Genome-Wide Association Study of Brown Rot (Monilinia spp.) Tolerance in Peach

Abstract

Brown rot, caused by Monilinia spp., is one of the most important diseases on stone fruit worldwide. Severe yield loss can be caused by pre- and post-harvest fruit decay. Although some degree of tolerance has been reported in peach and almond, the genetic resistance in peach cultivars is still lacking. To date, only few genomic regions associated with brown rot response in fruit skin and flesh have been detected in peach. Previous studies suggested brown rot tolerance in peach being a polygenic quantitative trait. More information is needed to uncover the genetics behind brown rot tolerance in peach. To identify the genomic regions in peach associated with this trait, 26 cultivars and progeny from 9 crosses with ‘Bolinha’ sources of tolerance, were phenotyped across two seasons (2015 and 2016) for brown rot disease severity index in wounded and non-wounded fruits and genotyped using a newly developed 9+9K peach SNP array. Genome wide association study using single- and multi-locus methods by GAPIT version 3, mrMLM 4.0, GAPIT and G Model, revealed 14 reliable SNPs significantly associated with brown rot infection responses in peach skin (10) and flesh (4) across whole genome except for chromosome 3. Candidate gene analysis within the haplotype regions of the detected markers identified 25 predicted genes associated with pathogen infection response/resistance. Results presented here facilitate further understanding of genetics behind brown rot tolerance in peach and provide an important foundation for DNA-assisted breeding.

Mapping the genomic landscape of peach and almond with PrunusMap

“…6G243800 ), known as major disease resistance genes in plants. For instance, in peach they have been reported to be involved in pathogen recognition and innate immune responses (Fu et al, 2021).…”

“…Several genes encode disease resistance proteins with LRR and NB-ARC domains (Prupe.1G165300, Prupe.6G243700 and Prupe.6G243800), known as major disease resistance genes in plants. For instance, in peach they have been reported to be involved in pathogen recognition and innate immune responses (Fu et al, 2021).…”

Genetic Diversity and Genome-Wide Association Study of Morphological and Quality Traits in Peach Using Two Spanish Peach Germplasm Collections

“…SNPs classified as “Monomorphic”, “Failed”, and “NullAllele-Failed” were removed ( Di Guardo et al, 2015 ). Subsequently, the SNPs which overcome the previous step with minor allele frequency (MAF) higher than 0.05, were filtered in the Genotyping Analysis Module of GenomeStudio™ v2.0.5 to be used as the high-quality subset of SNPs for further analysis ( Vanderzande et al, 2019 ; Fu et al, 2021 ).…”

“…More recently, different resources using next-generation sequencing (NGS) technologies have been generated to study and manage peach germplasm collections ( Verde et al, 2012 , 2013 , 2017 ), with the most recent being the new version of the peach 18K SNP v2 array ( Gasic et al, 2019 ). Such tools are providing new knowledge for peach breeding regarding genetic control of fruit maturity ( Pirona et al, 2013 ; Nuñez-Lillo et al, 2015 ; Elsadr et al, 2019 ), fruit quality and flower traits ( Font i Forcada et al, 2019 ; Lobato et al, 2021 ), tolerance to diseases ( Cirilli et al, 2017 ; Fu et al, 2021 ), agronomical traits ( da Silva Linge et al, 2021 ; Fu et al, 2021 ), and genetic diversity ( Thurow et al, 2020 ; Fu et al, 2021 ; Mas-Gómez et al, 2021 ). However, only a small fraction of the Spanish peach germplasm has been studied using NGS methodologies ( Font i Forcada et al, 2019 ; Mas-Gómez et al, 2021 ).…”

Re-sequencing and morphological data revealed the genetics of stone shell and kernel traits in apricot

“…The link between genetic markers and a particular trait can be determined using genome-wide association studies (GWAS) based on next-generation high-throughput sequencing techniques. G WAS are widely used to dissect complex genetic traits ( Cao et al., 2016 ; Fu et al., 2021 ). In the present study, we re-sequenced 339 apricot accessions and analyzed the diversity among the materials and the population structure of kernel-using apricots.…”