Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping

Abstract

Breeding forest species can be a costly and slow process because of the extensive areas needed for field trials and the long periods (e.g., five years) that are required to measure economically and environmentally relevant phenotypes (e.g., adult plant biomass or plant height). Genomic selection (GS) and indirect selection using early phenotypes (e.g., phenotypes collected in greenhouse conditions) are two ways by which tree breeding can be accelerated. These approaches can both reduce the costs of field-testing and the time required to make selection decisions. Moreover, these approaches can be highly synergistic. Therefore, in this study, we used a data set comprising DNA genotypes and longitudinal measurements of growth collected from a population of Populus deltoides W. Bartram ex Marshall (eastern cottonwood) in the greenhouse and the field, to evaluate the potential impact of integrating large-scale greenhouse phenotyping with conventional GS. We found that the integration of greenhouse phenotyping and GS can deliver very early selection decisions that are moderately accurate. Therefore, we conclude that the adoption of these approaches, in conjunction with reproductive techniques that shorten the generation interval, can lead to an unprecedented acceleration of selection gains in P. deltoides and, potentially, other commercially planted tree species.

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

“…The study showed a moderate correlation (0.39-0.42) between greenhouse height measurements at weeks 13 and 15 and field measurements at years 3-5. By combining multiple greenhouse phenotypes into a selection index, a relative efficiency of~0.48 was achieved, which is comparable with the results of GS models based on field phenotypes only [71].…”

“…On the other hand, quite opposite results have been obtained lately. In order to reduce the breeding cycle, Alves et al [71] integrated indirect phenotypic selection based on greenhouse phenotypes with traditional GS. Plants of the same genotypes of Populus deltoides were grown in the field and in a greenhouse, with plant height measurements collected from week 1 to 15 in the greenhouse and at years 1 to 5 in the field.…”

Genomic Breeding for Diameter Growth and Tolerance to Leptocybe Gall Wasp and Botryosphaeria/Teratosphaeria Fungal Disease Complex in Eucalyptus grandis

“…This approach would require the integration of nursery and field phenotypes to develop a more accurate GS model. Such an approach was demonstrated in Populus deltoids for tree height to accelerating its breeding strategies (Alves et al, 2020). The proposed GS approach in this involves challenging potted families with L. invasa and scoring Lepto tolerance 6 months after potting and then advancing the most tolerant individuals across families for BotryoTera tolerance scoring at 12 months after potting.…”

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

“…Well studied benefits of GS for forest tree breeding programs, in increasing genetic gains by shortening generation intervals and increasing prediction accuracies (Grattapaglia and Resende, 2011 ; Iwata et al, 2011 ; Grattapaglia et al, 2018 ), and combining the methodology with clonal propagation and somatic embryo-genesis (Li and Dungey, 2018 ), can be utilized in the Swedish conifer breeding programs to decrease generation intervals. Another advantage of GS in forest tree breeding is the possibility to increase the selection intensities and getting larger genetic gains, by reducing the breeding cycle through skipping or reducing the field-testing periods (Harfouche et al, 2012 ; Isik, 2014 ; Grattapaglia et al, 2018 ).…”