Molecular characterization of two novel null waxy alleles in Mexican bread wheat landraces

•A collection of wheat landraces was analyzed for waxy proteins polymorphism.•A novel Wx-A1 null allele was characterized at molecular level.•A molecular marker was developed for the detection of novel Wx-A1 allele (Wx-A1o).•A novel Wx-B1 null allele was characterized at molecular level (Wx-B1l).•The Wx-B1l allele does not imply the deletion of 67 kb as the Wx-B1b allele.

Starch is composed of two glucose polymers: amylose, formed by long linear chains, and amylopectin, which is larger and highly branched. The ratio between the two polymers (usually 22–35% amylose, 68–75% amylopectin) affects the starch properties, thereby determining different aspects of wheat quality. Waxy protein, which is the sole enzyme responsible for amylose synthesis, showed polymorphism in a collection of one hundred and three Mexican landraces, including null alleles at Wx-A1 and Wx-B1 loci, respectively. Molecular characterization of these alleles showed that the null Wx-A1 allele presented in only one accession was novel (Wx-A1o) and involved a deletion spanning the three and a half last exons of the gene. Some of the accessions lacking the Wx-B1 protein contained the common allele Wx-B1b (12.6%) (deletion of approximately 67 kb), while four others (3.8%) possessed the novel Wx-B1l, characterized by the deletion of one cytosine in the second exon of the gene and leading to a change in the ORF. This novel allele is particularly interesting because the absence of the Wx-B1 protein in this case was not associated with the lack of the other genes included in the approximately 67 kb region lost with the common null allele Wx-B1b.