Comparing modeling methods of genomic prediction for growth traits of a tropical timber species, Shorea macrophylla

Introduction

Shorea macrophylla is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to S. macrophylla.

Methods

To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of S. macrophylla in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for diameter at breast height and total height in the 7th year from planting (D7 and H7).

Results and discussion

These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 6 methods and their derivatives with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability for D7 and H7 with the sets of selected SNPs and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high predictive abilities for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. Predictive abilities were higher in H7 when smaller number of SNP subsets selected by GWAS p-value was used, However, D7 showed the contrary tendency, which might have originated from the difference in genetic architecture between primary and secondary growth of the species. This study suggests that GS with GWAS-based SNP selection can be used in breeding for non-cultivated tree species to improve initial growth and reduce genotyping costs for next-generation seedlings.

Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield

Dangers confronting forest ecosystems are many and the strength of these biological systems is deteriorating, thus substantially affecting tree physiology, phenology, and growth. The establishment of genetically engineered trees into degraded woodlands, which would be adaptive to changing climate, could help in subsiding ecological threats and bring new prospects. This should not be resisted due to the apprehension of transgene dispersal in forests. Consequently, it is important to have a deep insight into the genetic structure and phenotypic limits of the reproductive capability of tree stands/population(s) to endure tolerance and survival. Importantly, for a better understanding of genes and their functional mechanisms, gene editing (GeEd) technology is an excellent molecular tool to unravel adaptation progressions. Therefore, GeEd could be harnessed for resolving the allelic interactions for the creation of gene diversity, and transgene dispersal may be alleviated among the population or species in different bioclimatic zones around the globe. This review highlights the potential of the CRISPR/Cas tools in genomic, transcriptomic, and epigenomic-based assorted and programmable alterations of genes in trees that might be able to fix the trait-specific gene function. Also, we have discussed the application of diverse forms of GeEd to genetically improve several traits, such as wood density, phytochemical constituents, biotic and abiotic stress tolerance, and photosynthetic efficiency in trees. We believe that the technology encourages fundamental research in the forestry sector besides addressing key aspects, which might fasten tree breeding and germplasm improvement programs worldwide.

Stability of Transgene Inheritance in Progeny of Field-Grown Pear Trees over a 7-Year Period

Breeding woody plants is a very time-consuming process, and genetic engineering tools have been used to shorten the juvenile phase. In addition, transgenic trees for commercial cultivation can also be used in classical breeding, but the segregation of transgenes in the progeny of perennial plants, as well as the possible appearance of unintended changes, have been poorly investigated. We studied the inheritance of the uidA gene in the progeny of field-grown transgenic pear trees for 7 years and the physical and physiological parameters of transgenic seeds. A total of 13 transgenic lines were analyzed, and the uidA gene segregated 1:1 in the progeny of 9 lines and 3:1 in the progeny of 4 lines, which is consistent with Mendelian inheritance for one and two transgene loci, respectively. Rare and random deviations from the Mendelian ratio were observed only for lines with one locus. Transgenic seeds' mass, size, and shape varied slightly, despite significant fluctuations in weather conditions during cultivation. Expression of the uidA gene in the progeny was stable. Our study showed that the transgene inheritance in the progeny of pear trees under field conditions occurs according to Mendelian ratio, does not depend on the environment, and the seed vigor of transgenic seeds does not change.

A Roadmap for Participatory Chestnut Breeding for Nut Production in the Eastern United States

Chestnut cultivation for nut production is increasing in the eastern half of the United States. Chinese chestnuts (Castanea mollissima Blume), or Chinese hybrids with European (C. sativa Mill.) and Japanese chestnuts (C. crenata Sieb. & Zucc.), are cultivated due to their high kernel quality, climatic adaptation, and disease resistance. Several hundred thousand pounds of high-quality fresh nuts are taken to market every fall, and several hundred additional orchards are entering bearing years. Grower-led on-farm improvement has largely facilitated this growth. A lack of significant investments in chestnut breeding in the region, paired with issues of graft incompatibility, has led many growers to cultivate seedlings of cultivars rather than grafted cultivars. After decades of evaluation, selection, and sharing of plant materials, growers have reached a threshold of improvement where commercial seedling orchards can be reliably established by planting offspring from elite selected parents. Growers recognize that if cooperation persists and university expertise and resources are enlisted, improvement can continue and accelerate. To this end, the University of Missouri Center for Agroforestry (UMCA) and chestnut growers throughout the eastern United States are partnering to formalize a participatory breeding program - the Chestnut Improvement Network. This partnership entails the UMCA providing an organizational structure and leadership to coordinate on-farm improvement, implement strategic crossing schemes, and integrate genetic tools. Chestnut growers offer structural capacity by cultivating seedling production orchards that provide financial support for the grower but also house segregating populations with improved individuals, in situ repositories, and selection trials, creating great value for the industry.

Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America

Earth's atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taeda L.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.

Identification of early and late flowering time candidate genes in endodormant and ecodormant almond flower buds

Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.

Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits

With climate change, the pressure on tree breeding to provide varieties with improved resilience to biotic and abiotic stress is increasing. As such, pest resistance is of high priority but has been neglected in most tree breeding programs, given the complexity of phenotyping for these traits and delays to assess mature trees. In addition, the existing genetic variation of resistance and its relationship with productivity should be better understood for their consideration in multitrait breeding. In this study, we evaluated the prospects for genetic improvement of the levels of acetophenone aglycones (AAs) in white spruce needles, which have been shown to be tightly linked to resistance to spruce budworm. Furthermore, we estimated the accuracy of genomic selection (GS) for these traits, allowing selection at a very early stage to accelerate breeding. A total of 1,516 progeny trees established on five sites and belonging to 136 full-sib families from a mature breeding population in New Brunswick were measured for height growth and genotyped for 4,148 high-quality SNPs belonging to as many genes along the white spruce genome. In addition, 598 trees were assessed for levels of AAs piceol and pungenol in needles, and 578 for wood stiffness. GS models were developed with the phenotyped trees and then applied to predict the trait values of unphenotyped trees. AAs were under moderate-to-high genetic control (h 2: 0.43-0.57) with null or marginally negative genetic correlations with other traits. The prediction accuracy of GS models (GBLUP) for AAs was high (PAAC: 0.63-0.67) and comparable or slightly higher than pedigree-based (ABLUP) or BayesCπ models. We show that AA traits can be improved and that GS speeds up the selection of improved trees for insect resistance and for growth and wood quality traits. Various selection strategies were tested to optimize multitrait gains.

Genetic Improvement of Sawn-Board Stiffness and Strength in Scots Pine (Pinus sylvestris L.)

Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (r_A > 0.65) for sawn-board stiffness while MOE_TREE, VEL_HIT and resistograph wood density (DEN_RES) measured on standing trees and MOE_LOG and VEL_FAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability ( h i 2 ) for VEL, MOE and MOR were weak (0.05-0.26) but were substantially stronger for wood density (0.34-0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4% to 9.1%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOE_TREE, DEN_RES or stem straightness (STR) could improve several structural wood traits simultaneously.

Forest genomics: Advancing climate adaptation, forest health, productivity, and conservation

Forest ecosystems provide important ecological services and resources, from habitat for biodiversity to the production of environmentally friendly products, and play a key role in the global carbon cycle. Humanity is counting on forests to sequester and store a substantial portion of the anthropogenic carbon dioxide produced globally. However, the unprecedented rate of climate change, deforestation, and accidental importation of invasive insects and diseases are threatening the health and productivity of forests, and their capacity to provide these services. Knowledge of genetic diversity, local adaptation, and genetic control of key traits is required to predict the adaptive capacity of tree populations, inform forest management and conservation decisions, and improve breeding for productive trees that will withstand the challenges of the 21st century. Genomic approaches have well accelerated the generation of knowledge of the genetic and evolutionary underpinnings of nonmodel tree species, and advanced their applications to address these challenges. This special issue of Evolutionary Applications features 14 papers that demonstrate the value of a wide range of genomic approaches that can be used to better understand the biology of forest trees, including species that are widespread and managed for timber production, and others that are threatened or endangered, or serve important ecological roles. We highlight some of the major advances, ranging from understanding the evolution of genomes since the period when gymnosperms separated from angiosperms 300 million years ago to using genomic selection to accelerate breeding for tree health and productivity. We also discuss some of the challenges and future directions for applying genomic tools to address long-standing questions about forest trees.

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.

Impact of genetic variation and long-term limited water availability on the ecophysiology of young Sitka spruce (Picea sitchensis (Bong.) Carr.)

