QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

Abstract

Sitka spruce (Picea sitchensis (Bong.) Carr) is the most common commercial plantation species in Britain and a breeding programme based on traditional lines has been in operation since the early 1960s. Rotation lengths of 40-years have led breeders to adopt a process of indirect selection at younger ages based on traits well correlated with final selection, but still the generation interval is unlikely to reduce much below twenty years. Recent successful developments with genomic selection in animal breeding have led tree breeders to consider the application of this technology. In this study a RAD sequence assay was developed as a means of investigating the potential of molecular breeding in a non-model species. DNA was extracted from nearly 500 clonally replicated trees growing in a single full-sibling family at one site in Britain. The technique proved successful in identifying 132 QTLs for 5-year bud-burst and 2 QTLs for 6-year height. In addition, the accuracy of predicting phenotypes by genomic selection was strikingly high at 0.62 and 0.59 respectively. Sensitivity analysis with 200 offspring found only a slight fall in correlation values (0.54 and 0.38) although when the training population reduced to 50 offspring predictive values fell further (0.33 and 0.25). This proved an encouraging first investigation into the potential use of genomic selection in the breeding of Sitka spruce. The authors investigate how problems associated with effective population size and linkage disequilibrium can be avoided and suggest a practical way of incorporating genomic selection into a dynamic breeding programme.

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

“…We have been unable to find published studies reporting RAD-Seq based genotyping of maize lines and thus it was not possible to directly compare the number of SNP sites identified by this method and tGBS. However, a report has recently been published using double digestion RAD-Seq and the REs PstI and Alw1 to genotype Sitka spruce ( 39 ). This study relied on pilot sequencing studies to select the REs.…”

Genomic selection of juvenile height across a single-generational gap in Douglas-fir

“…Early deterministic simulations by Grattapaglia and Resende (2011) of GS that modeled forest tree species reported promising results. Following this, several experimental investigations have built upon this concept with varying success (Bartholomé et al 2016; Beaulieu et al 2014a, 2014b; Fuentes-Utrilla et al 2017; Gamal El-Dien et al 2015; Grattapaglia 2014; Isik et al 2016; Müller et al 2017a; Ratcliffe et al 2015; Resende et al 2012a, 2012b, 2012c, 2017; Tan et al 2017; Thistlethwaite et al 2017). In general, the following phases are involved in the GS process: (1) the genetic and phenotypic evaluation of a random subset of samples from within a selected population forming the training set from the tree breeding population under investigation; (2) creating a predictive model using this data, in which alleles at all marker loci have their effects simultaneously estimated; (3) implementing a validation or cross-validation process to test the developed models’ robustness; and (4) genomic prediction on a different subset of individuals from the same breeding population and selection of candidates from this population for next-generation breeding based on their genomic estimated breeding values (GEBVs) (Meuwissen et al 2001; Grattapaglia 2014).…”

Genomic architecture of complex traits in loblolly pine

“…This made it possible to detect larger numbers of polymorphisms in close proximity to QTL or even QTL themselves, although effect sizes are reported to be smaller than those detected by QTL mapping (Neale & Savolainen, 2004;Neale & Kremer, 2011;Hall et al, 2016;Plomion et al, 2016). With the absence of reference genomes, these studies focused only on candidate genes or specific regions (although see Fuentes-Utrilla et al, 2017;Lu et al, 2017). As a result, most of the associations explained a very small proportion of the genetic variation in complex traits (Plomion et al, 2016).…”