A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.

Climate Change Impacts on Stream Water Temperatures in a Snowy Cold Region According to Geological Conditions

This study clarifies how climate change affects stream temperatures in snowy cold regions, where groundwater impacts vary with geological conditions. We developed a physics-based water circulation model that incorporates an atmospheric and land surface process model considering snow processes, a runoff model, and a water temperature estimation model. Small watersheds in the mountainous area of Hokkaido formed the study area, and the runoff model was assigned different parameters depending on the geological characteristics. Using these parameters, changes in water temperature were calculated with respect to changes in the meteorological data in historical and future simulations. Current water temperatures were effectively reproduced by the model, and following the IPCC RCP 8.5 scenario, future water temperatures in the distribution area for new pyroclastic flows were predicted to remain lower in summer than in the distribution area of older formations. The findings of this study will be useful in informing conservation measures for river ecosystems, including the prioritization of streams where cold-water fish need to be conserved.