Development of High-Resolution Simple Sequence Repeat Markers through Expression Profiling of Genes Associated with Pod Maturity of Soybean

Abstract

In soybeans (Glycine max L.), the time required to attain maturity is a quantitative trait controlled by multiple genes and quantitative trait loci (QTL), which enable soybean cultivars to adapt to various regions with diverse day lengths. In this study, depending on the days to maturity, 100 soybean varieties were classified into eight maturity groups numbered from 0 to VII. The maturity groups were further sorted into three maturity ecotypes: early, middle, and late maturity. The analysis of 55,589 soybean genes revealed a total of 1147 related to the growth and development of soybean pods, including 211 genes with simple sequence repeats (SSRs). We further identified 42 SSR markers that amplified over two alleles in three different ecotypes, including six genes that were up- or downregulated in pods of more than one ecotype. The agglomerative hierarchical tree constructed for the newly identified SSR markers had three clusters. Clusters B-I, B-II, and B-III were found to be strongly related with the early, middle, and late maturity ecotypes, respectively. Therefore, the newly identified set of SSR markers can serve as an effective high-resolution tool for the genotyping and QTL mapping of soybean pod maturity.