Future limited water availability may reduce the potential of tree improvement to increase timber yields. We investigated ecophysiological variation between full-sibling families of Sitka spruce (Picea sitchensis (Bong.) Carr.) growing under contrasting water availability conditions: control (optimal) water availability and limited water availability. One-year-old seedlings of nine improved families plus an unimproved seed lot were grown in pots in a greenhouse and the two water availability treatments imposed via drip irrigation. Whole-plant water use varied between families. Stomatal conductance and the light-saturated quantum yield of photosystem II at times differed between families, but not consistently. Certain families showed considerably greater increases in electron transport rate with increasing photosynthetically active radiation. Limited water availability resulted in reduced branch water potential, leaf stomatal conductance and transpiration per unit leaf area, and increased whole-plant water-use efficiency, in all genetic material. The responses of plant water use and leaf carbon isotope composition to water limitation, were, however, initially influenced by variation in vigour between families-with conservative growth in some material slowing the decline in substrate moisture content. As the duration of water deficit extended, these variables showed a more uniform response across families. Between-family variation in physiological mechanisms of drought tolerance was not detected. Thus, for Sitka spruce, assessing juvenile material may not allow selection to prevent reductions in productivity associated with long-term sub-optimal growing conditions, but screening for conservative growth (within families as well as between families) may be beneficial where survival of relatively short-term water limitation is the primary concern.

Plant hormone-assisted early family selection in Pinus densiflora via a retrospective approach

In an even-aged pine forest trees can vary considerably in stem size. We examined the basis for this anomaly using a retrospective approach. Twelve open-pollinated families of Pinus densiflora Sieb. et Zucc. were deliberately chosen for their variation in stem volumes at age 32 years. Seedlings obtained from these families were grown to age 6 months under optimal nursery conditions. Endogenous levels of growth hormones (auxin [IAA] and gibberellins [GAs]) and expression of the GA biosynthesis gene, PdGA20ox1, all assessed at age 3 months, were significantly correlated, across family, with seedling stem and/or shoot dry biomass at age 6 months. Retrospective comparisons of seedling growth, seedling stem tissue GA(20) and seedling stem expression levels of PdGA20ox1 were then made, across family, with tree stem growth at age 32 years. Age 6 months length and shoot dry biomass at age 6 months showed positive and significant Pearson's correlations with age 32 years tree stem diameters and a tree stem volume index, as did seedling stem tissue GA(20). Even seedling stem PdGA20ox1 expression levels were positively and near significantly (P = 0.088) correlated with age 32 years tree stem diameters. Auxin and GAs control nursery growth of seedlings at the family level, and this control also extends, for GAs at least, to field growth of older trees. We propose that family differences in PdGA20ox1 gene expression, and thus endogenous GA levels, may explain much of the natural variation seen for tree stem size in even-aged pine forests. If our hypothesis is correct, then the heritable components of variation in tree stem growth capacity should be predictable by hormonal and gene expression profiling. Such profiling, combined with the measurement of seedling phenotypic growth characters, could have the potential to accelerate the early selection of those conifer families that possess traits for inherently rapid stem wood growth.

Successful crossings with early flowering transgenic poplar: interspecific crossings, but not transgenesis, promoted aberrant phenotypes in offspring

In forest tree species, the reproductive phase is reached only after many years or even decades of juvenile growth. Different early flowering systems based on the genetic transfer of heat-shock promoter driven flowering-time genes have been proposed for poplar; however, no fertile flowers were reported until now. Here, we studied flower and pollen development in both HSP::AtFT and wild-type male poplar in detail and developed an optimized heat treatment protocol to obtain fertile HSP::AtFT flowers. Anthers from HSP::AtFT poplar flowers containing fertile pollen grains showed arrested development in stage 12 instead of reaching phase 13 as do wild-type flowers. Pollen grains could be isolated under the binocular microscope and were used for intra- and interspecific crossings with wild-type poplar. F1-seedlings segregating the HSP::AtFT gene construct according to Mendelian laws were obtained. A comparison between intra- and interspecific crossings revealed that genetic transformation had no detrimental effects on F1-seedlings. However, interspecific crossings, a broadly accepted breeding method, produced 47% seedlings with an aberrant phenotype. The early flowering system presented in this study opens new possibilities for accelerating breeding of poplar and other forest tree species. Fast breeding and the selection of transgene-free plants, once the breeding process is concluded, can represent an attractive alternative even under very restrictive regulations.