Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm (original) (raw)
Related papers
Genome‐wide association mapping identifies novel loci underlying fire blight resistance in apple
The Plant Genome
Fire blight, caused by epiphytotic gram-negative bacteria Erwinia amylovora, is the most destructive bacterial disease of apple (Malus spp.). Genetic mechanisms of fire blight resistance have mainly been studied using traditional biparental quantitative trait loci (QTL) mapping approaches. Here, we use large-scale historic shoot and blossom fire blight data collected over multiple years and genotyping-by-sequencing (GBS) markers to identify significant marker-trait associations in a diverse set of 566 apple [Malus domestica (Suckow) Borkh.] accessions. There was large variation in fire blight resistance and susceptibility in these accessions. We identified 23 and 38 QTL significantly (p < .001) associated with shoot and blossom blight resistance, respectively. The QTL are distributed across all 17 chromosomes of apple. Four shoot blight and 19 blossom blight QTL identified in this study colocalized with previously identified QTL associated with resistance to fire blight or apple scab. Using transcriptomics data of two apple cultivars with contrasting fire blight responses, we also identified candidate genes for fire blight resistance that are differentially expressed between resistant and susceptible cultivars and located within QTL intervals for fire blight resistance. However, further experiments are needed to confirm and validate these marker-trait associations and develop diagnostic markers before use in markerassisted breeding to develop apple cultivars with decreased fire blight susceptibility.
Horticulture Research
Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr...
Acta Horticulturae, 2009
Fire blight, caused by Erwinia amylovora (Ea), is a destructive disease of Malus (apple), Pyrus (pear) and some woody ornamentals in the rose family (Rosaceae). The goal of this project is to use a functional genomics approach to develop tools to breed fire blight resistant apples. Suppression subtractive hybridization (SSH) and cDNA-AFLP analysis were used to identify 650 expressed sequence tags (ESTs) associated with fire blight from Ea-challenged apple leaf tissue. ESTs were ranked for their potential impact on resistance based on bioinformatics and inferences drawn from model systems. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from highly ranked fire blight-associated ESTs were mapped in a 'M.9' × 'Robusta 5' population in which a major QTL for fire blight resistance has been located on Linkage Group 03. Highly ranked fire blight-associated ESTs were mapped to this QTL, as well as to the positions corresponding to the location of at least two QTLs reported in other populations. A secretory class III peroxidase mapped to the LG03 fire blight resistance QTL and a serine/threonine protein kinase mapped at a 4 cM distance. To date, 6 out of 28 candidate fire blight resistance gene markers that have been mapped, have co-located to or near known fire blight resistance QTLs. This research will facilitate new methods of marker-assisted selection to efficiently breed superior apple cultivars with fire blight resistance.
BMC Genetics, 2012
Background: Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus 'Robusta 5'. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases.
Horticulturae
Fire blight of fruit crops is one of the most dangerous diseases for apple trees and other plants of the Rosaceae family, and in Kazakhstan, it is subject to quarantine. To study the spread of fire blight, a phytopathological evaluation of 59 apple varieties of domestic and foreign breeds was carried out in various regions of the south and southeast of Kazakhstan while also considering climatic conditions. The susceptibility of an apple tree to fire blight is influenced by the climatic conditions prevailing in a particular fruit region of Kazakhstan. Samples were collected from various varieties of apple trees with fire blight symptoms for molecular genetic analysis. The phytopathological evaluation and results of the PCR analysis made it possible to identify the causative agent of the disease and its spread to apple varieties in the main fruit regions of Kazakhstan. A molecular study of the resistance to the fire blight pathogen was carried out using the most effective molecular ma...
