Sometimes referred to as a ‘clone bank’, an archive is a set of plants that are stored in living form, usually for breeding and/or gene conservation purposes. For radiata pine, an archive will usually contain cloned copies (‘ramets’) of selected trees.
Backward selection is selection of parent trees based on results from a progeny test. The selected parent trees will then be cloned (usually using grafts) and planted into seed orchards for commercial seed production, and into archives for breeding purposes.
The rate of improvement achievable in a breeding programme is determined by the ‘breeder’s equation’, summarised as:
A clone is a group of plants produced from cuttings, tissue culture, or add some other method that produces offspring genetically identical to the original plant. Cloning is used in radiata pine breeding to reproduce selections, both as seed orchard parent trees and as juvenile trees to be used for plantations.
Seed produced by methods of controlled pollination in CP orchards. CP orchards are planted with a selection of genetically superior ‘mother trees’ (selections) and pollen from another genetically superior tree is blown into bags covering receptive immature cones on each tree. Bags over the cones prevent stray pollen from entering during this critical period. CP pollinations are intentional; the result is that the genetic identify of both parents is known. CP seed is genetically rated for each trait with GF Plus™ values derived from the related Estimated Breeding Values.
Breeding Values are not known exactly (see EBV Accuracy), but it is possible to make good estimates of the performance of selections, and so they are referred to as Estimated Breeding Values (i.e. EBVs) from an analysis of the trial measurement data. An EBV is the genetic value of an individual as determined by the average value of its progeny. An EBV may be estimated based on either individual traits or a selection index. In a full-sib cross, half of the genetic merit of each parent is passed into its offspring (progeny). An EBV is specific to each genotype (referred to as a 'selection' by RPBC) for each breeding trait. The EBV for a selection is the difference between the average of its measured values for a trait and the average of the measured values for the whole base population. For example, for the growth trait of Diameter (DBH), the RPBC base population average is approximately 19.6cm (2017 EBVs); a selection with an EBV of +1.6 has an average DBH of 21.2cm which is 16 mm larger than the base population mean value. EBVs can be either positive or negative due to their variance above or below the population average. The absolute values of the EBV are not critical; what is important is the differences in EBVs among selections, and whether the EBV for a selection is above or below the population average.
The accuracy of a Breeding Value describes how close the BV estimate is to the real, underlying performance of the individual for a specific trait, or Index of traits. For radiata pine, the accuracy can be improved with an increased heritability, and by improving the definition of the trait to be measured.
A family is a set of closely-related genotypes. For tree breeding, families are usually comprised of half-sibs (with one parent in common) or full-sibs (with both parents in common). Families are ranked for their performance in breeding trials, and new selections are made of the best trees within the best families. Each CP cross produces one family, unless a mix of pollen is used.
Forward selection involves choosing the best individuals out of a progeny test for use in seed orchards and/or subsequent generations of breeding. It is ‘forward’ in the sense that the breeding population is being advanced from the ‘backward-selected’ parents to selection in the next generation.
Genetic gain is the change achieved by artificial selection in a specific trait. Gain is usually expressed as the change per generation or the change per year. Gain is influenced by selection intensity, parental variation, and heritability. The RPBC recognises two types of genetic gain. First is genetic gain delivered through the breeding programme. It is the average amount of improvement achieved through selection in the current breeding population compared to the previous breeding generation. This form of genetic gain is estimated from measurements of specific traits (e.g. DBH) in the breeding trials, and is expressed in breeding values and GF Plus™ values summarised for the population. In future, RPBC will also express genetic gain from breeding in terms of $NPV.
Actual or realised genetic gain is the gain from genetic improvement realised in forest operations. This is also referred to as operational gain. Genetic gain can be measured and compared between genotypes grown under consistent, controlled conditions, often in purpose-designed long-term growth and yield trials. Yield is a measure of realised gain for growth that integrates the effects of site conditions and management regime. Quality gains can be estimated from log grade outturns and premiums associated with improved wood quality.
The genome of a tree is the whole of its hereditary information encoded in its DNA. This includes both the genes and the non-coding sequences of the DNA. Genomic selection uses genome-wide genetic markers to select individuals with the desired overall combination of breeding traits. The RPBC is developing GS capability using a marker system based on Single Nucleotide Polymorphisms (SNPs). When applied to the RPBC breeding population, GS promises to shorten the time and expense required for progeny testing, as well as to improve understanding of the pedigree of individual RPBC selections.
The genotype is the specific set of genes possessed by an individual, including both expressed and recessive genes. Every individual radiata pine tree has its own unique genotype. Tree breeding selection aims to increase the frequencies of favourable genes, while retaining the genetic diversity represented by all other genes in the genotypes of the selections.
