QTL mapping of fire blight resistance in apple

Fire blight caused by the bacterium Erwinia amylovora is a severe threat to apple and pear orchards worldwide. Apple varieties exhibit a wide range of relative susceptibility/tolerance to fire blight. Although, no monogenic resistance against fire blight has been identified yet, recent evidence indicates the existence of quantitative resistance. Potential sources of fire blight resistance include several wild Malus species and some apple cultivars. F1 progenies of ‘Fiesta’בDiscovery’ were inoculated with the Swiss strain Ea 610 and studied under controlled conditions to identify quantitative trait loci (QTLs) for fire blight resistance. Disease was evaluated at four time points after inoculation. Shoot lesion length and the area under disease progress curve (AUDPC) values were used for QTL analysis. One significant (LOD score of 7.5–8.1, p<0.001) QTL was identified on the linkage group 7 of ‘Fiesta’ (F7). The F7 QTL explained about 37.5–38.6% of the phenotypic variation.     

QTL mapping of fire blight resistance in Malus ×robusta 5 after inoculation with different strains of Erwinia amylovora

Fire blight caused by Erwinia amylovora is one of the most disastrous diseases in apple production. Whereas most apple cultivars are susceptible to fire blight, several wild apple species accessions like Malus ×robusta 5 (Mr5) bear significant resistance. The resistance of Mr5 is mainly inherited by a major quantitative trait locus (QTL) on linkage group 3. QTL mapping was performed after inoculation of the population 04208 (Idared × Mr5) using strains differing in their virulence to Mr5. The QTL mapping approach demonstrated that the major QTL on linkage group 3 could be confirmed after inoculation with strains non-virulent to Mr5. In contrast, the major QTL disappeared after inoculation with strains virulent to Mr5. Only after inoculation with the resistance breaking strain Ea 3049 was a minor QTL with a LOD >3 found on linkage group 3. Additionally, several minor QTLs were detected on linkage groups 5, 7, 11 and 14 of Mr5 after inoculation with virulent strains able to overcome the major resistance QTL of Mr5. Their usefulness for further breeding activities will be discussed. The strain-specific results obtained in the present study provide further evidence for the existence of gene-for-gene relationships in the host–pathogen system Mr5–E. amylovora. Of the newly discovered minor QTLs, the one detected on LG7 contributes significantly to fire blight resistance in the presence of the major QTL, independently of the strain used.     

Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies

Although fire blight, caused by the bacterium Erwinia amylovora, is one of the most destructive diseases of apple (Malus × domestica) worldwide, no major, qualitative gene for resistance to this disease has been identified to date in apple. We conducted a quantitative trait locus (QTL) analysis in two F₁ progenies derived from crosses between the cultivars Fiesta and either Discovery or Prima. Both progenies were inoculated in the greenhouse with the same strain of E. amylovora, and the length of necrosis was scored 7 days and 14 days after inoculation. Additive QTLs were identified using the mapqtl software, and digenic epistatic interactions, which are an indication of putative epistatic QTLs, were detected by two-way analyses of variance. A major QTL explaining 34.3–46.6% of the phenotypic variation was identified on linkage group (LG) 7 of Fiesta in both progenies at the same genetic position. Four minor QTLs were also identified on LGs 3, 12 and 13. In addition, several significant digenic interactions were identified in both progenies. These results confirm the complex polygenic nature of resistance to fire blight in the progenies studied and also reveal the existence of a major QTL on LG7 that is stable in two distinct genetic backgrounds. This QTL could be a valuable target in marker-assisted selection to obtain new, fire blight-resistant apple cultivars and forms a starting point for discovering the function of the genes underlying such QTLs involved in fire blight control.     

