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Fig. 1 | BMC Genetics

Fig. 1

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

Fig. 1

The Hfr-1 (AF483596.1) gene comprises four exons and three introns. The numbers at start and end of the structure indicate the nt positions of the coding sequence in the Hfr-1 mRNA sequence (AF483596.1). The 5′ and 3′ untranslated regions (UTR) are not shown. BLAST analysis with the wheat genome repository (https://wheat-urgi.versailles.inra.fr/Seq-Repository/) retrieved the complete genomic sequences of three alleles; one on chromosome 7DS and two on 4AL. The coding sequences on these 3 contigs are: 7DS contig 3,851,079 (9354 bp, Expect = 0) - (2067..2428, 2590..2785, 2870..3088, 3192..3452), 4AL contig 7,100,402 (9669 bp) - (6726..7087, 7246..7441, 7526..7743, 7847..8107) and 4AL contig 7,061,271 (2643 bp)- (1056..1404, 1567..1762, 1845..2063, 2167..2427). Allelic variations were observed in the sizes of intron I and 2, and the SNPs identified in the exons of the three alleles (Additional file 1: Table S1). Sequence alignment enabled the design of four primer pairs (Table 1) to sequence the exons of Hfr-1 for wheat cultivars in this study. Analysis (see ‘Results’ and ‘Discussion’) facilitated the development of a SNP assay at nt 883 (SNP883_Hfr-1 assay) for the selection of Hfr-1 from resistant sources with the R allele. The closely related protein, AAC49284.1 also has four exons and three introns. BLAST analysis retrieved complete genomic sequences of three alleles on chromosomes 4DS, 4BS, 4AL and a partial sequence on chromosome 4DL. The coding sequences on these contigs are: 4DS contig 2,315,729 (11,564 bp, Expect = 3e− 79)- complement (4882..5142, 5253..5483, 5601..5787, 6022..6374); 4BS contig 4,932,707 (9792 bp) - complement (2403..2663, 2773..3003, 3121..3307, 3542..3894); 4AL contig 7,126,572 (9728 bp)- complement (1441..1701, 1812..2042, 2160..2346, 2578..2891) and a 4DL contig 14,119,728 (430 bp) – complement (< 1..91, 209..395>). Like the Hfr-1 protein, this closely related protein has a dirigent domain and a jacalin-like lectin domain.

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