In the framework of the EU-PRIMA research project FREECLIMB (FRUIT CROPS RESILIENCE TO CLIMATE CHANGE IN THE MEDITERRANEAN BASIN), we are investigating genotype by environment (GxE) interactions for resilience traits in peach trees (Prunus persica). This is a multi-year, multi-site experiment: samples from 4 different locations across Southern Europe (Italy, Spain, Greece) have been collected, with data available over multiple production years. The target phenotypes include: i) maturation time; ii) flowering time; iii) fruit developmental period. The standard GBLUP model for whole-genome predictions is going to be extended to include repeated records over time and the GxE term. Cross-validation schemes have been designed to take into account data stratification (year, site, genetic background) in order to obtain unbiased estimates of the attainable predictive ability of the models. About 400 peach samples have been sequenced with two approaches: whole-genome resequencing (WGS) and SPET (Single Primer Enrichment Technology) sequencing. SNPs (single-nucleotide polymorphisms) have been called with a Nextflow-based BWA-MEM resequencing pipeline. As a preliminary step, the accuracy of imputing missing SNP genotypes has been measured with results, in terms of Cohen's kappa, ranging from 0.55 to 0.90, depending on the peach population and the missing rate.
Modelling GxE Interactions in Peach Trees (Prunus persica): A Multi-Year, Multi-Site Trial
Filippo Biscarini;T Bobbo
2023
Abstract
In the framework of the EU-PRIMA research project FREECLIMB (FRUIT CROPS RESILIENCE TO CLIMATE CHANGE IN THE MEDITERRANEAN BASIN), we are investigating genotype by environment (GxE) interactions for resilience traits in peach trees (Prunus persica). This is a multi-year, multi-site experiment: samples from 4 different locations across Southern Europe (Italy, Spain, Greece) have been collected, with data available over multiple production years. The target phenotypes include: i) maturation time; ii) flowering time; iii) fruit developmental period. The standard GBLUP model for whole-genome predictions is going to be extended to include repeated records over time and the GxE term. Cross-validation schemes have been designed to take into account data stratification (year, site, genetic background) in order to obtain unbiased estimates of the attainable predictive ability of the models. About 400 peach samples have been sequenced with two approaches: whole-genome resequencing (WGS) and SPET (Single Primer Enrichment Technology) sequencing. SNPs (single-nucleotide polymorphisms) have been called with a Nextflow-based BWA-MEM resequencing pipeline. As a preliminary step, the accuracy of imputing missing SNP genotypes has been measured with results, in terms of Cohen's kappa, ranging from 0.55 to 0.90, depending on the peach population and the missing rate.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
