Previsual and Early Detection of Myrtle Rust on Rose Apple Using Indices Derived from Thermal Imagery and Visible-to-Short-Infrared Spectroscopy.

Myrtle rust, caused by the fungus , is a serious disease, which affects many Myrtaceae species. Commercial nurseries that propagate Myrtaceae species are prone to myrtle rust and require a reliable method that allows previsual and early detection of the disease. This study uses time-series thermal imagery and visible-to-short-infrared spectroscopy measurements acquired over 10 days from 81 rose apple plants () that were either inoculated with myrtle rust or maintained disease-free.

High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata.

Background: The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes.

Results: Our mapping approach used probabilistic error correction of the marker data, followed by an iterative approach based on stringent parameters.

Genomic selection for resistance to mammalian bark stripping and associated chemical compounds in radiata pine.

The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark.

Chasing genetic correlation breakers to stimulate population resilience to climate change.

Global climate change introduces new combinations of environmental conditions, which is expected to increase stress on plants. This could affect many traits in multiple ways that are as yet unknown but will likely require the modification of existing genetic relationships among functional traits potentially involved in local adaptation. Theoretical evolutionary studies have determined that it is an advantage to have an excess of recombination events under heterogeneous environmental conditions.

Genetic Variation in Drought-Tolerance Traits and Their Relationships to Growth in D. Don Under Water Stress.

The selection of drought-tolerant genotypes is globally recognized as an effective strategy to maintain the growth and survival of commercial tree species exposed to future drought periods. New genomic selection tools that reduce the time of progeny trials are required to substitute traditional tree breeding programs. We investigated the genetic variation of water stress tolerance in New Zealand-grown D.

Genetic Variation for Economically Important Traits in in New Zealand.

Increasing productivity and tolerance against cypress canker disease is an important goal in the Mexican white cypress breeding program in New Zealand, and screening has been in place since 1983. Cypress canker disease is caused by and , the current study presents the results of two progeny trials within the breeding program in the North Island of New Zealand. The trials were established as open-pollinated progeny tested and were assessed for diameter at breast height, branch size, canker severity score, malformation score, and stem straightness score and acceptability score.

Spatial Models With Inter-Tree Competition From Airborne Laser Scanning Improve Estimates of Genetic Variance.

Phenotyping individual trees to quantify interactions among genotype, environment, and management practices is critical to the development of precision forestry and to maximize the opportunity of improved tree breeds. In this study we utilized airborne laser scanning (ALS) data to detect and characterize individual trees in order to generate tree-level phenotypes and tree-to-tree competition metrics. To examine our ability to account for environmental variation and its relative importance on individual-tree traits, we investigated the use of spatial models using ALS-derived competition metrics and conventional autoregressive spatial techniques.

Marker Selection in Multivariate Genomic Prediction Improves Accuracy of Low Heritability Traits.

Multivariate analysis using mixed models allows for the exploration of genetic correlations between traits. Additionally, the transition to a genomic based approach is simplified by substituting classic pedigrees with a marker-based relationship matrix. It also enables the investigation of correlated responses to selection, trait integration and modularity in different kinds of populations.

Indication of Quantitative Multiple Disease Resistance to Foliar Pathogens in in New Zealand.

Increasing resistance against foliar diseases is an important goal in the D.Don breeding program in New Zealand, and screening for resistance has been in place for some time, since the late 1960s. The current study presents results of four progeny trials within the breeding program to investigate whether multiple disease resistance could be detected against three different needle diseases in : needle blight (DNB) caused by , needle cast (CNC) caused by , and red needle cast (RNC) caused by Four progeny trials in the North Island of New Zealand were available to estimate heritabilities and between-trait genetic correlations.

Effect of trait's expression level on single-step genomic evaluation of resistance to Dothistroma needle blight.

Background: Many conifer breeding programs are paying increasing attention to breeding for resistance to needle disease due to the increasing importance of climate change. Phenotyping of traits related to resistance has many biological and temporal constraints that can often confound the ability to achieve reliable phenotypes and consequently, reliable genetic progress. The development of next generation sequencing platforms has also enabled implementation of genomic approaches in species lacking robust reference genomes.

