## 4 Discussion
### Large-Scale Genic SSR Marker Development in the Soybean
In Arabidopsis, JA is associated with the timing of senescence processes in both somatic tissues and reproductive organs [62; 63]. We found that Glyma.07g057900.3, which encodes a jasmonic acid-amido synthetase (JAR1), was downregulated in the pods of the EM and MM ecotypes. Taken together, these results imply that all six genes are related to the growth and development of soybean pods. From these results, we predicted that thenewly developed SSR markers derived from the six genes could serve for the high-resolution detection and characterization of genetic diversity based on the DTM of soybean varieties. Allelic Variations for the New SSR Markers Are Sufficient for Generating a Cluster and Distinguishing the Soybean Varieties by Ecotype Group  
Several studies have reported that the 5'-UTR of a gene influences the efficiency of translation by regulating its secondary structure [64; 65; 66], suggesting that it plays an important role in expression regulation. The 5'- and 3'-UTRs can also regulate mRNA stability [67; 68]. Out of the six SSR markers described in this study, five were predicted to lie within the 5'- or 3'-UTR. The sixth SSR, Glyma.19g164800.1, was predicted to be in the CDS regions. Moreover, our preliminary SSR deletion results indicate that the molecular markers do not affect the signal peptide or the main domains on the CDS of this gene. However, further studies are required to establish whether the SSRs affect the mRNA stability and regulation of gene expression. Genic SSR markers have been reported to not only be less polymorphic than non-genic markers [69] but to also have 3.5 alleles per locus, with a higher PIC of 0.824 among the mulberry species [70]. Similarly, previous studies reported that the genic SSR markers for jute (2.7 alleles and a PIC of 0.34) [71] and flax (2.3 alleles and a PIC of 0.35) [72] show high polymorphism and are expected to be of use for the characterization of germplasm, as well as for variety identification and marker-assisted breeding. Therefore, although the average number of alleles and PIC values of the six newly developed genic SSR markers were low (3.1 alleles and a PIC of 0.61) compared to those of the previously established six SSR markers (3.8 alleles and a PIC of 0.70), the allelic variations exhibited by the new SSR markers were sufficient for generating clustering and distinguishing the soybean varieties by ecotype group. Finally, these alleles can serve as a marker for the characterization of populations, varieties, and germplasm, as previously reported in wheat [73], jatropha [74], and oil palm [75]. Agglomerative Clustering Shows That the Six New Genic SSR Markers Can Serve for the Genotyping and Fine QTL Mapping of Soybean Pod Maturity  
We used agglomerative hierarchical clustering, a common bottom-up clustering method that uses the neighbor-joining method, for creating the phylogenetic trees [30]. This method provides a snapshot of the data that can facilitate more detailed analysis, while rapidly producing well-scaled informative networks for several hundred taxa [76]. The agglomerative clusters constructed for the six new genic SSR markers showed a strong relationship with each maturity ecotype. The EM, MM, and LM ecotypes were found to be dominant in the B-I, B-II, and B-III clusters, respectively. However, our results showed that the new set of six SSR markers based on the maturity of the soybean pod had high sensitivity for detecting genetic diversity. Thus, the six new SSR markers can serve as effective and high-resolution tools for the genotyping and fine QTL mapping of soybean pod maturity.