Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

Abstract

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot.

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

“…Although there is a similarity between the present work and that of Martinez-Garcia et al (2013a) in terms of experimental approach, these works differ in fundamental points that have led to different results. First, the genetic backgrounds of the analyzed populations in the cited and the present study are different: in Martinez-Garcia et al (2013a), the studied population is PopDF (cross "Dr. Davis"×"F8,1-42"), with pedigrees including mostly historical canning peach cultivars and almond introgressions; by contrast, most accessions constituting the pedigrees of Contender and Elegant Lady (parents of the population used in the present study) correspond to traditional, melting fleshed peach cultivars, characterized by a recurrent presence of "Chinese Cling" and "JH Hale," and any introgression from other Prunus species is observed in their lineages. In the case of quantitative traits, like BR resistance, favorable alleles segregating in a population can be absent in populations with a different genetic background, carrying to the discovery of different QTLs, depending on the population studied.…”

“…Markers linked with ESTs related with resistance to powdery mildew (a biotrophic pathogen) were found in Lalli et al (2005) in a similar map position of LG4 (markers CC136A, AG8A, and CC138, positioned near BPPCT015 and thus to EPPISF032). A QTL was recently found in Martinez-Garcia et al (2013a) in LG4 of "PopDF" (see below); however, the QTL resulted significant only 1 year, and significance interval is in a position around 8,500,000 bp of scaffold 4, far from the position of QTLs SK-if_2009.4 and SK-if_2010.4b (near EPPISF032, around 12.77 Mb of the same scaffold).…”

“…Recently, QTL analysis for BR resistance in peach has been published (Martinez-Garcia et al 2013a). In the cited work, the authors found two candidate QTLs on the LG1, significantly associated with skin BR resistance in 2 out of 3 years of phenotypic analysis.…”

Peach Brown Rot: Still in Search of an Ideal Management Option

“…Other different parts have been used to study the genetic resistance to pathogens of plant parts, such as flowers in apricots [186] and fruits in peaches [180,181,187]. Moreover, the evaluations have consistently been performed in situ with attached fruits, in natural ambient situations in the field on peaches and nectarines [180,188], or ex situ on apples [189] and stone fruits [40,190,191], involving detached apricots [45,46] and peaches, under controlled conditions [48,190,192].…”

“…[51,179], there could exist genetic disease control elements [180,181] to be introgressed in high-quality fruit's genetic backgrounds [40]. Hence, the relative tolerance or susceptibility of fruits to disease has often been used for selecting disease-resistant genotypes for subsequent peach breeding.…”