Forest-Scale Phenotyping: Productivity Characterisation Through Machine Learning.

Advances in remote sensing combined with the emergence of sophisticated methods for large-scale data analytics from the field of data science provide new methods to model complex interactions in biological systems. Using a data-driven philosophy, insights from experts are used to corroborate the results generated through analytical models instead of leading the model design. Following such an approach, this study outlines the development and implementation of a whole-of-forest phenotyping system that incorporates spatial estimates of productivity across a large plantation forest.

Genotype-by-environment interaction in coast redwood outside natural distribution - search for environmental cues.

Background: Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environments was undertaken to assess genotype x environment interaction (GxE) of coast redwood in order to understand the performance of genotypes across environments.

Results: The quantitative genetic analysis discovered no GxE between investigated environments for diameter at breast height (DBH).

Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information.

Background: Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external resin bleeding and internal checking are examples of such traits and are targeted for improvement in radiata pine research programmes.

Modelling of population structure through contemporary groups in genetic evaluation.

Background: Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained.

A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata.

Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absence of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.

Expected benefit of genomic selection over forward selection in conifer breeding and deployment.

Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical conifer breeding program. Methods of speeding the deployment of selected material were also considered, including top-grafting onto mature seed orchard ortets, using additional replicates of clones in archives for crossing, and embryogenesis and clonal propagation.

Correction to: Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories.

Published online: 6 July 2018This article was originally published under standard licence, but has now been made available under a [CC BY 4.0] license. The PDF and HTML versions of the paper have been modified accordingly.

Genotype by environment interaction for growth and Dothistroma resistance and clonal connectivity between environments in radiata pine in New Zealand and Australia.

Twenty-eight clonal trials of radiata pine planted across Australia and New Zealand were used to investigate genetic variation and genotype by environment (G×E) interaction for diameter-at-breast-height (DBH), height and Dothistroma resistance (DO_R). The average narrow-sense heritabilities were 0.11, 0.

Effect of Hidden Relatedness on Single-Step Genetic Evaluation in an Advanced Open-Pollinated Breeding Program.

Open-pollinated (OP) mating is frequently used in forest tree breeding due to the relative temporal and financial efficiency of the approach. The trade-off is the lower precision of the estimated genetic parameters. Pedigree/sib-ship reconstruction has been proven as a tool to correct and complete pedigree information and to improve the precision of genetic parameter estimates.

Phenotyping Whole Forests Will Help to Track Genetic Performance.

Phenotyping is the accurate and precise physical description of organisms. Accurate and quantitative phenotyping underpins the delivery of benefits from genetic improvement programs in agriculture. In forest trees, phenotyping at an equivalent precision has been impossible because trees and forests are large, long-lived, and highly variable.

Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories.

Genomic selection is expected to enhance the genetic improvement of forest tree species by providing more accurate estimates of breeding values through marker-based relationship matrices compared with pedigree-based methodologies. When adequately robust genomic prediction models are available, an additional increase in genetic gains can be made possible with the shortening of the breeding cycle through elimination of the progeny testing phase and early selection of parental candidates. The potential of genomic selection was investigated in an advanced Eucalyptus nitens breeding population focused on improvement for solid wood production.

Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens.

Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population. Our study investigates the efficiency of sib-ship reconstruction in an advanced breeding population of Eucalyptus nitens with only partially tracked pedigree.

Improvement of non-key traits in radiata pine breeding programme when long-term economic importance is uncertain.

Diameter at breast height (DBH), wood density (DEN) and predicted modulus of elasticity (PME) are considered as 'key traits' (KT) in the improvement in radiata pine breeding programmes in New Zealand. Any other traits which are also of interest to radiata pine breeders and forest growers are called 'non-key traits' (NKTs). External resin bleeding (ERB), internal checking (IC), number of heartwood rings (NHR) are three such non-key traits which affect wood quality of radiata pine timber.

Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K).