The development of a co-dominant marker for the β-conglycinin α′ subunit in soybeans

Abstract

The development of soybean varieties that lack the β-conglycinin α′ subunit is an attractive goal because the β-conglycinin α′ subunit exerts a negative influence on nutrition and tofu gelation, and is also a major allergen. We sought to develop a co-dominant DNA marker for the β-conglycinin α′ subunit (Cgy-1) gene for use in marker-assisted selection (MAS). We identified a deleted sequence responsible for the null allele of Cgy-1 in a soybean variety lacking the β-conglycinin α′ subunit known as ‘Keburi’. The deletion spanned 12,998 bp and included Cgy-1 and its incomplete tandem duplicate on chromosome 10. Based on the Cgy-1 sequence from both the Williams 82 soybean reference sequence and the Keburi variety, a set of three allele-specific primers was designed for multiplex PCR assay. These primers enabled allelic discrimination by the sizes of PCR products. This amplified two distinct DNA fragments of 913 and 649 bp in Williams 82 and Keburi, respectively. The practicality of the developed co-dominant marker for Cgy-1 was also confirmed by amplification in five other soybean varieties including three wild types and two mutants. The heterozygosity of the F1 plants at the Cgy-1 locus was ascertained using our novel co-dominant marker. This PCR-based co-dominant marker is capable of detecting the presence or absence of β-conglycinin α′ subunit for soybean marker assisted breeding system.