| Summary: | <p>Abstract</p> <p>Background</p> <p>In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat.</p> <p>Findings</p> <p>In the present study, three genome-specific primer sets for the <it>waxy </it>(<it>Wx</it>) genes and four genome-specific primer sets for the <it>starch synthase II </it>(<it>SSII</it>) genes were developed mainly from single nucleotide polymorphisms (SNPs) and/or insertions or deletions (Indels) in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the <it>Wx </it>genes and 59.5%-61.6% of the <it>SSII </it>genes. Five genome-specific primer sets for the <it>Wx </it>genes (one for Wx-7A, three for Wx-4A and one for Wx-7D) could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the <it>Wx </it>and <it>SSII </it>genes produced amplifications in hexaploid wheat, cultivated durum wheat, and <it>Aegilops tauschii </it>accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions.</p> <p>Conclusions</p> <p>For the first time, we report on the development of genome-specific primers from three homoeologous <it>Wx </it>and <it>SSII </it>genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous <it>Wx </it>and <it>SSII </it>genes in natural populations of both hexaploid wheat and cultivated tetraploid wheat. The strategies used in this paper can be used to develop genome-specific primers for homoeologous genes in any allopolypoid species. They may be also suitable for (i) the development of gene-specific primers for duplicated paralogous genes in any diploid species, and (ii) the development of allele-specific primers at the same gene locus.</p>
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