Data from: Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories

Genomic selection is expected to enhance the genetic improvement of forest tree species by providing more accurate estimates of breeding values through marker-based relationship matrices compared with pedigree-based methodologies. When adequately robust genomic prediction models are available, an additional increase in genetic gains can be made possible with the shortening of the breeding cycle through elimination of the progeny testing phase and early selection of parental candidates. The potential of genomic selection was investigated in an advanced Eucalyptus nitens breeding population focused on improvement for solid wood production. A high-density SNP chip (EUChip60K) was used to genotype 691 individuals in the breeding population, which represented two seed orchards with different selection histories. Phenotypic records for growth and form traits at age six, and for wood quality traits at age seven were available to build genomic prediction models using GBLUP which were compared to the traditional pedigree-based alternative using BLUP. GBLUP demonstrated that breeding value accuracy would be improved and substantial increases in genetic gains towards solid wood production would be achieved. Cross-validation within and across two different seed orchards indicated that genomic predictions would likely benefit in terms of higher predictive accuracy from increasing the size of the training data sets through higher relatedness and better utilization of L

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

Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population. Our study investigates the efficiency of sib-ship reconstruction in an advanced breeding population of Eucalyptus nitens with only partially tracked pedigree. The sib-ship reconstruction allowed the identification of selfs (4% of the sample) and the exploration of their potential effect on inbreeding depression in the traits studied. We detected signs of inbreeding depression in diameter at breast height and growth strain while no indications were observed in wood density, wood stiffness and tangential air-dry shrinkage. After the application of a corrected sib-ship relationship matrix, additive genetic variance and heritability were observed to increase where signs of inbreeding depression were initially detected. Conversely, the same genetic parameters for traits that appeared to be free of inbreeding depression decreased in size. It therefore appeared that greater genetic variance may be due, at least in part, to contributions from inbreeding in these studied populations rather than a removal of inbreeding as is traditionally thought

Data_for_DRYAD

Compressed file containing genomic information, pedigree and phenotypic data used in the analysi

Variance components, heritability, their standard errors and Akaike Information Criterion (AIC) estimated on the basis of pedigree information, sib-ship reconstruction using only additive relationship matrix (Sib-ship A) and sib-ship reconstruction using additive and dominant relationship matrix (Sib-ship AD).

<p>Variance components, heritability, their standard errors and Akaike Information Criterion (AIC) estimated on the basis of pedigree information, sib-ship reconstruction using only additive relationship matrix (Sib-ship A) and sib-ship reconstruction using additive and dominant relationship matrix (Sib-ship AD).</p

Relatedness agreement.

<p>Agreement in relatedness inferred from the pedigree and from sib-ship analysis and number of cases detected are given in the lower triangular relationship matrix (including diagonal) for each scenario.</p

Correspondence of estimated genetic gain and breeding values.

<p>Correspondence of genetic gain and breeding values estimated on the basis of information from pedigree (dashed line) or from sib-ship reconstruction (solid line); a) Wood density [kg/m3], b) Growth strain 1.4-3 m log [mm], c) Growth strain 3-6 m log [mm], d) Stiffness 1.4-3 m log [km/s], e) Stiffness 3-6 m log [km/s], f) Diameter at breast height [mm], g) Tangential air-dry shrinkage average 3-6 m log [%].</p

Breeding program history.

<p>History of the <i>E. nitens</i> breeding program established in New Zealand. The number of selected parents are given in the arrows between the different generations.</p

Inbreeding depression effect.

<p>Comparison of performance between outbred and inbred individuals after sib-ship reconstruction and Welch t-test p-values; x-axis represents presence (1) or absence (0) of selfing.</p

Accuracy of breeding values estimated in single trait model, multi-trait model based on documented pedigree and multi-trait model based on information from sib-ship reconstruction.

<p>Accuracy of breeding values estimated in single trait model, multi-trait model based on documented pedigree and multi-trait model based on information from sib-ship reconstruction.</p