Fine mapping of quantitative trait loci for sucrose and oligosaccharide contents in soybean [Glycine max (L.) Merr.] using 180 K Axiom® SoyaSNP genotyping platform

Soybean [Glycine max (L.) Merr.] is one of the major legume crops in the world and two types of soluble sugars, sucrose and oligosaccharides, are important determinants for consumer acceptance of soybean products. Thus, understanding soluble sugar profiling in seeds is important in breeding. The recombinant inbred lines have a number of advantages in genetic and breeding researches, even though it is a time-consuming and labor-intensive process. However, their application has been limited, because of the number of available molecular markers and lack of high-throughput genotyping technology. Today, high density fine mapping is available due to the development of single nucleotide polymorphism markers and various advanced microarray technologies. The Axiom(A (R)) 180 K SoyaSNP is state-of-the-art genotyping technology with 180,961 markers, with 96-well or 384-well microarray formats. The objective of this study was to revisit the previously constructed mapping population, which was from the cross between Keunolkong and Iksan 10, with 180 K SoyaSNP assay, and conduct fine mapping for quantitative traits locus (QTL) for sucrose and oligosaccharide contents. Total 26,054 among 180,961 markers showed polymorphism and 8967 high quality markers, average 448 markers per each chromosome, covered the whole 20 chromosomes with 0.6 cM of average distance of each marker and used to construct highly saturated linkage map. Through inclusive composite interval mapping method, 5 QTLs on 4 chromosomes were identified. Also, most QTLs were defined within 65-650 kbps region of genome with 10-42 annotated genes. This result showed that, with the aid of high saturated linkage map using Axiom(A (R)) 180 K SoyaSNP genotyping technology, we could narrow down the QTL regions to gene level to identify the traits responsible genes, instead of broad range of QTL region.