Use of EUChip60K for the genetic diversity characterization of an Eucalyptus dunnii breeding population of Argentina

AGUIRRE, NC; FILIPPI, C; VILLALBA, PV; GARCIA, MN; RIVAS, JG; MARTINEZ, MC; ACUÑA, CV; LOPEZ, A; LOPEZ, J; CAPPA, EP; PATHAUER, P; PALAZZINI D.; HARRAND, L.; OBERSCHELP, J; MARCÓ, M; CISNEROS F.; CARRERAS R.; HOPP, HE; RODRIGUEZ, JG; GRATTAPAGLIA, D; MARCUCCI POLTRI, SN

Monpellier

Congreso; Improvement and culture of Eucalyptus, Managing Eucalyptus plantations under global changes.; 2018

IUFRO - CIRAD

In Argentina, the Eucalyptus breeding program is mainly carried out by INTA (National Institute of Agricultural Technology) with the aim to provide an improved material for forestry sector.In a climate change context, Eucalyptus dunnii has been included in INTA´s breeding program due to its tolerance to low temperatures. In order to apply molecular breeding strategies into the genetic program, different genotyping platforms are being used.The multispecies EUChip60K represents an outstanding tool to address population genomics questions in Eucalyptus and to empower Genomic Selection (GS), Genome Wide Association Studies (GWAS) and the broader study of complex trait variation in this species.In this work, an E. dunnii progeny trial population (308 individuals, coming from 6 different geographic Australian origins and a local selection), which has already been phenotyped for 7 different traits related to wood quality (NIR analysis) and 3 traditional growing traits, was genotyped with the EUChip60K (NEOGEN, USA) for future GWAS and GS analysis. The 64638 markers of the chip were filtered by minor allele frequency (MAF) lower than 0.05 and a percentage of missing data up to 20%, keeping a total of 14123 SNPs, with only 3.39% of missing data, according to Silva-Junior et al (2015) who reported 17014 SNPs with MAF >0.01 for this species. Based on the reported SNP genomic position, a uniform distribution of these markers across the E. grandis genome was also observed. The expected and observed heterozygosity were 0.322 and 0.326 respectively across the total 308 samples, which were separated by DAPC analysis into two genetic groups, one of them with 87% of the individuals.To our knowledge, this is the first report of applying EUChip60K to a breeding population of E. dunnii for molecular breeding purposes, validating its usefulness in this species.