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.

Genome wide selection in Citrus breeding

“…GWS could explain a greater proportion of the observed variance in traits compared with methods based on the identification of individual QTL. This was observed by Viana et al (2016) who compared MAS and genomic selection in a grape breeding population consisting of 143 individuals obtained from a cross between (Vitis rupestris x Vitis arizonica/girdiana) x Vitis vinifera. The efficiency of genomic selection was 1.7 to 11.6-fold higher than that obtained by traditional QTL analysis.…”

“…GWS has rarely been applied to fruit trees, being restricted to apples (Kumar et al, 2012), pears (Iwata et al, 2013), and grapes (Viana et al, 2016). To our knowledge, the present study represents the first attempt to investigate the feasibility of genomic selection in Citrus.…”

Triple categorical regression for genomic selection: application to cassava breeding

“…On the other hand, the TCR method provided lower accuracy than the G-BLUP and BLASSO methods did, with the BLASSO method standing out in terms of prediction accuracy. In GWS studies for genetic improvement of table grapes, Viana et al (2016a) also reported the superiority of the BLAS-SO method over the ridge regression BLUP method (reparametrization of G-BLUP method) for its efficiency in predicting additive genomic values. ), accuracy (r âa ), and bias (b yâ ), with respective standard deviations, of the additive genomic values estimated by the triple categorical regression (TCR), genomic best linear unbiased predictor (G-BLUP), and Bayesian least absolute shrinkage and selection operator (BLASSO) methods, considering the additive-dominance model on simulated data.…”

Seleção Genômica Ampla (Gws) E Associação Genômica Ampla (Gwas) No Melhoramento De Forrageiras: Abordagem Conceitual, Genética Quantitativa E Aplicações

“…No Brasil, esta técnica começou a ser aplicada recentemente com sucesso em culturas anuais e perenes (CASTRO et al, 2016;LIMA et al, 2019;RESENDE et al, 2012a;VIANA et al, 2016). Em espécies forrageiras, apesar do uso da pastagem como principal componente das dietas de ruminantes, poucos estudos nacionais trazem tal abordagem, apontando, porém, para seu grande potencial (PEREIRA et al, 2018).…”