Analysis of Environment-Marker Associations in American Chestnut

A Review of the Stress Resistance, Molecular Breeding, Health Benefits, Potential Food Products, and Ecological Value of Castanea mollissima

Chestnut (Castanea spp., Fagaceae family) is an economically and ecologically valuable species. The main goals of chestnut production vary among species and countries and depend on the ecological characteristics of orchards, agronomic management, and the architecture of chestnut trees. Here, we review recent research on chestnut trees, including the effects of fungal diseases (Cryphonectria parasitica and Phytophthora cinnamomi) and insect pests (Dryocosmus kuriphilus Yasumatsu), molecular markers for breeding, ecological effects, endophytic fungi, and extracts with human health benefits. We also review research on chestnut in the food science field, technological improvements, the soil and fertilizer used for chestnut production, and the postharvest biology of chestnut. We noted differences in the factors affecting chestnut production among regions, including China, the Americas, and Europe, especially in the causal agents of disease and pests. For example, there is a major difference in the resistance of chestnut to C. parasitica in Asian, European, and American countries. Our review provides new insights into the integrated disease and pest management of chestnut trees in China. We hope that this review will foster collaboration among regions and help to clarify differences in the direction of breeding efforts among countries.

Frozen in time: rangewide genomic diversity, structure, and demographic history of relict American chestnut populations

American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the eastern United States. In the first half of the 20th century, an exotic fungal pathogen - Cryphonectria parasitica - decimated the species, killing billions of chestnut trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted restoration populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant genetic populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.

Genetic Diversity and Association Analysis among Germplasms of Diospyros kaki in Zhejiang Province Based on SSR Markers

In subtropical to temperate regions, persimmon (Diospyros kaki Thunb.) is an economically important fruit crop cultivated for its edible fruits. Persimmons are distributed abundantly and widely in Zhejiang Province, representing a valuable resource for the breeding of new cultivars and studying the origin and evolution of persimmon. In this study, we elucidated the genetic structures and diversity patterns of 179 persimmon germplasms from 16 different ecologic populations in Zhejiang Province based on the analysis of 17 SSR markers. The results show that there was a medium degree of genetic diversity for persimmon found in Zhejiang Province. With the exception of the Tiantai Mountain and Xin’an River populations, we found extensive gene exchange had occurred among the other populations. The 179 D. kaki germplasms from the 16 populations could be separated into three distinct clusters (I, II, and III) with a higher mean pairwise genetic differentiation index (FST) (0.2714). Nearly all samples of Cluster-I were distributed inland. Cluster-II and Cluster-III contained samples that were widely distributed throughout Zhejiang Province including all samples from the coastal populations and the Northeast Plain populations. In addition, we performed association mapping with nine traits (fruit crude fiber content, fruit calcium content, fruit water content, fruit longitudinal diameter, fruit aspect ratio, seed width, seed length, leaf aspect ratio, and number of lateral veins) using these markers. This led to the identification of 13 significant marker–trait associations (MTAs; p < 0.00044, 0.1/228) using a general linear model, of which, six MTAs with a correlation coefficient (R2) >10% were consistently represented in the general linear model with p < 0.00044 in the two models. The genetic structures and diversity patterns of the persimmon germplasms revealed in this study will provide a reference for the efficient conservation and further utilization of persimmon germplasms. The MTAs identified in this study will be useful for future marker-assisted breeding of persimmon.

Abiotic genetic adaptation in the Fagaceae

Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.