Identification of a major quantitative trait locus for resistance to fire blight in the wild apple species Malus fusca

Fire blight, caused by the Gram-negative bacterium Erwinia amylovora, is the most important bacterial disease affecting apple (Malus × domestica) and pear (Pyrus communis) production. The use of antibiotic treatment, though effective to some degree, is forbidden or strictly regulated in many European countries, and hence an alternative means of control is essential. The planting of fire blight-resistant cultivars seems to be a highly feasible strategy. In this study, we explored a segregating population derived from a cross between the wild apple species Malus fusca and the M. × domestica cultivar Idared. F1 progenies used for mapping were artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 10⁹ cfu/ml in three different years. The averages of percentage lesion length of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal–Wallis analysis was used to determine marker–phenotype association and revealed a linkage group with Diversity Arrays Technology (DArT) markers significantly linked with fire blight. After locating the positions of the DArT markers on the Golden Delicious genome, simple sequence repeat (SSR) markers were developed from chromosome 10 to replace the DArT markers and to determine the quantitative trait locus (QTL) region. Multiple QTL mapping (MQM) revealed a strong QTL (Mfu10) on linkage group 10 of M. fusca explaining about 65.6 % of the phenotypic variation. This is the first report on a fire blight resistance QTL of M. fusca.     

First report on the presence of fire blight resistance in linkage group 11 ofPyrus ussuriensis Maxim

Fire blight, caused by the gram-negative bacteriumErwinia amylovora (Burrill) Winslow et al., is a dangerous disease of pome fruits, including pear. A pear breeding program for fire blight resistance was initiated in 2003 at the Department of Pomology, Warsaw University of Life Sciences, Poland. Since several Asian species are considered to be potential sources of resistance to fire blight, the susceptiblePyrus communis ‘Doyenne du Comice’ was crossed with the resistantP. ussuriensis. The F₁ full-sib progeny composed of 155 seedlings was tested for susceptibility to fire blight by artificial shoot inoculation. A framework linkage map of both parents was constructed based on 48 AFLP and 32 SSR markers and covered a length of 595 cM and 680 cM in ‘Doyenne du Comice’ andP. ussuriensis, respectively. For the first time a putative QTL for fire blight resistance inP. ussuriensis linkage group 11 was identified. Another putative QTL in linkage group 4 of ‘Doyenne du Comice’ seems to indicate that sources of fire blight resistance can be identified also in the susceptible cultivars.     

Identifying QTLs for fire-blight resistance via a European pear (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.) genetic linkage map

The existence of different levels of susceptibility to fire blight (Erwinia amylovora) in European pear (Pyrus communis L.) cultivars suggests that it is possible to identify QTLs related to resistance in pear germplasm. Given the polygenic nature of this trait, we designed two genetic maps of the parental lines 'Passe Crassane' (susceptible) and 'Harrow Sweet' (resistant) using SSRs, MFLPs, AFLPs, RGAs and AFLP-RGAs markers. RGA-related markers should theoretically map in chromosome regions coding for resistance genes. The 'Passe Crassane' map includes 155 loci, for a total length of 912 cM organised in 18 linkage groups, and the 'Harrow Sweet' map 156 loci, for a total length of 930 cM divided in 19 linkage groups; both maps have a good genome coverage when compared to the more detailed apple maps. Four putative QTLs related to fire blight resistance were identified in the map. A suite of molecular markers, including two AFLP-RGAs, capable of defining resistant and susceptible haplotypes in the analysed population was developed.     

Development of molecular markers linked to the 'Fiesta' linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection.

A fire blight resistance QTL explaining 34.3%-46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar 'Fiesta' (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of 'Fiesta' with these markers enabled tracking of the F7 QTL allele back to 'Cox's Orange Pippin'. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between 'Milwa', a susceptible cultivar, and '1217', a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS.     

Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments

Powdery mildew, caused by the ascomycete fungus Podosphaera leucotricha, is one of the most damaging diseases of apple worldwide. Polygenically determined resistance might contribute to a significant increase of resistance to this disease in new cultivars. A quantitative trait locus (QTL) analysis was performed in an F₁ progeny derived from a cross between the apple cultivar Discovery and the apple hybrid TN10-8. Powdery mildew incidence was assessed during four years (five seasons) in spring and/or autumn in a French local orchard. Seven additive and/or dominant QTLs were detected over the five seasons, with effects (R ²) ranging from 7.5% to 27.4% of the progeny phenotypic variation. Two QTLs, on linkage groups (LGs) 2 and 13, were consistently identified and accounted together from 29% to 37% of the phenotypic variation according to the year of assessment. The other QTLs were identified during one (LGs 1, 14), two (LG10), or three (LGs 8, 17) seasons. Their instability indicated a changing genetic determinism according to the year of assessment, for which several hypotheses may be put forward. The QTLs on LGs 2 and 8 mapped close to clusters of resistance gene analogs (RGAs) and major genes for resistance to mildew or apple scab previously identified. The stable QTLs identified on LGs 2 and 13, together with the strong effect QTL located on LG 8, are of special interest for breeding purposes, especially if combined with other major resistance genes.     

