A study in the Forest Molecular Genetics (FMG) Programme at the University of Pretoria’s Forestry and Agricultural Biotechnology Institute (FABI) interrogates the benefits of implementing genomic selection for growth and wood quality traits in an established Eucalyptus grandis breeding programme in South Africa. Outcomes from this study appear in an article in Tree Genetics & Genomes.
Eucalyptus species such as E. grandis are highly adaptable, fast-growing and produce wood of superior quality, making them a critical resource for the timber, pulp and paper industries, as well as emerging bioenergy, biochemical and biomaterial industries. Faster and more agile breeding approaches are needed to ensure the future sustainability of Eucalyptus plantation forestry and to meet the increasing demand for renewable carbon resources for the South African bioeconomy. However, this is not easy with traditional tree breeding approaches due to the long generation times of forest trees and the fact that many commercially important traits such as wood quality are only expressed at maturity.
Tree breeders can bypass these long breeding cycles with the use of genomic selection. Genomic selection predicts the genetic merit of individuals based on the aggregate of genome-wide DNA markers to obtain genome estimated breeding values of individual trees in a breeding population. A main advantage of this tool is that tree breeders can estimate the breeding value of trees at seedling stage when only genotypic information (for 10,000s of DNA markers) is available, while it would take many years to obtain trait measurements such as stem volume, density and wood quality. Genomic selection technology is a step-change for a tree breeder because it can significantly shorthen the breeding cycle, while increasing the accuracy of selection and reducing the cost of land to host large breeding trials over long periods of time.
As part of his PhD study, Mmoledi Mphahlele developed a genomic selection model for E. grandis, trained from 1,575 trees that were genotyped with the Eucalyptus (EUChip60K) single-nucleotide polymorphism (SNP) chip and phenotyped for growth and wood quality traits. The predictive accuracy of the genomic selection model rangedfrom 0.47 (diameter) to 0.67 (fibre width). A simulated approach was used to estimate the relative efficiency of an accelerated genomic selection breeding strategy (four years seed-to-seed breeding cycle) compared to the traditional breeding strategy (eight years seed-to-seed breeding cycle), achieving relative efficiencies ranging from 1.20 (wood density) to 1.62 (fibre length) over 17 years. The study further demonstrated that the genetic gains benefit over 17 years of adopting the accelerated genomic selection strategy compared to the traditional breeding strategy should result in improved genetic gains per unit time ranging from 1.53 (diameter) to 3.35 (wood density). The study highlights that in order for tree breeders to implement genomic selection and realise these genetic gains per unit time in E. grandis, significant adjustments have to be made to integrate genomic selection into practical operational breeding operations. The research demonstrates to tree breeders that genomic selection is a viable approach for molecular breeding of E. grandis, however it requires significant modification of operational breeding processes.