Development of SNP assays for hessian fly response genes, Hfr-1 and Hfr-2, for marker-assisted selection in wheat breeding

Table 1 Sequences of primer pairs for the amplification of exon segments in Hfr-1 and Hfr-2 genes

Primer names	Primer sequence (5′ to 3′)	Amplicon size (bp)	Exon	Overall outcomes
Hfr-1
Hfr-1_F1	CCTCAGTCTTTCACCTTGGAGACC	294	I	The sequences were poor.
Hfr-1_R1	CCCGAGGTGCAAACCTTGAGC	294	I	The sequences were poor.
Hfr-1_F2	GGTTTACAGGTTCCAGTTTCAAGG	205	II	7 SNPs occurred randomly across cultivars
Hfr-1_R2	CACCAGAGGTCTTAAGAAGGAGAG	205	II	7 SNPs occurred randomly across cultivars
Hfr-1_F3	CCGAGTCCGACCAGCTTTCTC	237	III	7 SNPs were detected –some result in no amino acid change, some result in amino acid substitution but did not differentiate any R cultivar from S ones.
Hfr-1_R3	CTACCGTGTCCTTGTTATCCCCAC	237	III
Hfr-1_F4	CCTTCAGAGATCGTTACGGAAGT	210	IV	8 SNPs were detected. The SNP at nt 883 (AF483596) was found to differentiate some R cultivars from S cultivars (Table 3).
Hfr-1_R4	CTCCACGTAYTTACCAGCGCAC	210	IV
Hfr-2
Hfr-2_F1	GCAAGTACCTAGGTAGCGTGC	340	I	2 SNPs were observed to occur in random.
Hfr-2_R1	CGTACCTGATGGATAGATTATTGTCC	340	I	2 SNPs were observed to occur in random.
Hfr-2_F2a	CTTCCGTCCYCAGCAGACAAC	678	II	29 SNPs were detected but were found across both S and R cultivars.
Hfr-2_R2a	GGTGTCATTGGTTGAAGTCATGCTGG	678	II
Hfr-2_F2b	CTATGGCGTGGAGTTCAAGCTC	433	II	The SNP at nt 1294 (GenBank AY587018) was found to differentiate some R cultivars from S cultivars (Table 3). 16 other SNPs found were not informative.
Hfr-2_R2b	TCTTGTAGGTAACAACCTCTCCTG	433	II

Refer to Additional file 1: Table S1 for details of the SNPs observed in the exon fragments of Hfr-1 and Hfr-2 of S and R wheat accessions sequenced

ISSN: 2730-6844