Genetic control of fruit vitamin C contents

An F(1) progeny derived from a cross between the apple (Malus x domestica) cultivars Telamon and Braeburn was used to identify quantitative trait loci (QTL) linked to the vitamin C (l-ascorbate [l-AA]) contents of fruit skin and flesh (cortex) tissues. We identified up to three highly significant QTLs for both the mean l-AA and the mean total l-AA contents of fruit flesh on both parental genetic linkage maps, confirming the quantitative nature of these traits. These QTLs account for up to a maximum of 60% of the total population variation observed in the progeny, and with a maximal individual contribution of 31% per QTL. QTLs common to both parents were identified on linkage groups (LGs) 6, 10, and 11 of the Malus reference map, while each parent also had additional unique QTLs on other LGs. Interestingly, one strong QTL on LG-17 of the Telamon linkage map colocalized with a highly significant QTL associated with flesh browning, and a minor QTL for dehydroascorbate content, supporting earlier work that links fruit l-AA contents with the susceptibility of hardfruit to postharvest browning. We also found significant minor QTLs for skin l-AA and total l-AA (l-AA + dehydroascorbate) contents in Telamon. Currently, little is known about the genetic determinants underlying tissue l-AA homeostasis, but the presence of major, highly significant QTL in both these apple genotypes under field conditions suggests the existence of common control mechanisms, allelic heterozygosity, and helps outline strategies and the potential for the molecular breeding of these traits.     

Mapping of quantitative trait loci (QTLs) for oil yield using SSRs and gene-based markers in African oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis> Jacq.)

The identification of quantitative trait loci (QTLs) based on anchor markers, especially candidate genes that control a trait of interest, has been noted to increase the power of QTL detection. Since these markers can be scored as co-dominant data, they are also valuable for comparing and integrating the QTL linkage maps from diverse mapping populations. To estimate the position and effects of QTLs linked to oil yield traits in African oil palm, co-dominant microsatellites (SSR) and candidate gene-based sequence polymorphisms were applied to construct a linkage map for a progeny showing large differences in oil yield components. The progeny was genotyped for 97 SSR markers, 93 gene-linked markers, and 12 non-gene-linked SNP markers. From these, 190 segregating loci could be arranged into 31 linkage groups while 12 markers remained unmapped. Using the single marker linkage, interval mapping and multiple QTL methods, 16 putative QTLs on seven linkage groups affecting important oil yield related traits such as fresh fruit bunch yield (FFB), ratio of oil per fruit (OF), oil per bunch (OB), fruit per bunch (FB) and wet mesocarp per fruit (WMF) could be identified in the segregating population with estimated values for explained variance ranging from 12.4 % to 54.5 %. Markers designed from some candidate genes involved in lipid biosynthesis were found to be mapped near significant QTLs for various economic yield traits. Associations between QTLs and potential candidate genes are discussed.     

Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

The identification of quantitative trait loci (QTLs) affecting agronomically important traits enable to understand their underlying genetic mechanisms and genetic basis of their complex interactions. The aim of the present study was to detect QTLs for 12 agronomic traits related to staygreen, plant early development, grain yield and its components, and some growth characters by analyzing replicated phenotypic datasets from three crop seasons, using the population of 168 F₇ RILs of the cross 296B × IS18551. In addition, we report mapping of a subset of genic-microsatellite markers. A linkage map was constructed with 152 marker loci comprising 149 microsatellites (100 genomic- and 49 genic-microsatellites) and three morphological markers. QTL analysis was performed by using MQM approach. Forty-nine QTLs were detected, across environments or in individual environments, with 1–9 QTLs for each trait. Individual QTL accounted for 5.2–50.4% of phenotypic variance. Several genomic regions affected multiple traits, suggesting the phenomenon of pleiotropy or tight linkage. Stable QTLs were identified for studied traits across different environments, and genetic backgrounds by comparing the QTLs in the study with previously reported QTLs in sorghum. Of the 49 mapped genic-markers, 18 were detected associating either closely or exactly as the QTL positions of agronomic traits. EST marker Dsenhsbm19, coding for a key regulator (EIL-1) of ethylene biosynthesis, was identified co-located with the QTLs for plant early development and staygreen trait, a probable candidate gene for these traits. Similarly, such exact co-locations between EST markers and QTLs were observed in four other instances. Collectively, the QTLs/markers identified in the study are likely candidates for improving the sorghum performance through MAS and map-based gene isolations.     