A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR
Tree Genetics & Genomes, 2013
Fire blight is the most important bacterial disease in apple (Malus×domestica) and pear (Pyrus communis) production. Today, the causal bacterium Erwinia amylovora is present in many apple-and pear-growing areas. We investigated the natural resistance of the wild apple Malus×robusta 5 against E. amylovora, previously mapped to linkage group 3. With a fine-mapping approach on a population of 2,133 individuals followed by phenotyping of the recombinants from the region of interest, we developed flanking markers useful for marker-assisted selection. Open reading frames were predicted on the sequence of a BAC spanning the resistance locus. One open reading frame coded for a protein belonging to the NBS-LRR family. The in silico investigation of the structure of the candidate resistance gene against fire blight of M.×robusta 5, FB_MR5, led us hypothesize the presence of a coiled-coil region followed by an NBS and an LRR-like structure with the consensus 'LxxLx[IL]xxCxxLxxL'. The function of FB_MR5 was predicted in agreement with the decoy/guard model, that FB_MR5 monitors the transcribed RIN4_MR5, a homolog of RIN4 of Arabidopsis thaliana that could interact with the previously described effector AvrRpt2 EA of E. amylovora.
Horticulture Research
Apple cultivars with durable resistance are needed for sustainable management of fire blight, the most destructive bacterial disease of apples. Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples, more research is needed to understand the molecular mechanisms underlying host-pathogen interaction and differential genotypic responses to fire blight infection. We have analyzed phenotypic and transcriptional responses of 'Empire' and 'Gala' apple cultivars to fire blight by infecting them with a highly aggressive E. amylovora strain. Disease progress, based on the percentage of visual shoot necrosis, started showing significant (p < 0.001) differences between 'Empire' and 'Gala' 4 days after infection (dai). 'Empire' seems to slow down bacterial progress more rapidly after this point. We further compared transcriptome profiles of 'Empire' and 'Gala' at three different time points after fire blight infection. More genes showed differential expression in 'Gala' at earlier stages, but the number of differentially expressed genes increased in 'Empire' at 3 dai. Functional classes related to defense, cell cycle, response to stress, and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes. Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12, and can serve as functional candidates for future research. These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E. amylovora-Malus pathosystem.
Fire blight (Erwinia amylovora) causes serious damage to pome fruit orchards, and identification of germplasm with heritable disease resistance is therefore crucial. Two dominant SCAR (sequence characterised amplified region) marker alleles (AE10-375 and GE-8019), flanking a previously identified QTL (quantitative trait locus) for resistance to fire blight on 'Fiesta' linkage group 7 in apple cultivars related to 'Cox's Orange Pippin', were screened on 205 apple cultivars. Both marker alleles were present in 22% of the cultivars, indicating presence of the QTL allele for tolerance, and both were lacking in 25%, indicating homozygosity for absence of the QTL tolerance allele. However, 33% had only the marker allele AE10-375, while 20% had only GE-8019, suggesting that some cultivars with the dominant alleles for both of the flanking markers can carry these on separate chromosomes and may lack the QTL allele for tolerance. In 2009 and 2010, terminal shoots of greenhouse-grown grafted trees of 21 cultivars (only 20 in 2010) were inoculated with Erwinia amylovora. 'Idared' (susceptible) and 'Enterprise' (tolerant) were included as controls. Disease severity for each cultivar was expressed as percentage of necrosis in relation to entire length of shoot, and the ranking of cultivars in 2009 and 2010 was compared with a Spearman rank correlation test, P \ 0.01. A relationship between presence of both flanking marker alleles for tolerance and level of fire blight tolerance was confirmed with a Mann-Whitney U-test, P \ 0.01 in 2009, and P \ 0.05 in 2010. A PCO (principal coordinate) analysis based on band profiles obtained with 12 SSR (simple sequence repeat) loci produced three loose clusters, two of which contained known offspring of 'Cox's Orange Pippin', and one with cultivars that were either unrelated or had an unknown origin. Cases where DNA markers did not predict level of fire blight damage as expected, were, however, as common among descendants of 'Cox's Orange Pippin' as among apparently unrelated cultivars. Obviously the 'Fiesta' LG 7 QTL has some predictive value, both for known 'Cox' relatives and others, but more efficient markers would be desirable for marker-assisted selection.