Germplasm is living tissue from which new plants can be grown. It can be a seed or another plant part – a leaf, a piece of stem, pollen or even just a few embryonic cells that can be turned into a whole plant. Germplasm contains the information for a species’ genetic makeup, a valuable natural resource of plant diversity (Source: Seed Biotechnology Center, UC Davis). Germplasm is the base material used in a tree breeding programme.
Other terms used by the RPBC carry somewhat similar meanings, including ‘genotype’, 'genetic materials’, and ‘genetic entities’.
GF refers to ‘growth and stem form’. The GF rating scheme was used to rate the genetic quality of radiata pine seedlots before being replaced by the GF Plus™ scheme. Seedlots were given a GF rating based on the growth and form of the parents used to create the seedlot. Ratings ranged from zero (no improvement) to 30 (maximum improvement available at the time). The GF scheme is no longer in use and genetic improvement has increased beyond that available under the GF scheme.
The GF Plus™ scheme introduced seedlot ratings for individual selection traits, including; diameter, straightness, branching habit, wood density and Dothistroma resistance. As for GF, GF Plus ratings range from zero (no improvement) to 40 (maximum available improvement at present). The RPBC may modify the GF Plus™ system to reflect $NPV ratings in future.
OP seedlot refers to seed produced from radiata pine cones that are ‘open’ or wind pollinated. Commercial seed orchards plant a range of genetically improved trees, called ‘mother trees’ in an OP orchard, which is designed to limit the risk of inbreeding; that is, trees being self-pollinated. OP orchards are typically large, and isolated from other radiata pine stands, such that the main pollen source for the orchard is from the selected mother trees planted in the orchard.
The seed collected from cones produced is collected and combined by the orchard manager into one or more ‘OP mixes’ each of which becomes an OP seedlot. The proportion of seed from each mother-tree may vary between mixes but each OP seedlot would typically include seed from approximately 40 mother trees.
The original plant selection from which grafts are taken to create vegetative clones subsequently planted in a seed orchard. Each individual plant of that vegetative clone is called a ramet.
The phenotype is the sum of the physical characteristics of a tree. The phenotype is determined by the genotype interacting with the environment in which it is grown. All clones and progenies in RPBC trials have distinct phenotypes, and it is the phenotype that is measured for the development of breeding values..
A progeny trial is a field trial aimed at comparing the offspring of different parents. The RPBC manages both seedling and clonal breeding trials in order to rank candidate parents, families and individual trees for selection purposes.
A ramet is a vegetatively reproduced copy of a plant; for example, a cutting. Together, ramets of the same plant are clones. Copies of parent clones in radiata pine seed orchards are ramets. Juvenile clones of radiata are being tested in RPBC clonal breeding trials are also ramets.
In the rolling front strategy, crosses are made between the best available trees in each year, and new breeding trials are established using the crosses done in the previous year, rather than waiting for all crosses in that generation to be completed.
A scion is a branch, bud, or other vegetative plant part that may be grafted onto the root-system of another plant. For radiata pine, grafting is used to create copies (ramets) of selected trees to establish in both breeding archives and seed orchards.
Commercial seed orchards produce seedlots for forest growers and nurseries. A seedlot is a unique mix of seeds available for purchase, labelled with a specific code (e.g. 19/201). A seedlot may comprise seed from one parent cross or from a mix of different crosses. The seedlot code prefix is the year of collection, while the following three digit code is the unique identifier for one seedlot in that year of seed production. Seedlot numbers are also used to identify specific units of genetic materials that are tested within the RPBC tree breeding programme. CP seedlots are given an overall GF Plus rating as it is anticipated that OP seedlots will also be able to be rated in the near future.
Selections are individual trees with desirable traits that are chosen to achieve genetic improvement.
Single Nucleotide Polymorphisms or SNPs, are small variations in the DNA sequence called markers. A unique set of markers creates a unique individual with unique trait characteristics. Related individuals will have more variations in common. A SNP panel is a set of markers that can be used to identify related individuals and therefore predict what their trait characteristics are likely to be.
The more individuals we can catalogue with both their marker and trait profiles, the more accurate our predictions for the next generation become.
A clonal plant produced by the development of embryos from diploid somatic cells in tissue culture
Traits are specific characteristics of trees that may be selected for in a tree breeding programme. Radiata pine examples include growth rate, wood density, corewood stiffness, and Dothistroma resistance.
A varietal is a clone derived using somatic embryogenesis (SE clone) and then propagated from stoolbeds using cuttings. Production varietals are selected from forest screening trials to then be deployed in clonal forestry operations.
A clonal plant (ramet) vegetatively propagated, most commonly by taking cuttings from a mother plant (ortet).
Propagation from the vegetative material of a plant by asexual means, as in budding, grafting and rooting of cuttings. The clones (ramets) that result are genetically identical with those of the original plan (ortet or mother plant).