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

AGUIRRE, NATALIA CRISTINA; VILLALBA, PAMELA VICTORIA; GARCÍA, MARTÍN NAHUEL; FILIPPI, CARLA VALERIA; RIVAS, JUAN GABRIEL; MARTÍNEZ, MARÍA CAROLINA; ACUÑA, CINTIA VANESA; LÓPEZ, AUGUSTO J.; LÓPEZ, JUAN ADOLFO; PATHAUER, PABLO; PALAZZINI, DINO; HARRAND, LEONEL; OBERSCHELP, JAVIER; MARCÓ, MARTÍN ALBERTO; CISNEROS, ESTEBAN FELIPE; CARRERAS, ROCÍO; MARTINS ALVES, ANA MARIA; RODRIGUES, JOSÉ CARLOS; HOPP, H. ESTEBAN; GRATTAPAGLIA, DARIO; CAPPA, EDUARDO PABLO; PANIEGO, NORMA BEATRIZ; MARCUCCI POLTRI, SUSANA NOEMÍ

Frontiers in Genetics

Frontiers

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 provenance-progeny trial. 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 predictiveability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulosecontent, Total and Ethanolic extractives, Total and Klason lignin content andSyringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PAvalues for six traits, meanwhile, the values estimated using ddRADseq gave highervalues for three other traits. The PAs correlated positively with narrow senseheritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, aregenerally comparable for population genetics and genomic prediction,demonstrating the utility of the former when subjected to rigorous SNP filtering.The results of this study provide a basis for future whole-genome studies usingddRADseq in non-model forest species for which SNP arrays have not yetbeen developed.