Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.

A transcription-aided selection (TAS) strategy is proposed in this paper, which utilizes the positive regulatory roles of genes involved in the plant immunity pathways to screen crops with high disease resistance. Increased evidence has demonstrated that upon pathogen attack, the expression of diverse genes involved in salicylic acid (SA)-mediated SAR are differentially expressed and transcriptionally regulated. The paper discusses the molecular mechanisms of the SA signaling pathway, which plays a central role in plant immunity, and identifies differentially expressed genes (DEGs) that could be targeted for transcriptional detection. We have conducted a series of experiments to test the TAS strategy and found that the level of GmSAGT1 expression is highly correlated with soybean downy mildew (SDM) resistance with a correlation coefficient R2 = 0.7981. Using RT-PCR, we screened 2501 soybean germplasms and selected 26 collections with higher levels of both GmSAGT1 and GmPR1 (Pathogenesis-related proteins1) gene expression. Twenty-three out of the twenty-six lines were inoculated with Peronospora manshurica (Pm) in a greenhouse. Eight showed HR (highly resistant), four were R (resistant), five were MR (moderately resistant), three were S (susceptible), and three were HS (highly susceptible). The correlation coefficient R2 between the TAS result and Pm inoculation results was 0.7035, indicating a satisfactory consistency. The authors anticipate that TAS provides an effective strategy for screening crops with broad-spectrum and long-lasting resistance.