Genome selection in fruit breeding: application to table grapes

ABSTRACT Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger nematode and Pierce’s disease (PD), and ‘B90-116’, a susceptible Vitis vinifera cultivar with desirable fruit characteristics. Our aim was to enhance the knowledge on the genomic variation of agronomical traits in table grape populations for future use in marker-assisted selection (MAS) and GS, by discovering a set of molecular markers associated with genomic regions involved in this variation. A number of Quantitative Trait Loci (QTL) were discovered but this method is inaccurate and the genetic architecture of the studied population was better captured by the BLasso method of genomic selection, which allowed for efficient inference about the genetic contribution of the various marker loci. The technology of genomic selection afforded greater efficiency than QTL analysis and can be very useful in speeding up the selection procedures for agronomic traits in table grapes

Selective Genotyping and Phenotyping strategies in a complex trait context

Selective genotyping and phenotyping strategies are used to lower the cost of quantitative trait locus studies. Their efficiency has been Studied primarily in simplified contexts-when a single locus contributes to the phenotype, and when the residual error (phenotype conditional on the genotype) is normally distributed. It is unclear how these strategies will perform in the context of complex traits where multiple loci, possibly linked or epistatic, may contribute to the trait. We also do not know what genotyping strategies should be used for nonnormally distributed phenotypes. For time-to-event phenotypes there is the additional question of choosing follow-tip time duration. We use an information perspective to examine these experimental design issues in the broader context of complex traits and make recommendations on their use

3D graphical visualization of the genetic architectures underlying complex traits in multiple environments

An approach for generating interactive 3D graphical visualization of the genetic architectures of complex traits in multiple environments is described. 3D graphical visualization is utilized for making improvements on traditional plots in quantitative trait locus (QTL) mapping analysis. Interactive 3D graphical visualization for abstract expression of QTL, epistasis and their environmental interactions for experimental populations was developed in framework of user-friendly software QTLNetwork ( http://ibi.zju.edu.cn/software/ qtlnetwork ). Novel definition of graphical meta system and computation of virtual coordinates are used to achieve explicit but meaningful visualization. Interactive 3D graphical visualization for QTL analysis provides geneticists and breeders a powerful and easy-to-use tool to analyze and publish their research results