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Fig. 2 | BMC Genetics

Fig. 2

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

Fig. 2

The Hfr-2 (AY587018.1) gene comprises two exons and one intron. The numbers at start and end of the structure indicate the nt positions of the mRNA sequence in Hfr-2 (AY587018.1). The 5′ and 3′ untranslated regions (UTR) are not shown. BLAST analysis with the wheat genome repository ( retrieved (Expect = 0) the complete genomic sequence of alleles on chromosomes 4BS, 4BL, 2BS and 5AL; and partial sequences of alleles on chromosomes 5BL, 4BS, 4BL and 2DL. The complete coding sequences on four contigs are: 4BS contig 4,958,329 (4018 bp) – complement (447..1537, 1856..2243); 4BL contig 7,039,907 (8364 bp) - (2916..3303, 3619..4709); 2BS contig 5,190,813 (2627 bp) - (714..1101, 1420..2510); 5AL contig 2,765,398 (12,008 bp) - (8239..8639, 8964..10053). The partial coding sequence on the 5BL contig 10,798,540 (1553 bp) - (< 27..1117>). Allelic variations were observed in the intron sizes and the SNPs identified in the exons of these 5 alleles (Additional file 1: Table S1). Sequence alignment enabled the design of three primer pairs (Table 1) to sequence the exons of Hfr-2 for wheat cultivars in this study. Analysis (see ‘Results’ and ‘Discussion’) facilitated the development of a SNP assay at nt 1294 (SNP1294_Hfr-2 assay) for the selection of Hfr-2 from R sources. Contigs not illustrated are 4BS contig 4,958,328 (3162 bp)-complement (447..1537, 1858..2245); 4BS contig 4,888,577 (1419 bp)- (< 1..973), partial exon II; 2DL contig 9,762,580 (542 bp)- (< 26..542>), partial exon II; 4BL contig 7,014,725 (700 bp)- complement (< 1..700>), partial exon II; 4BL 7,009,722 (1814 bp)- complement (< 306..692>), partial exon I. Ten alleles of this gene have been identified

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