Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm

The Population Divergence and Genetic Basis of Local Adaptation of Wild Soybean (Glycine soja) in China

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.

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

Genetic origin and dispersal of the invasive soybean aphid inferred from population genetic analysis and approximate Bayesian computation

Biological invasion is considered among the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines, is among the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using 8 microsatellite loci and the mitochondrial cytochrome c oxidase subunit I gene. We were able to identify a significant isolation by distance pattern and 3 genetic lineages in the microsatellite data but not in the mtDNA dataset. The genetic structure showed that the USA population had the closest relationship with those from Korea and Japan, indicating that the 2 latter populations might be the sources of the invasion to the USA. Both population genetic analyses and approximate Bayesian computation showed that the northeastern populations in China were the possible sources of the further spread of A. glycines to Indonesia. The dispersal history of this aphid can provide useful information for pest management strategies and can further help predict areas at risk of invasion.

The Untapped Genetic Reservoir: The Past, Current, and Future Applications of the Wild Soybean (Glycine soja)

There is a considerable demand for crop improvement, especially considering the increasing growth of world population, continuing climatic fluctuations, and rapidly evolving plant pests and pathogens. Crop wild relatives hold great potential in providing beneficial alleles for crop improvement. Wild soybean, Glycine soja (Siebold & Zucc.), the wild ancestor to the domesticated soybean (Glycine max (L.) Merr.), harbors a high level of genetic variation. Research on G. soja has been largely devoted to understanding the domestication history of the soybean, while little effort has been made to explore its genetic diversity for crop improvement. High genomic diversity and expanded traits make G. soja populations an excellent source for soybean improvement. This review summarizes recent successful research examples of applying wild soybeans in dissecting the genetic basis of various traits, with a focus on abiotic/biotic stress tolerance and resistance. We also discuss the limitations of using G. soja. Perspective future research is proposed, including the application of advanced biotechnology and emerging genomic data to further utilize the wild soybean to counterbalance the rising demand for superior crops. We proposed there is an urgent need for international collaboration on germplasm collection, resource sharing, and conservation. We hope to use the wild soybean as an example to promote the exploration and use of wild resources for crop improvement in order to meet future food requirements.