of six microsatellite loci

Figure 3. Electrotraces for identification of the cultivar ‘Rose de Côte d’Or’ based on combination of six microsatellite loci

Figure 4. Electrotraces for identification of the cultivar ‘Meeker’ based on combination of seven microsatellite loci

Figure 5. Electrotraces for identification of the raspberry genotype Dieffenbach based on combination of six microsatellite loci

Figure 6. Electrotraces for identification of the raspberry genotype Sicoly based on combination of six microsatellite loci

Figure 7. Electrotraces for identification of the cultivar ‘Polka’ based on combination of six microsatellite loci

Figure 8. Neighbor-joining dendrogram showing similarities among six raspberry genotypes based on 12 SSR markers