Abstract
Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource available with the EuCHIP60k, opens a whole new array of opportunities for high-throughput, genome-wide or targeted genotyping in species of Eucalyptus.
Highlights
Eucalyptus nitens (Dean et Maiden) Maiden has shown promise as a vigorous species for planted forests, well-suited to many New Zealand sites
The EuCHIP60K was designed as a multi-species assay [30], and we would not expect all single nucleotide polymorphism (SNP) probes on the chip to be assayable in E. nitens
For the replicate samples of parental tree 896.829, we observed four discrepancies out of 54,149 genotyped SNPs which equates to a mistyping rate of 0.0074%
Summary
Eucalyptus nitens (Dean et Maiden) Maiden has shown promise as a vigorous species for planted forests, well-suited to many New Zealand sites. Microsatellite markers have been the major tool for a number of genetic analyses, including verification of clonal identity, pedigree reconstruction, monitoring genetic diversity, inbreeding, population structure, and detection and quantification of linkage disequilibrium [10]. This was due to their high multiallelism that translates in high polymorphic information content (PIC) [11] and heterozygosity. Analysis of genetic diversity and population structure in wine grape was performed with both microsatellites and SNPs, which were Both able to distinguish two subspecies, the estimates of heterozygosity differed between the two marker types [14]. We examined the relative contribution of different pollen parents in the progeny tested and discuss the results in the context of the New Zealand E. nitens breeding program
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