Identification and molecular mapping of the semi-dwarf locus (sdf-1) in soybean by SLAF-seq method

Plant height is one of the most important agronomic traits in soybean. The semi-dwarf soybean cultivars could improve lodging resistance and solar radiation use efficiency so as to increase soybean yield. However, the inheritance of semi-dwarf traits has not been intensively studied and few semi-dwarf genes have been isolated in soybean. In this study, we use specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to map the semi-dwarf gene in soybean. Plant height of 213 F2:3 families, derived from a cross between ‘Jimidou-1’ (semi-dwarf) and ‘Gongjiao9112’ (tall), was evaluated under field conditions. Genetic analysis indicated that the semi-dwarf trait was controlled by one single recessive gene. Associated with the semi-dwarf trait, SLAF-seq combined with BSA was used to develop polymorphic SLAF markers and identify a 1.04 Mb genomic region, which was designated as sdf-1. The sdf-1 locus was delimited to 80.72 kb region on chromosome 19 by KASP SNP markers developed from the SLAF markers and 6 K SNP chip. There were 14 putative genes in the associated region. From annotation information, three genes (Glyma.19g194800, Glyma.19g194500 and Glyma.19g195200) might be interesting candidate genes that are highly related to plant height growth or semi-dwarf trait. The successful identification and localization of sdf-1 could help reveal molecular mechanisms underlying soybean semi-dwarfism and to indirectly improve total yield.