Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2018
Publication Date: 5/17/2018
Citation: Ibba, M., Kiszonas, A., Morris, C.F. 2018. Development of haplotype-specific molecular markers for the low-molecular-weight glutenin subunits. Molecular Breeding. 38:68. https://doi.org/10.1007/s11032-018-0827-9.
Interpretive Summary: In the present study, a total of three PCR-based molecular marker sets specific for the linkage groups at the Glu-A3 and Glu-B3 loci, and five marker sets for the linkage groups at the Glu-D3 locus were developed. Each of these molecular markers were found to be specific for the different Glu-3 loci and for each linkage group. The LMW-GS genic profile detected using these molecular markers corresponded to the results obtained in previous studies confirming the reliability of these linkage-group-specific molecular markers. In many cases, the markers developed here were more efficient than those previously reported. Specifically, compared to the molecular markers developed for the Glu-A3 and Glu-B3 allele discrimination, the markers developed here were more accurate since they were able to detect most of the LMW-GS genes rather than the polymorphism of single genes. They could discriminate different Glu-A3, and most of the Glu-B3 alleles by performing a single PCR reaction as opposed to seven, ten, or four as previously reported. The linkage-group-specific molecular markers developed here are easier to interpret, unambiguous and selectively amplify only specific LMW-GS genes/haplotypes rather than a relatively large number of amplicons. These markers could be effectively used for the discrimination of the known Glu-A3 and Glu-B3 alleles, to solve the ambiguities from the previous molecular marker, and in the future, could be employed for the selection of specific LMW-GS linkage groups more highly involved in wheat end-use quality.
Technical Abstract: Low-molecular-weight glutenin subunits (LMW-GSs) are one of the major components of gluten and their allelic variation has been widely associated with numerous wheat end-use quality parameters. These proteins are encoded by multigene families located at the orthologous Glu-3 loci (Glu-A3, Glu-B3 and Glu-D3); the genes at each locus are divided by large intergenic and highly recombinogenic regions. Among the methods used for the LMW-GS allele identification, polymerase chain reaction (PCR)-based molecular markers have the advantages of being simple, accurate and independent from the plant stage of development. However, the available LMW-GS molecular markers are either incapable of capturing the complexity of the LMW-GS gene family or difficult to interpret. In the present study, we report the development of a set of PCR-based molecular markers specific for the LMW-GS linkage groups present at each Glu-3 locus. Based on the LMW-GS gene sequences available in GenBank, single nucleotide polymorphisms (SNPs) specific for each Glu-3 linkage group were identified and the relevant PCR primers were designed. In total, we developed three molecular markers for the Glu-A3 and Glu-B3 loci, respectively, and five molecular markers for the Glu-D3 locus. The markers were tested on 44 bread wheat varieties previously characterized for their LMW-GS genic profile and found to be equally or more efficient than previously developed LMW-GS PCR-based markers. This set of markers allows an easier and unambiguous identification of specific LMW-GS genes/haplotypes connected with gluten strength and can facilitate the marker-assisted breeding for wheat quality.