Comparative Analysis and EST Mining Reveals High Degree of Conservation among Five Brassicaceae Species

Table 5

Details of the SSR markers used for evaluation of amplification among cultivars of Brassica and cultivar of Raphanus sativus.

S. no.	Primer_Id^#	Forward primer sequence (5^′→3^′)	Reverse primer sequence (5^′→3^′)	Product Size^∗	Anneal. temp.^$
1	Bn_Genomic114	TGGTATTCGGGCATTGGTAT	GCAACCACACAGAAGGACAA	153	60
2	Bn_Genomic29	GAGTCTGATCCTGCCTCCAT	CTTTGTTAGCGGCTCCATGT	171	55
3	Bn_Genomic33	CTAACGACCCTTTTCCGTCA	AAACCCCACGTTCATTTTTG	194	55
4	Bo_Genomic166	GCATGCTATGTTGGGAACCT	AAGAAGACGAGCAAGGACGA	181	65
5	Bo_Genomic76	CAAGGCCAAGGTATCTGGAA	CTCTCTGACCGAGCCATCAT	160	55
6	Bo_Genomic77	GATTGAAGGCGCTTAGGAGA	ACATGCGGGATTTTGAAGAC	151	60
7	Bo_Genomic85	GAGGCGAGTACGGTTCAAGT	CCCAAATGAGGGAAAACAAA	160	65
8	Bo_Genomic90	AGCAAGAAGAGGCTCACCAA	CCGAATAGTGATGCACCAAA	199	55
9	Br_Genomic654	GGCTCTAAGCAAGTGGGACA	AAGTGCCGATGACGAAGAAG	165	60
10	Br_Genomic664	CTCTTTCCCTTTCCGGTAGC	CTCAATCGGTTCTTCTGCTG	187	55
11	Br_Genomic665	CGGCCATTCATACCATCTCT	ACAGGAGAAAGGAGCCCGTA	152	55
12	Br_Genomic674	CGAAGCAAATGAAGCAGACA	GAGGAACGGTTCAGCAAGAG	159	55
13	Br_Genomic677	TTTTACCAACGCCTTGATCG	ACCGCCTTCATCGTATTGAC	184	55
14	Br_Genomic684	TCATTCATCCGCAGCACTAC	CACGTCTGGTTGTGCGTATC	171	55
15	Br_Genomic692	AATGTTTGCAGGAGGAGAGC	ATGCAACTGAATGTGGTGGA	156	60
16	Br_Genomic697	CTCTTTACTTGCGGGAGACG	CAGCCTCCTTCACCAAGAAC	198	55
17	Br_Genomic708	TCCCCATCGACCTTTCTTCT	GGGAACCAGCATCATCAGTT	153	NA
18	Br_Genomic709	GCTTGCTTGGCTGATTTGTT	CAAGCATTCACGACATCACC	154	65
19	Br_Genomic718	CCTCGTGTCAGCGACCATA	AAGAACACATCGCCTCCTTC	178	55
20	Br_Genomic730	ACTAGGAAGAAGAAGGGAGAAACC	CCGAGCCCATTTCATTGTAT	150	55
21	Br_Genomic732	AGCATTTGCACATGTTGGTT	ATGTGCCTCGCATGTGAAT	159	55
22	Br_Genomic739	TAGGGTGAAAGGGAAGCTCA	CGCTAATAATGGCGCTAAGG	150	60
23	Br_Genomic773	GTTTCTATCGGTGCCTCGTG	TGGCCACTATGGTTTTGTCA	163	55
24	Br_Genomic777	GCACTCAGGAGAACAGAGCA	CCTGGTAAAACGTGTTGCATT	163	55
25	Br_Genomic910	AACCCCGCTGAGCTTTACTC	GTTTCCAGGAATCGCTTTGA	159	55
26	Br_Genomic935	TACCCAGTCCCAACTTGCTC	GATCTGCTGGTTGGGGATAG	192	55
27	Br_Genomic938	TTTTGTCCCTTTCCCAAATC	AGCACAAACCACACCCAAA	173	55
