Identification of candidate gene mutation associated with low Stachyose Phenotype in soybean line PI200508
To investigate the genetic factors underlying a major quantitative trait locus (QTL) contributing to low seed stachyose content in two separate populations derived from soybean [Glycine max (L.) Merr.] line PI200508, the recently released ‘Williams 82’ whole genome shotgun (WGS) sequence was exploited for candidate gene discovery. The physical interval containing a low stachyose QTL from PI200508 was identified in the WGS, and screened for areas that could be exploited for linkage mapping purposes. Microsatellite sequences designed in these areas were used to develop new markers, creating tighter linkage with the QTL. Examination of the Williams 82 sequence in this interval and the corresponding glyma0.1b gene model, available through the Phytozome website (http://www.phytozome.org), revealed one candidate gene with significant homology to previously characterized galactosyltransferase genes from Arabidopsis, pea, and cucumber. Sequencing of the annotated coding region for this gene revealed a single unique sequence polymorphism between PI200508, and lines exhibiting wild-type expression of stachyose content. The mutant phenotype appears to have arisen from a 3 bp deletion, and is easily distinguished from the wild-type allele via a marker presented in this study. This mutation-specific marker explained 88 to 94% of the phenotypic variation for seed stachyose content, and 76% for seed sucrose content, traits that exhibited a strong negative correlation in this study (p < 0.01).