Genetic Dissection of Growth and Eco-Physiological Traits Associated with Altitudinal Adaptation in Sakhalin Fir (Abies sachalinensis) Based on QTL Mapping.

(1) Background: The genetic basis of local adaptation in conifers remains poorly understood because of limited research evidence and the lack of suitable genetic materials. Sakhalin fir (Abies sachalinensis) is an ideal organism for elucidating the genetic basis of local adaptation because its altitudinal adaptation has been demonstrated, and suitable materials for its linkage mapping are available. (2) Method: We constructed P336 and P236 linkage maps based on 486 and 516 single nucleotide polymorphisms, respectively, that were derived from double digest restriction site-associated DNA sequences. We measured the growth and eco-physiological traits associated with morphology, phenology, and photosynthesis, which are considered important drivers of altitudinal adaptation. (3) Results: The quantitative trait loci (QTLs) for growth traits, phenology, needle morphology, and photosynthetic traits were subsequently detected. Similar to previous studies on conifers, most traits were controlled by multiple QTLs with small or moderate effects. Notably, we detected that one QTL for the crown area might be a type-A response regulator, a nuclear protein responsible for the cytokinin-induced shoot elongation. (4) Conclusion: The QTLs detected in this study include potentially important genomic regions linked to altitudinal adaptation in Sakhalin fir.

Temperature-related cline in the root mass fraction in East Asian wild radish along the Japanese archipelago.

Wild plants with a wide distribution, including those exposed to a wide variety of environmental conditions, may have variations in key functional traits relevant for agricultural applications. The East Asian wild radish (Raphanus sativus var. raphanistroides) is an appropriate model plant because it is widely distributed and has outstanding sink capacity as well as two cultivars within the species. Multiple common garden trials with 14 populations and three testing sites were conducted across the Japanese archipelago to quantify variations in yield and allocation. Significant inter-population variations and interaction effects with testing sites were detected for the root and shoot mass and the root mass fraction (RMF). While the rank order of the population changed drastically among sites and the variance components of genetic effects were small in yield traits (2.4%-4.7%), RMF displayed a large genetic variance (23.2%) and was consistently higher in the northern populations at all sites. Analyses revealed that the mean temperature of growing season of the seed origin was the most prominent factor explaining variation in RMF, irrespective of the sites. We concluded that the trait of resource allocation had a temperature-related cline and plants in cooler climates could invest more resources into their roots.

TodoFirGene: Developing Transcriptome Resources for Genetic Analysis of Abies sachalinensis.

Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected the transcriptome from the female and male flower, leaf and inner bark. De novo assembly with 34.7 Gb of sequencing reads produced 158,542 transcripts from 69,618 loci, whose estimated coverage reached 95.6% of conserved eukaryotic genes. Homology searches against publicly available databases identified 134,190 (84.6%) transcripts with at least one hit. In total, 28,944 simple sequence repeats (SSRs) and 80,758 single nucleotide variants (SNVs) were detected from 23,570 (14.9%) and 25,366 (16.0%) transcripts, which were valuable for use in genetic analysis of the species. All the annotations were included in a relational database, TodoFirGene, which provides an interface for various queries and homology search, and can be accessed at http://plantomics.mind.meiji.ac.jp/todomatsu/. This database hosts not only the A. sachalinensis transcriptome but also links to the proteomes of 13 other species, allowing a comparative genomic study of plant species.

Influence of low- and high-elevation plant genomes on the regulation of autumn cold acclimation in Abies sachalinensis.

Boreal coniferous species with wide geographic distributions show substantial variation in autumn cold acclimation among populations. To determine how this variation is inherited across generations, we conducted a progeny test and examined the development of cold hardening in open-pollinated second-generation (F2) progeny of Abies sachalinensis. The F1 parents had different genetic backgrounds resulting from reciprocal interpopulational crosses between low-elevation (L) and high-elevation (H) populations: L × L, L × H, H × L, and H × H. Paternity analysis of the F2 progeny using molecular genetic markers showed that 91.3% of the fathers were located in surrounding stands of the F1 planting site (i.e., not in the F1 test population). The remaining fathers were assigned to F1 parents of the L × L cross-type. This indicates that the high-elevation genome in the F1 parents was not inherited by the F2 population via pollen flow. The timing of autumn cold acclimation in the F2 progeny depended on the cross-type of the F1 mother. The progeny of H × H mothers showed less damage in freezing tests than the progeny of other cross-types. Statistical modeling supported a linear effect of genome origin. In the best model, variation in freezing damage was explained by the proportion of maternally inherited high-elevation genome. These results suggest that autumn cold acclimation was partly explained by the additive effect of the responsible maternal genome. Thus, the offspring that inherited a greater proportion of the high-elevation genome developed cold hardiness earlier. Genome-based variation in the regulation of autumn cold acclimation matched the local climatic conditions, which may be a key factor in elevation-dependent adaptation.

Development of 32 EST-SSR markers for Abies firma (Pinaceae) and their transferability to related species.

PREMISE OF THE STUDY: We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Abies firma, a conifer endemic in Japan, to facilitate evaluation of the population genetic structure in this species. • METHODS AND RESULTS: We designed primers for 153 EST-SSRs identified from 486322 ESTs from A. sachalinensis ESTs, and tested 96 of them for PCR amplification. Thirty-two primers provided clear amplification, and 14 of those 32 displayed clear polymorphic patterns in multiple populations of A. firma and in two closely related species. The number of alleles per locus and mean expected heterozygosity ranged from one to six and 0 to 0.476, respectively. • CONCLUSIONS: The EST-SSR markers developed in this study may be useful for phylogeography and population genetic studies of A. firma. Successful amplifications were obtained for two other Abies species, suggesting that these markers may also be useful for similar applications in other fir species.

Modeling intraspecific adaptation of Abies sachalinensis to local altitude and responses to global warming, based on a 36-year reciprocal transplant experiment.

Intraspecific adaptation in Abies sachalinensis was examined using models based on long-term monitoring data gathered during a reciprocal transplant experiment with eight seed source populations and six transplantation sites along an altitudinal gradient. The consequence of local adaptation was evaluated by testing the home-site advantage for upslope and downslope transplants at five ages. The populations' fitness-linked trait was set as their productivity (tree height × survival rate) at each age. The effects of global warming were evaluated on the basis of the 36-year performance of downslope transplants. Evidence was found for adaptive genetic variation affecting both height and survival from an early age. Increasing the distance between seed source and planting site significantly reduced productivity for both upslope and downslope transplantation, demonstrating the existence of a significant home-site advantage. The decrease in productivity was most distinct for upslope transplantations, indicating strong local adaptation to high altitudes. Global warming is predicted to increase the productivity of high-altitude populations. However, owing to their existing local adaptation, all tested populations exhibited lower productivity under warming than demes that were optimal for the new climate. These negative predictions should be considered when planning the management of locally adapted plant species such as A. sachalinensis.