水稻纹枯病抗性QTL分析

对灿稻窄叶青8号（ZYQ8）和粳稻京系17（JX17）以及由它们构建的加倍单倍体（DH）群体,分别在杭州和海南岛,采用注射器接种法进行纹枯病抗性鉴定,并使用该群体的分子链锁图谱进行数量性状座位（QTL）分析。共检测到4个抗纹枯病的QTL（qSBR-2、qSBR-3、qSBR-7和qSBR-11）,分别位于第2、第3、第7和第11染色体。其中qSBR-2、qSBR-3、qSBR-7的抗性基因由抗病亲本ZYQ8贡献,而qSBR-11的抗性基因来自感病亲本JX17。qSBR-2、qSBR-3、qSBR-7在杭州和海南岛都能检测到,而qSBR-11只在杭州检测到。在杭州的实验中,纹枯病病级与秆长和抽穗期呈显著负相关;在控制秆长和抽穗期的QTL中,控制秆长的qCL-3与qSBR-3位于同一染色体区域,其余QTL与抗纹枯病的QTL之间无连锁关系。     

Identification and validation of genomic regions that affect shoot fly resistance in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

Shoot fly is one of the most important pests affecting the sorghum production. The identification of quantitative trait loci (QTL) affecting shoot fly resistance enables to understand the underlying genetic mechanisms and genetic basis of complex interactions among the component traits. The aim of the present study was to detect QTL for shoot fly resistance and the associated traits using a population of 210 RILs of the cross 27B (susceptible) × IS2122 (resistant). RIL population was phenotyped in eight environments for shoot fly resistance (deadheart percentage), and in three environments for the component traits, such as glossiness, seedling vigor and trichome density. Linkage map was constructed with 149 marker loci comprising 127 genomic-microsatellite, 21 genic-microsatellite and one morphological marker. QTL analysis was performed by using MQM approach. 25 QTL (five each for leaf glossiness and seedling vigor, 10 for deadhearts, two for adaxial trichome density and three for abaxial trichome density) were detected in individual and across environments. The LOD and R ² (%) values of QTL ranged from 2.44 to 24.1 and 4.3 to 44.1%, respectively. For most of the QTLs, the resistant parent, IS2122 contributed alleles for resistance; while at two QTL regions, the susceptible parent 27B also contributed for resistance traits. Three genomic regions affected multiple traits, suggesting the phenomenon of pleiotrophy or tight linkage. Stable QTL were identified for the traits across different environments, and genetic backgrounds by comparing the QTL in the study with previously reported QTL in sorghum. For majority of the QTLs, possible candidate genes were identified. The QTLs identified will enable marker assisted breeding for shoot fly resistance in sorghum.     

Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple.

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus x domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has bee n inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.     

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Whole‐genome sequencing‐based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next‐generation sequencing (NGS)‐based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR‐01 and CPR‐02. Eleven QTLs in CPR‐01 and six QTLs in CPR‐02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR‐01 using conventional biparental mapping approach were used to compare the efficiency of NGS‐based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR‐01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS‐based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR‐02 population. This study demonstrated the efficiency of NGS‐based BSA as a rapid and cost‐effective method to identify QTLs associated with ascochyta blight in chickpea.     

