Markers:SSR

From RadishDB

Contents 1 Computationally identified 2 Tested 2.1 Raphanus raphanistrum, NY population, variable 2.2 Raphanus raphanistrum, NY population, little variation

Computationally identified

• SSRs from all 7 libraries, ~25,000 clones each:
  • Data table: Radish_est25000_ssr_map_080529.xls.gz
  • Methods: see here

Tested

Raphanus raphanistrum, NY population, variable

Locus	Fwd Primer	Rev Primer	Repeat	Allele Size	Mg (mM)	DNA(ng)	Tm (C)	Anneal (C)
Bn26A	TAAACTTGTCAGACGCCGTTATC	CCCGTAAATCAAGCAAATGG	GA	90-120	2.5	6	53	52
Bn35d	GCAGAAGGAGGAGAAGAGTTGG	TTGAGCCGTAAAGTTGTCACCT	GA	222-251	2.5	6	58	61
BRMS-005	ACCTCCTGCAGATTCGTGTC	GCTGACCTTTCTTACCGCTC	GA	132-175	2.5	6	56	50
Na10-D07	CTACTTTGATGGACACTTGCC	TCTGAAGTTGATTAGTCGGTCC	CA-TA	126-164	2.5	6	54	50
Na10-G10	TGGAAACATTGGTGTTAAGGC	CATAGATTCCATCTCAAATCCG	GA	120-140	5	6	52	50
Na10-H06	AGAATGAGACCCAGAAACCG	GCCACACTCTCTCTTACTAGGGC	CT	120-140	2.5	6	56	52
Na12-E05	CGTATGTTTGTTCCACCTGC	ACTAGCAACCACAACGGACC	CA	133-150	2.5	6	55	52
Na14-E08	TTACTATCCCCTCTCCGCAC	GCGGATTATGATGACGCAG	GCC	85-122	2.5	6	55	50
Ni3-D03	ACCGGAGACGAAACTACCG	CCTCTTCGACGTTTTTGGTG	GCC	115-118	2.5	6	56	52
Ol10-G05	TCAATGCTCTTGTAGTCTTTGACC	AGAATGAGAGCGTGGAGAGG	CT	L1 116-130	5	6	57	50
Ol10-G05	TCAATGCTCTTGTAGTCTTTGACC	AGAATGAGAGCGTGGAGAGG	CT	L2 103-105	5	6	57	50
Ra1-H08	GTCGATGATCACGGAAGAGG	CTTGACAGCTACGGTTTGTCC	AGG/CGG	184-204	2.5	6	56	52
Ra2-E11	GGAGCCAGGAGAGAAGAAGG	CCCAAAACTTCCAAGAAAAGC	CT	167-191	2.5	6	54	61
JKC1	TGCACGTGGTATGTGATAAA	GAATGAGCAAATTAACTTAAGG	AG	159-185	1.25	6	52	40
JKC2	TAACCCGTCAGGGAAGACAC	AATGGCACCCACTACCATTT	AG	207-227	1.25	6	56	50
JKC4	AGAAGCGAGAATGGCTTTCA	CACGAAAGCAGACCAAGACA	AG	207-215	1.25	6	54	50
JKC15	AGCAACAGAAGGCAAACACA	CCTGGTGCTTCCAACAATTT	AG	106-118	1.25	6	55	40

Raphanus raphanistrum, NY population, little variation

Locus	Fwd Primer	Rev Primer	Repeat	Allele Size	Mg (mM)	DNA(ng)	Tm (C)	Anneal (C)
Na10-A08	CATGGTTAAAACAATGGCCC	CAAGAAACACCATCATTTCTCA	CT	140-145	5	6	53	49
Na10-F08	AAACTTGCTTTCGAGGATGG	AAACCAGTTGACTCCATCGG	GCC	165	5	6	54	52
Na12-H02	CTATGGTTCATCTTTCGCCG	GCTGCACATCCATCTCTCG	GA	210	5	6	55	61
Na14-F11	CTATGGTTCATCTTTCGCCG	CATGCTCCAACCACAGTTTG	GT	240	2.5	6	55	52
Na14-G06	AAACGGCTTGCATTGTTCTC	GGCTTGCTTGATCCAGTCTC	GT	184	5	6	56	58
Ni2-A02	GAGTGGAATCTTGCTACTGTCG	AAGGTCTGTGGAAATGACAGG	CT	150	2.5	6	56	52
Ni2-C12	ACATTCTTGGATCTTGATTCG	AAAGGTCAAGTCCTTCCTTCG	GA	180	2.5	6	52	49
Ni2-E05	CTCGTCTCAGGGATTATGTCG	CAGACAGAGGATAGACCGAACC	CT	165	2.5	6	55	43
Ol10-F09	AGAGAGCGAGATTGATTGGC	AAACGACCACGAGTGATTCC	GA	123	5	6	56	58
Ol11-E03	GCTCTCCCAGTGAGAATCAC	GAAAACCAATCCAGTGCCTG	GCC	145	2.5	6	55	52
Ra3-D02B	CACAGGAAACCGTGGCTAGA	AACCCAACCTCAACGTCTTG	GA	256	2.5	12	56	52
JKC3	CCACTTCTTCCCCACACTA	TTCATCAATGGTGACCAAAT	AG	193-204	2.5	6	50	52
JKC6	TTTGCGGAAGAGAAATAGGT	GCAAGCTATTTTCGATTAAGG	AG	196-204	2.5	6	50	52
JKC9	ATCCAACAAAAGGAAGGAGA	GGAGACAACCAAACACAAAG	AG	224	2.5	6	52	52
JKC10	GCTACACCAAGGGCCAATCT	GCCCTGCAGAGATCAGTCTT	AG	250-260	2.5	6	57	52
JKC11	GAATCAAGGTCTCAAGAGCA	GAATCAAGGTCTCAAGAGCA	AG	166	2.5	6	51	52
JKC12	ATTTGCGGAAGAAAGATAGG	TCATCACAACTATGAATCAAGA	AG	175	5	6	50	40
JKC16	TGGAAAACCCTGTGAAAATTG	TTGCCTAGCCATTGTCTTTG	AG	194	2.5	6	53	52
JKC18	CCTTTTCCTCTCTGTTTCCTTC	TCGGTAAGAATCCCGTCTTG	AG	166	2.5	6	54	50
JKC19	CGACATCACACCGGTAACAG	TGTTTCTAGGCTTTGGACTTTTG	AG	200	2.5	6	54	50
JKC21	ATGCTTCCGCAAAACTCAAG	CGCAGTTTGAGCTCCTTTGT	AG	240	2.5	6	56	50
JKC22	TGCGGAAGTTAGATTCGGTTT	TTTGCCATTTTCAACTTAAGGAA	AG	209-211	1.25	6	55	40
JKC23	AGGAGAGATTGCGTGAGAGAA	CGCATCTCAGACCCATTTGT	AG	210-215	2.5	6	55	50
JKC24	TGTGGAGATTAATCAAGAACAGGA	ATCAGGCGCATGAATCAGAC	AG	200	2.5	6	55	50
JKC28	TGATGTTGCGGAAGAGAAAGG	TCACACTGAGTAAAATTAAGGGAAA	AG	177	2.5	6	53	50
JKC29	ATGCCTTGGGCTGATTCATA	GCAACTTGCCAAGCTTACTCT	AG	246	2.5	6	56	50