Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

AGUIRRE, NATALIA C.; PAMELA V. VILLALBA; GARCIA MARTIN N.; CARLA FILIPPI; JUAN RIVAS; MARTINEZ MARÍA CAROLINA; ACUÑA, CINTIA V.; AUGUSTO J. LOPEZ; LÓPEZ, JUAN ADOLFO; PABLO S. PATHAUER; PALAZZINI, DINO A.; HARRAND, LEONEL; JAVIER OBERSCHELP; MARCÓ M.; CISNEROS, FELIPE E.; ROCIO CARRERAS; ANA MARIA MARTINS ALVES; JOSÉ RODRIGUEZ; HORACIO ESTEBAN HOPP; GRATTAPAGLIA, DARIO; CAPPA E.P.; NORMA PANIEGO; MARCUCCI POLTRI, SUSANA N.

Frontiers in Genetics

Frontiers Media SA

Lugar: Lausanne; Año: 2024 vol. 15

Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiberpulp production in regions where other species of the genus are affected by poorsoil and climatic conditions. In this context, E. dunnii holds promise as a resourceto address and adapt to the challenges of climate change. Despite its rapid growthand favorable wood properties for solid wood products, the advancement of itsimprovement remains in its early stages. In this work, we evaluated theperformance of two single nucleotide polymorphism, (SNP), genotypingmethods for population genetics analysis and Genomic Selection in E. dunnii.Double digest restriction-site associated DNA sequencing (ddRADseq) wascompared with the EUChip60K array in 308 individuals from a provenanceprogenytrial. The compared SNP set included 8,011 and 19,008 informative SNPsdistributed along the 11 chromosomes, respectively. Although the two datasetsdiffered in the percentage of missing data, genome coverage, minor allelefrequency and estimated genetic diversity parameters, they revealed a similargenetic structure, showing two subpopulations with little differentiation betweenthem, and low linkage disequilibrium. GS analyses were performed for eleventraits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventionalpedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl andGuaiacyl lignin monomer ratio). When contrasting the SNP datasets used toestimate PAs, the GBLUP-EUChip60K model gave higher and significant PA valuesfor six traits, meanwhile, the values estimated using ddRADseq gave higher values forthree other traits. The PAs correlated positivelywith narrow sense heritabilities,with thehighest correlations shown by the ABLUP and GBLUP-EUChip60K. The twogenotyping methods, ddRADseq and EUChip60K, are generally comparable forpopulation genetics and genomic prediction, demonstrating the utility of theformer when subjected to rigorous SNP filtering. The results of this study provide abasis for future whole-genome studies using ddRADseq in non-model forest speciesfor which SNP arrays have not yet been developed.