拔节期与抽穗期玉米抗纹枯病相关QTL的初步定位

以玉米自交系R15(抗)×478(感)的F_2分离群体为作图群体,构建了包含146个SSR标记位点的遗传连锁图谱,覆盖玉米基因组1666 cM,平均图距11．4 cM。通过麦粒嵌入法对229个F_(2：4)家系进行人工接种纹枯病菌,于玉米拔节期和抽穗期进行纹枯病的抗性鉴定。应用复合区间作图法分析两个时期的抗病QTL及遗传效应。结果共检测到17个抗性QTL,其中以拔节期病情指数为指标共检测到9个QTL,分别位于第1、2、3、4、5、6、和10染色体上,可解释的表型变异为3．72%-9．26%;以抽穗期的病情指数为指标共在7条染色体上检测到10个抗玉米纹枯病的QTL,分布于第2、3、4、5、6、8和9染色体上。单个QTL可解释的表型变异为4．27%-9．27%。两个时期共检测出2个共同QTL,它们分别位于第2染色体的bnlgl662-bnlg1940区间和第6染色体的umc1006-umc1723区间。定位结果表明两个时期检测出的抗性QTL的差异表达与玉米不同发育时期基因的时空表达有密切关系,从而反映在纹枯病的抗性位点差异性上．这为玉米抗病选育提供新的信息。     

Identification of Novel Strain-Specific and Environment-Dependent Minor QTLs Linked to Fire Blight Resistance in Apples

Since its first report almost 200 years ago, fire blight, caused by the gram-negative bacterium Erwinia amylovora, has threatened apple and pear production globally. Identifying novel genes and their functional alleles is a prerequisite to developing apple cultivars with enhanced fire blight resistance. Here, we report 13 strain-specific and environment-dependent minor QTLs linked to fire blight resistance from a segregating Malus sieversii × Malus × domestica mapping population. Interval mapping at 95% confidence and Kruskal–Wallis analysis at P value =?0.005 were used to identify QTLs for three strains of E. amylovora differing in virulence and pathogenicity. The QTLs identified explain a small to moderate part of resistance variability, and a majority was not common between years or E. amylovora strains. These QTLs are distributed in eight linkage groups of apples and comparison of their map position to previously identified fire blight resistance QTLs indicates that most are novel loci. Interaction between experimental conditions in the greenhouse and field, and between years, and differences in virulence levels of strains might be responsible for strain- and year-specific QTLs. The QTLs identified on LG10 for strain Ea273 in 2011 and strain LP101 in 2011, and on LG15 for strain LP101 could be the same QTLs identified previously with strain CFBP1430 in cultivar “Florina” and “Co-op16 × Co-op17” mapping population, respectively. We discuss the potential impact of newly identified minor fire blight QTLs and major gene-based resistance on the rate of mutation in pathogen populations to overcome resistance and durability of resistance.     

Validation of quantitative trait loci for Ascochyta blight resistance in pea (Pisum sativum L.), using populations from two crosses

Resistance to Ascochyta blight of pea was genetically characterized by mapping quantitative trait loci (QTLs) using two crosses, 3147-A26 (A26, partially resistant) × cultivar Rovar (susceptible) and 3148-A88 (A88, partially resistant) × Rovar, with the aim of developing an increased understanding of the genetics of resistance and of identifying linked molecular markers that may be used to develop resistant germplasm. Molecular linkage maps for both crosses were aligned so that the results of QTL mapping could be compared. Ascochyta blight disease severity in response to natural epidemics was measured in field trials conducted in Western Australia and New Zealand. Eleven putative QTLs for Ascochyta blight resistance were identified from the A26 × Rovar population and 14 putative QTLs from the A88 × Rovar population. Six QTLs were associated with the same genomic regions in both populations. These QTLs reside on linkage groups II, III, IV, V, and VII (two QTLs). The severity of Ascochyta blight disease symptoms on pea increases during field epidemics as plants mature; therefore, QTLs for plant reproductive maturity were mapped. Six QTLs were detected for plant maturity in the A26 × Rovar population, while five plant maturity QTLs were mapped in the A88 × Rovar population. QTLs for plant maturity coincide with Ascochyta blight resistance QTLs in four genomic regions, on linkage groups II (two regions), III, and V. The plant maturity and Ascochyta blight resistance QTLs on III were linked in repulsion phase. Therefore, the coincidence of these QTLs may be explained by linkage of distinct loci for the two traits. The QTLs on linkage groups II and V were linked in coupling phase; therefore, linked QTLs for resistance and maturity may be present in these regions, or the Ascochyta blight resistance QTLs detected in these regions are the result of pleiotropic effects of plant-maturity genetic loci.