Dissection of complex traits in forest trees — opportunities for marker-assisted selection

Abstract

Due to their long reproductive cycles and the time to expression of mature traits, markerassisted selection is particularly attractive for tree breeding. In this review we discuss different approaches used for developing markers and propose a method for application of markers in low linkage disequilibrium (LD) populations. Identification of useful markers for application in tree breeding is mainly based on two approaches, quantitative trait locus mapping (QTL) and association genetic studies. While several studies have identified significant markers, effect of the individual markers is low making it difficult to utilize them in breeding programs. Recently genomic selection (GS) was proposed for overcoming some of these difficulties. In GS, high density markers are used for predicting phenotypes from genotypes. Currently small effective populations with high LD are being tested for GS in tree breeding. For wider application, GS needs to be applied in low LD populations which are found in many tree breeding programs. Here we propose an approach in which the significant markers from association studies may be used for developing prediction models in low LD populations using the same methods as in GS. Preliminary analyses indicate that a modest numbers of markers may be sufficient for developing prediction models in low LD populations. Genomic selection based on large numbers of random markers or small numbers of associated markers is poised to make marker-assisted selection a reality in forest tree breeding.

Estimation of number and size of QTL effects in forest tree traits

“…Recent common garden trials in Populus along with the completion of the Populous trichcarpa genome sequence (Tuskan et al 2006) have resulted in a few genome-wide association mapping studies on P. trichocarpa where the number of markers is much greater than previous candidate gene approaches (Evans et al 2014;McKown et al 2014;Porth et al 2013). However, several mapping studies in forest trees suggest that most traits have a large number of underlying QTL, and to date, there are very few studies that have a mapping population size that provide the power needed to capture a large proportion of the genetic variation (Neale and Savolainen 2004;Thavamanikumar et al 2013). Investigating the expected number of underlying QTL effects and their distribution can enhance our understanding of the genetic architecture of important quantitative traits, design better experiments to uncover missing factors of heritability, and facilitate implementation of marker-assisted selection (MAS) and genomic selection (Isik 2014;Meuwissen and Goddard 2010;Thavamanikumar et al 2013).…”

“…However, several mapping studies in forest trees suggest that most traits have a large number of underlying QTL, and to date, there are very few studies that have a mapping population size that provide the power needed to capture a large proportion of the genetic variation (Neale and Savolainen 2004;Thavamanikumar et al 2013). Investigating the expected number of underlying QTL effects and their distribution can enhance our understanding of the genetic architecture of important quantitative traits, design better experiments to uncover missing factors of heritability, and facilitate implementation of marker-assisted selection (MAS) and genomic selection (Isik 2014;Meuwissen and Goddard 2010;Thavamanikumar et al 2013). In this paper, we suggest a modified method from Otto and Jones (2000) in order to estimate the number of underlying QTL from the reported size of phenotypic variance explained of significant markers for eight different trait types.…”

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

“…The identification of relevant markers from LA and LD studies would therefore improve the prediction of breeding values for individuals from genotypic data alone, thereby increasing the efficiency of selection strategies [53–55]. In this study, we investigated the genetic architecture of height growth and stem straightness, two major traits in the maritime pine breeding program, through a combination of linkage and genome-wide association mapping.…”

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

“…This has led to the conclusion that GS is only likely to be successful in populations in which Ne is much reduced such as highly selected breeding sub-groups or seed orchards. (Thavamanikumar et al 2013, Beaulieu et al 2014. However, one advantage that forest trees do have over livestock is that very large full-sib families can be generated through controlled pollination followed by the collection of large quantities of cones and seed.…”