Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat

Singh, Amit Kumar; Chaurasia, Shiksha; Kumar, Sundeep; Singh, Rakesh; Kumari, Jyoti; Yadav, Mahesh C.; Singh, Nidhi; Gaba, Sonam; Jacob, Sherry Rachel

doi:10.1186/s12870-018-1476-1

BMC Plant Biology

Table 1 Details of cg-WSSR markers used for studying genetic diversity among wheat genotypes

From: Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat

Gene	Marker	Chr	Forward primer (5′ → 3′)	Reverse primer (5′ → 3′)	Annealing Temp (°C)	Allele size (bp)	No of alleles	PIC Value	Repeat Motif^a	Location of motif
TaSRG	WSSR1	2DL	GAAGAAGAGAGAATACCACTGC	ATCCTATCCTATCCTTGCTTG	54	120–130	2	0.153	(AGGA)4	5’UTR
TaSnRK2.8	WSSR4	5D	AACCCCGGCAATAATAAG	CTCCTCTCCCCTCGAATC	55	160–170	2	0.455	(TC)8	5’UTR
TaNAC47	WSSR13	3DS	TTGCTTGTATGATGGTCTTTT	CGCACACAAAATATAAATAAGC	53	150–165	3	0.618	(TG)10	Promoter
TabHLH39	WSSR14	5DL	GTACTCACACGTCTGCTCCT	GGCTGAAGAGAAGTGGATTC	53	145–155	3	0.543	(CCTC)5	5’UTR
TaPP2C1	WSSR25	2BL	GGGTCTTAATTTCGATGTTTT	AAAAACTGTACAAGGCCACTC	53	140–150	3	0.646	(TG)20	Exon
TaAOC1	WSSR40	6BL	TAAATAAGGAGCCTAGGGTGT	CTGACGGAGACGGAGGAG	55	135–145	3	0.663	(CCA)5	5’UTR
TaSOS1	WSSR44	3DS	TAGACTCCCTCTTTTCAGGTT	ACAATTCCCATCTAGGATGAC	55	150–175	5	0.653	(AAG)10	Promoter
F3H1	WSSR75	2DL	ATCACCTTCTCCGAGATGTA	AATTTCGTTGAGAGACTTGGT	52	170–180	2	0.439	(CAG)5	Intron
Tagpd1	WSSR79	2AL	AAATAAATGCGAGTACCAAGA	GCACACGTGAGTGAATATGT	52	150–160	3	0.553	(TTG)10	Promoter
TaAFP-A	WSSR85	2BS	AGGTCTTCCTGAGAATTTGG	GAACCTGCCCAAGAAGTC	55	130–145	3	0.581	(CT)7	5’UTR
TaOBF1b	WSSR89	5BS	CCGTCGTCTTCCTCTACTACT	TGCTGCTACCGTTCTTATTTA	54	150–160	2	0.499	(TCT)6	5’UTR
TaACO1	WSSR101	4AL	AACCTTTGACACCTAACTTGG	CTCAGGTGTGTCGATTAGGTA	53	140–148	3	0.636	(CTT)5	5’UTR
TaGAPC1	WSSR109	7DL	TTCAATTAGCAATTGTGTCCT	CAACCAAACCAACTAAACAAA	53	150–165	4	0.712	(AC)13	Intron
TaSOS1	WSSR111	3AS	GCATCCGTATCTGTAAGCTC	GAAGGAGATCAGGATTTATGG	53	160–170	2	0.480	(GTA)5	Exon
TdSOS1	WSSR112	3AS	CTACCACAGACTCCCTCTTTT	ATGATGTCACTCTTGTTACCG	53	130–170	5	0.770	(AAG)14	Promoter
TaMYB72	WSSR115	6DS	AGCGAGAAAGAAAGAAGACAC	GATTCAAGGACAAGGAATAGG	56	175–205	3	0.664	(GCA)5	Intron
TaSrg6	WSSR121	7BL	TACAACCATTTTGAGGACAAG	ACTAGGGTGTGCACAAAAATA	53	140–170	2	0.450	(TA)11	Exon
TaClpB2	WSSR126	1AL	AGGTCCGACATCCTCATC	TTCACTTCAGCTTCAGAGTTC	54	150–165	3	0.517	(CGG)6	Exon
TaClpB5	WSSR130	5BL	ATATGTGCAAACTTTTCATGG	TCCTGTAACATAATCCTCGAC	53	150–200	2	0.469	(AG)11	Promoter
TaCRY1a	WSSR132	6DL	CTTTTGAAAGCGAAGTGACTA	TCTGAAGTGGATGGTGCTAT	53	190–195	2	0.497	(CAG)5	3’UTR
TaSP	WSSR136	5BS	GCTCATCCTGATTCTTTCTCT	CCTCCGGAGTCCATCCAC	55	110–115	2	0.460	(AT)8	Promoter
TaWD40D	WSSR139	4BS	AGAAAGTGGCTAAGATTGAGG	AGACAATAAGTTTTGGGGAAC	53	150–160	3	0.644	(TA)6	Promoter
TaNAC47	WSSR12	6AS	GCACGATAAAGGATCGAC	GAGTCAAAGGGGTTCATCTT	53	120–140	2	0.495	(CCTT)5	Intron
TaSAP1-A1	WSSR42	7DL	TTGCCTAGATTTCTACTGCTC	TTTAAGAGACCAAGTGGTACG	53	150–165	4	0.688	(TC)8	Exon
TaRab7	WSSR76	3B	CCATCTCTCTCTCCTCCTTC	GTGGTGAATTCGATGTGATCT	53	140–170	4	0.742	(CT)6	5’UTR
BI-85	WSSR39	6BS	CACCACCACCCTATATATCC	CGTGGATTTTTCTCTTTTTCT	53	124–130	2	0.497	(ATCC)5	5’UTR
TaSST	WSSR98	3AS	ACAGACCTCAACCTCTTCTTC	GGTAGTCTGTTGTCAAGGTCA	53	190–210	3	0.664	(CT)10	Intron
TaClpB2	WSSR127	1AL	TATTGCTAGTCAAGCATGTGG	AGCCTCGTTTGTATTTTAGGT	54	165–170	2	0.193	(AAT)7	Promoter
TaABL1	WSSR95	6AL	TCCGATCTCTATCCCTC	ATTAAGTATGGCTGGCAGTG	53	120–130	3	0.616	(CT)8	5’UTR
TaeIF3g	WSSR88	6DL	AAATCACCCAGAAACTAATCC	GAAGCAGGAAGTCGAGGT	53	195–220	3	0.596	(AGCG)4	5’UTR

cg-WSSR markers details such as chromosomal location, targeted gene, primer sequence with Tm, number and size of alleles amplified, PIC value, types of SSR motifs and their location in the gene sequence,. ^asubscript denotes the number of repeats

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