Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness

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.

Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens

“…Genomic DNA was extracted from the leaf tissue of 691 individual trees using a commercial NucleoSpin Plant II kit (Machery-Nagel, Duren, Germany) [ 31 ] and sent to GeneSeek, Inc. (a Neogene company, Lincoln, NE, USA) for genotyping [ 24 ] using the Illumina Infinium EUChip60K SNP chip [ 32 ]. SNP calling was performed based on the Maidenaria section reference.…”

“…Additionally, the recovery of hidden relatedness enables the more efficient management of genetic diversity and prevents undesirable build-up of inbreeding in next generations of breeding populations. The selection of genetic markers, their type, quality and quantity is, however, crucial to obtain confident inference about relatedness [ 24 ] and improve accuracy in the genetic parameters [ 8 , 28 ].…”

An Axiom SNP genotyping array for Douglas-fir

“…For most applications, single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in a wide array of organisms. In forest trees, they are being used to understand the genetic architecture of natural populations, identify quantitative trait loci in pedigrees or natural populations, infer gene function, and assist tree breeding via parental analysis or genomic selection [1][2][3][4][5]. SNPs are desirable because they are found at a high frequency throughout the genome, codominant, usually biallelic, biochemically simple, and amenable to highthroughput genotyping.…”

“…The Infinium array is highly robust, but costs continue to be high on a per-sample basis [6]. The Infinium array has been used in many other plants and animals, including other tree species such as loblolly pine, black cottonwood, white spruce, Norway spruce, and eucalyptus [3,[18][19][20][21].…”

Properties of rotary peeled veneer and laminated veneer lumber (LVL) from New Zealand grown Eucalyptus globoidea

“…can also be found (Miller et al 2000). The development of these three species is supported by breeding programmes: E. nitens (Telfer et al 2015); E. fastigata (Kennedy et al 2011);and E. regnans (Suontama et al 2015). Eucalyptus nitens is currently grown for chip wood export for the pulp industry.…”