28	Br_Genomic939	TGAGAACAGAAGCTCAGAGTCG	TTCCTCTGTGACTGACTACAAAACA	150	NA
29	Br_Genomic940	TTTCTCCAAGGCAGAGAGGA	CACCGCATGATTTGATTGAA	178	55
30	Br_Genomic942	AGGGAGAAAACGCGTTGATA	CCTGGATGTTTGCACCCTAT	171	55
31	Br_Genomic944	ACTTGGCTCTCGATTTGCTC	TGGAGTGTTCCATCTTCCAT	176	NA
32	Br_Genomic945	CGGAACCACCTCCTTGTCTA	AACCGGTTTGTCAGGTTTTG	157	NA
33	Br_Genomic946	CGGTGAGAGAGAGGGAGATTC	TCTCCTTTGTTTGGGCTCAG	181	55
34	Br_Genomic948	AGTTCAAACCAGGTGCTGCT	GCCGGCCCTAAGATTTATGT	152	60
35	Br_Genomic952	TGAGCAGACGAAACCTGCT	AGAAGGGAGGAAGGAACGAA	168	55
36	GSS_Bn_154	CATGCTCAAAGTAGACGCAGA	GCCTTTGCTTCACAACACAA	170	55
37	GSS_Bn_313	TTCCGTCACCTAACTAGTCACC	ATATTGAGACGCCGCAGAAC	164	55
38	GSS_Bn_366	CCAAGGGGGAGTGTTATGAA	AGAGTGAAAAGGAAAACCTCCT	175	55
39	GSS_Bn_418	GAAGCAGCATCATGCCTGTA	CAAACCATAGTCAAGGCCTCA	158	55
40	GSS_Bn_423	TCAGTGTGCGTAGGAAACAAA	GGTGGGTACCTAATGGTTGG	150	NA
41	GSS_Bn_427	TTGGATCGTACTGGCCTGAT	GTCCTTGTTATGCGGCAAAG	153	55
42	GSS_Bn_432	CACATGAACAATTGCTTGGAG	TTCGTCAAGCTACCACTGGA	174	55
43	GSS_Bn_448	AGCGGAGATTGACTCAGACC	GGCTTCGTCTAAAGCCACAG	170	NA
44	GSS_Bn_450	AAGAGCAGGCAACAAATCGT	GCTTGGCGAAGTAAAAACAA	156	NA
45	GSS_Bn_464	TCCGACGCAAACTATCATCA	TCGATCACCGATGAAGTCAC	150	55
46	GSS_Bn_469	TCTCTGGTCACCCCTCTAGC	CTCCATCGAAGAAAGCCAAA	151	55
47	GSS_Bn_483	TGTTGCTGCTTCTTCGTTTG	AATCTTCACCAACGCTGCTT	158	55
48	GSS_Bn_506	GGGAAGACCCAGAAGGAAAC	AGGGAGAGGGAGAAGTGAGG	151	55
49	GSS_Bn_517	GTGGCGACTCTGGTGAAGAC	ATTCAATTCGCTTCCTCACG	161	55
50	GSS_Bn_546	AAATAGTCGCGATGCGTTTT	TCCTTTCGTTCCGACAATTC	159	55
51	GSS_Bn_549	GCCCTGCTCGTTAGAAGAAA	AGCTTGTCCCATTCCAACAC	164	60
52	GSS_Bn_552	TCCTTTCGTTCCGACAATTC	AAATAGTCGCGATGCGTTTT	165	65
53	GSS_Bn_561	TTGCCATCTCTCCTTCGATT	CTGGAGGTGCAGCTTTGACT	168	55
54	GSS_Bn_568	TCCCGTACGATCCTTTGAAC	ATGACGCGACGGATTATGA	151	55
55	GSS_Bn_570	GACAAAAAGAGCCCACATGAA	AGCAGGTTCTTCTCCACCAA	168	65
56	GSS_Bn_571	GGTTGCTACGGTGGAGCTAA	GAGGTTGAGACGGAAAAGCA	156	65
57	GSS_Bn_574	CTAATCGACGCAGACGACAG	TTTGGCTTCTCCTCGAACTC	179	55
58	GSS_Bn_577	GGCATTCTCAGGTCAGTGCT	GGTCCTGTTCCTGAATTCCTC	159	NA
59	GSS_Bn_579	CTACCACCGGGAAGAAAACA	CCCTCTGTCTCCCAGTACCA	150	55
60	GSS_Bn_583	TGGGAATTGCAACATGAAGA	CAAAGATCGGCGAAGAAGAC	190	55
