Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Abstract

BackgroundHighly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach.ResultsA repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average).ConclusionsThis study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3781-8) contains supplementary material, which is available to authorized users.

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“…Modelling traits simultaneously allows to achieve larger genomic prediction accuracy for the target trait, compared to single-trait genomic prediction (Dekkers 2007;Jia and Jannink 2012;Alimi 2016;Biscarini et al 2017;Sun et al 2017). The benefit from multi-trait genomic prediction using the target and intermediate traits simultaneously, relative to single trait prediction using the target trait exclusively depends on the trait correlations and trait heritability Jia and Jannink 2012), in the same way as discussed in Chapter 4 for the correlated selection response when measuring the same trait in two different regions (Atlin et al 2000;Piepho and Möhring 2005)…”

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