Soybean is one of the most important food crops worldwide.  Like other legumes, soybean can form symbiotic relationships with Rhizobium species.  Nitrogen fixation of soybean via its symbiosis with Rhizobium is pivotal for sustainable agriculture.  Type III effectors (T3Es) are essential regulators of the establishment of the symbiosis, and nodule number is a feature of nitrogen-affected nodulation.  However, genes encoding T3Es at quantitative trait loci (QTLs) related to nodulation have rarely been identified. Chromosome segment substitution lines (CSSLs) have a common genetic background but only a few loci with heterogeneous genetic information; thus, they are suitable materials for identifying candidate genes at a target locus.  In this study, a CSSL population was used to identify the QTLs related to nodule number in soybean.  Single nucleotide polymorphism (SNP) markers and candidate genes within the QTLs interval were detected, and it was determined which genes showed differential expression between isolines.  Four candidate genes (GmCDPK28, GmNAC1, GmbHLH, and GmERF5) linked to the SNPs were identified as being related to nodule traits and pivotal processes and pathways involved in symbiosis establishment.  A candidate gene (GmERF5) encoding a transcription factor that may interact directly with the T3E NopAA was identified.  The confirmed CSSLs with important segments and candidate genes identified in this study are valuable resources for further studies on the genetic network and T3Es involved in the signaling pathway that is essential for symbiosis establishment. 

Soluble sugar content in seeds is an important quality trait of soybean.  In this study, 57 quantitative trait loci (QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers.  After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified.  To further verify the consensus QTLs, a population of chromosome segment substitution lines (CSSLs) was analyzed.  Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents.  Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively.  Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes (Glyma.19G146800, Glyma.19G122500, and Glyma.19G128500) were identified in the genetic fragments introduced from wild soybean.  Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism (SNP) mutation in the coding sequence of Glyma.19G122500, causing a non-synonymous mutation in the amino acid sequence that affected the predicted protein structure.  A Kompetitive allele-specific PCR (KASP) marker was developed based on this SNP and used to evaluate the CSSLs.  These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding.