Ever since Darwin, one of the major challenges in evolutionary biology is to unravel the process and mechanisms of adaptation and speciation. Population genomics—the analysis of whole‐genome polymorphism data from large population samples—is a critical approach to study adaptation and speciation, as population genomics datasets enable us to: (1) perform genome‐wide association studies (GWAS) to find genes underlying adaptive phenotypic variations; (2) scan the footprints of selection across the genome to pinpoint loci under selection; and (3) infer the structure and demographic history of populations. Here, we review recent studies of plants using population genomics, covering those focusing on interactions with other organisms, adaptations to local climatic conditions, and the genomic causes and consequences of reproductive isolation. Integrative studies involving GWAS, selection scans, functional studies, and fitness measurements in the field have successfully identified loci for adaptation, revealed the molecular basis of genetic trade‐offs, and shown that fitness can be predicted by polygenic effects of a number of loci associated with local climate. We highlight the importance of the measurement of fitness and phenotypes in the field, which can be powerful tools when combined with population genomic analyses.

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

Grafting is a method used in agriculture to improve crop production and tolerance to biotic and abiotic stress. This technique is widely used in tomato, Solanum lycopersicum L.; however, the effects of grafting on changes in gene expression associated with stress tolerance in shoot apical meristem cells are still under-discovered. To clarify the effect of grafting, we performed a transcriptomic analysis between non-grafted and grafted tomatoes using the tomato variety Momotaro-scion and rootstock varieties, TD1, GS, and GF. Drought tolerance was significantly improved not only by a combination of compatible resistant rootstock TD1 but also by self-grafted compared to non-grafted lines. Next, we found the differences in gene expression between grafted and non-grafted plants before and during drought stress treatment. These altered genes are involved in the regulation of plant hormones, stress response, and cell proliferation. Furthermore, when comparing compatible (Momo/TD1 and Momo/Momo) and incompatible (Momo/GF) grafted lines, the incompatible line reduced gene expression associated with phytohormones but increased in wounding and starvation stress-response genes. These results conclude that grafting generates drought stress tolerance through several gene expression changes in the apical meristem.

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, FERONIA-receptor like kinase (LjFER) and a S-receptor-like kinase gene (LjLecRK) are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work suggests that recruiting a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering functional genetic insight into perennial herb evolution.

To understand the geographic distributions of rhizobia that associated with widely distributed wild legumes, 66 nodules obtained from 41 individuals including three sea-dispersed legumes (Vigna marina, Vigna luteola, and Canavalia rosea) distributed across the tropical and subtropical coastal regions of the world were studied. Partial sequences of 16S rRNA and nodC genes extracted from the nodules showed that only Bradyrhizobium and Sinorhizobium were associated with the pantropical legumes, and some of the symbiont strains were widely distributed over the Pacific. Horizontal gene transfer of nodulation genes were observed within the Bradyrhizobium and Sinorhizobium lineages. BLAST searches in GenBank also identified records of these strains from various legumes across the world, including crop species. However, one of the rhizobial strains was not found in GenBank, which implies the strain may have adapted to the littoral environment. Our results suggested that some rhizobia, which associate with the widespread sea-dispersed legume, distribute across a broad geographic range. By establishing symbiotic relationships with widely distributed rhizobia, the pantropical legumes may also be able to extend their range much further than other legume species.