61	GSS_Bn_606	CCGGATAGAGATGGAAATGG	ATTCTCCTCAGCAGCAGCA	189	55
62	GSS_Bn_612	GCTTGCATGTGCTAGGTTCA	ATACGAGCAAGGACGAGACG	183	NA
63	GSS_Bn_613	AGGAATGGGTCAGATCAAGC	GTCGCTGTCTCTCTCGTCCT	194	NA
64	GSS_Bn_614	GCCCACAAAAATGCTGAAAT	TTCGCTTGATTAGCTGGAAA	156	65
65	GSS_Bn_616	GAATCAAGCCACCAGCACTT	AGGAGTGATGAGCTGGCAGT	152	60
66	GSS_Bn_617	TCGAGTCATAACGCCTTTCG	AAACCGGTCGGTTAAAATCA	160	65
67	GSS_Bn_620	AAGGTGAAGCCTTTGGGTCT	AAGCCAACGAAAGCAAAAAC	165	55
68	GSS_Bn_622	TGTGGTGATTGCTGCTACAGA	TATGCAGCTGCTTTTGCTTC	189	NA
69	GSS_Bn_623	AAGACCCAAGACCCAAGACC	CAGCTTGGAGAGAGAGGAAGG	151	55
70	GSS_Bn_624	ATAACAGTCGTCCCCCTTCC	CAGCAGAGACTTGTGGGACA	189	55
71	GSS_Bn_625	CTTCGCCTCGATAAAGAACG	TGTTATATGGGGAAAGGTAGGC	177	55
72	GSS_Bn_626	AACCGAACCGAAAACCAAA	TGTTGCGCGGGATTATTTAT	152	55
73	GSS_Bn_628	GGGTGACCGTGATCATAGTGT	CTTCTGCATCGTCCAAATCA	167	55
74	GSS_Bn_629	CGGACCTATTCCTCAAGAGC	AGGAGACAAGGAGCCACTCA	199	55
75	U_Boleracea_320	AATCTGAATGGGCAGTTTGG	GAGCAGCCCTCATCATCATC	190	60
76	U_Boleracea_321	TGAGTCCACAAACCAGACCA	TCATCATCTTTGTTGGGACCT	162	55
77	U_Boleracea_404	AGAAGAAGAAGGGCCAAACC	TCCGAGCTTAGATCTGTCGAG	161	NA
78	U_Boleracea_433	GAACCGCTCATGAATGCTACT	CCCCAAGGATTAGGAAGTGG	200	55
79	U_Boleracea_447	CTATTCCGGCGAACTTCTCA	ACGATCCGTTACTCCCGTTA	150	55
80	U_Boleracea_460	CCCGGAAGAGTTTCCCTATC	ATCCCCTGAGAAGCTGGAAT	174	55
81	U_Boleracea_503	ATCAACACAGCCTCCAGCTT	GTTGATTCGGGTGCAAGAGT	153	55
82	U_Boleracea_504	TCCGATCAAGTCCCATCAAT	CACTGCTTCCCCTTTAGCAG	152	55
83	U_Boleracea_505	TAACCCAGGAGGTGGTCAAG	TTTGGGGTCATACCGTTTGT	171	NA
84	U_Boleracea_506	AAGGACGCTGAAGCTACCAA	TCAAGGCCGCTACCATTTAG	187	55
85	U_Boleracea_507	TGAAGAGCTTCGAAGGAAGG	ACCGTGTGAGAATCCGAAAG	175	55
86	U_Boleracea_508	TACCGGGGAAAGAAGAAGGT	TTTCAGAATCTGCAGCAACC	163	55
87	U_Brapa_244	ATCGCAGCCTCGAGATTACT	GATCGGTGAACGGATAAGGA	158	55
88	U_Brapa_421	GGCATGGCCAGCATATAAGT	CCTCCATGAGACTTCGTCAA	170	55
89	U_Brapa_422	GGCAGAAGCATCTCCTGAAG	CGCTATGGTCCCTTTTCAGT	172	55

#Primer Id denoted as Bn: Brassica napus, Bo: Brassica oleracea, Br: Brassica rapa, GSS: Genomic survey sequences, U: Unigene.
∗Expected product size in base pairs.
$Optimized annealing temperature in ^∘C,
NA: not amplified.