Across-population genomic prediction in grapevine opens up promising prospects for breeding

Abstract

Crop breeding involves two selection steps: choosing progenitors and selecting offspring within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.

Interest of phenomic prediction as an alternative to genomic prediction in grapevine

“…The half-diallel is composed of 676 individuals from ten bi-parental populations (hereafter named crosses) in a half-diallel mating design between five parents: Syrah (S), Grenache (G), Cabernet-Sauvignon (CS), Terret Noir (TN) and Pinot Noir (PN) (Tello et al, 2019). All of them, except Grenache, belong to the WW gene pool (Brault et al, 2021b). Each cross comprises between 64 and 70 offspring.…”

“…We studied the same 15 traits in both trials (diversity panel and half-diallel), related to (i) berry composition at harvest, with malic acid (mal.ripe), tartaric acid (tar.ripe), shikimic acid (shik.ripe) concentrations, and shikimic / tartaric acid (shiktar.ripe) and malic / tartaric acid (maltar.ripe) ratios, (ii) berry and cluster morphological traits, with mean berry weight (mbw), mean cluster weight (mcw), mean cluster length (mcl), mean cluster width (mcwi) and cluster compactness (clucomp), (iii) phenology traits, with véraison date (onset of ripening, verday), harvest date (samplday) and the interval between véraison and harvest (vermatu), (iv) vigor (vigour). Details about phenotypic measurements, statistical processing and heritability can be found in Brault et al (2021b). For prediction, we used the Best Linear Unbiased Predictors (BLUP) of genotypic values from Flutre et al (2020) in the diversity panel and Brault et al (2021b) in the half-diallel.…”

“…Details about phenotypic measurements, statistical processing and heritability can be found in Brault et al (2021b). For prediction, we used the Best Linear Unbiased Predictors (BLUP) of genotypic values from Flutre et al (2020) in the diversity panel and Brault et al (2021b) in the half-diallel. Briefly, a mixed linear model was fitted for eliminating experimental confounding effects and in order to extract BLUPs of genotypic values.…”

“…Details about genotyping and marker processing are given in (Tello et al, 2019) for the half-diallel and in Flutre et al (2020) for the diversity panel. The selection of common SNPs was done in Brault et al (2021b). 622 out of 676 individuals were successfully genotyped in the half-diallel, and 277 out of 279 individuals in the diversity panel.…”

“…Heritability values of phenotypic data were assessed for both populations in Flutre et al (2020) for the diversity panel and in Brault et al (2021b) for the half-diallel.…”