Introgression of homeologous quantitative trait loci (QTLs) for resistance to the root-knot nematode [Meloidogyne arenaria (Neal) Chitwood] in an advanced backcross-QTL population of peanut (Arachis hypogaea L.)

Resistance to root-knot nematodes [Meloidogyne arenaria (Neal) Chitwood] is needed for cultivation of peanut in major peanut-growing areas, but significant resistance is lacking in the cultivated species (Arachis hypogaea L.). Markers to two closely-linked genes introgressed from wild relatives of peanut have been identified previously, but phenotypic evidence for the presence of additional genes in wild species and introgression lines has eluded quantitative trait locus (QTL) identification. Here, to improve sensitivity to small-effect QTLs, an advanced backcross population from a cross between a Florunner component line and the synthetic amphidiploid TxAG-6 [Arachis batizocoi × (A. cardenasii × A. diogoi)]^4× was screened for response to root-knot nematode infection. Composite interval mapping results suggested a total of seven QTLs plus three putative QTLs. These included the known major resistance gene plus a second QTL on LG1, and a potentially homeologous B-genome QTL on LG11. Additional potential homeologs were identified on linkage group (LG) 8 and LG18, plus a QTL on LG9.2 and putative QTLs on LG9.1 and 19. A QTL on LG15 had no inferred resistance-associated homeolog. Contrary to expectation, two introgressed QTLs were associated with susceptibility, and QTLs at some homeologous loci were found to confer opposite phenotypic responses. Long-term functional conservation accompanied by rapid generation of functionally divergent alleles may be a singular feature of NBS-LRR resistance gene clusters, contributing to the richness of resistance alleles available in wild relatives of crops. The significance for peanut evolution and breeding is discussed.     

Identification of genome regions controlling cotyledon,pod wall/seed coat and pod wall resistance to pea weevil through QTL mapping

Pea weevil, Bruchus pisorum, is one of the limiting factors for field pea (Pisum sativum) cultivation in the world with pesticide application the only available method for its control. Resistance to pea weevil has been found in an accession of Pisum fulvum but transfer of this resistance to cultivated pea (P. sativum) is limited due to a lack of easy-to-use techniques for screening interspecific breeding populations. To address this problem, an interspecific population was created from a cross between cultivated field pea and P. fulvum (resistance source). Quantitative trait locus (QTL) mapping was performed to discover the regions associated with resistance to cotyledon, pod wall/seed coat and pod wall resistance. Three major QTLs, located on linkage groups LG2, LG4 and LG5 were found for cotyledon resistance explaining approximately 80 % of the phenotypic variation. Two major QTLs were found for pod wall/seed coat resistance on LG2 and LG5 explaining approximately 70 % of the phenotypic variation. Co-linearity of QTLs for cotyledon and pod wall/seed coat resistance suggested that the mechanism of resistance for these two traits might act through the same pathways. Only one QTL was found for pod wall resistance on LG7 explaining approximately 9 % of the phenotypic variation. This is the first report on the development of QTL markers to probe Pisum germplasm for pea weevil resistance genes. These flanking markers will be useful in accelerating the process of screening when breeding for pea weevil resistance.     

QTL mapping for bacterial wilt resistance in peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F₂ population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut. Genome-wide SNPs were identified from restriction-site-associated DNA sequencing tags using next-generation DNA sequencing technology. SNPs linked to disease resistance were determined in two bulks of 30 resistant and 30 susceptible plants along with two parental plants using bulk segregant analysis. Polymorphic SSR and SNP markers were utilized for construction of a linkage map and for performing the QTL analysis, and a moderately dense linkage map was constructed in the F₂ population. Two QTL (qBW-1 and qBW-2) detected for resistance to BW disease were located in the linkage groups LG1 and LG10 and account for 21 and 12 % of the bacterial wilt phenotypic variance. To confirm these QTL, the F₈ RIL population with 223 plants was utilized for genotyping and phenotyping plants by year and location as compared to the F₂ population. The QTL qBW-1 was consistent in the location of LG1 in the F₈ population though the QTL qBW-2 could not be clarified due to fewer markers used and mapped in LG10. The QTL qBW-1, including four linked SNP markers and one SSR marker within 14.4-cM interval in the F₈, was closely related to a disease resistance gene homolog and was considered as a candidate gene for resistance to BW. QTL identified in this study would be useful to conduct marker-assisted selection and may permit cloning of resistance genes. Our study shows that bulk segregant analysis of genome-wide SNPs is a useful approach to expedite the identification of genetic markers linked to disease resistance traits in the allotetraploidy species peanut.     

Mapping quantitative trait loci conferring partial physiological resistance to white mold in the common bean RIL population Xana?×?Cornell 49242

White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a devastating disease in common bean (Phaseolus vulgaris L.). Resistance to this pathogen can be due to physiological or avoidance mechanisms. We sought to characterize the partial physiological resistance exhibited by Xana dry bean in the greenhouse straw test using quantitative trait locus (QTL) analysis. A population of 104 F7 recombinant inbred lines (RILs) derived from an inter-gene pool cross between Xana and the susceptible black bean Cornell 49242 was evaluated against five local isolates of Sclerotinia. The effect of morphological traits (plant height, first internode length, and first internode width) on response to white mold was examined. The level of resistance exhibited by Xana to five isolates of S. sclerotiorum was similar to that of the well-known resistant lines PC50, A195, and G122. Eighteen QTL, involving the linkage groups (LG) 1, 3, 6, 7, 8, and 11, were found to be significant in at least one evaluation and in the mean of the two evaluations. The number of significant QTL identified per trait ranged from one to five. Four major regions on LG 1, 6, and 7 were associated with partial resistance to white mold, confirming the results obtained in other populations. A relative specificity in the number and the position of the identified QTL was found depending on the isolate used. QTL involved in the control of morphological traits and in the response to white mold were co-located at the same relative position on LG 1, 6, and 7. The role of these genomic regions in physiological resistance or avoidance mechanisms to white mold is discussed.     

Quantitative trait locus mapping reveals conservation of major and minor loci for powdery mildew resistance in four sources of resistance in mungbean [Vigna radiata (L.) Wilczek]

Powdery mildew (PM) is a common and serious disease of mungbean [Vigna radiata (L.) Wilczek]. A few quantitative trait loci (QTL) for PM resistance in mungbean have been reported. The objective of this study was to locate QTL for PM resistance in two resistant accessions V4718 and RUM5. Simple sequence repeat markers were analyzed in an F₂ population from a cross between Kamphaeng Saen 1 (KPS1; susceptible to PM) and V4718 (resistant to PM), and in F₂ and BC₁F₁ populations from a cross between Chai Nat 60 (CN60; susceptible to PM) and RUM5 (resistant to PM). Progenies of 134 F_2:3 and F_2:4 lines derived from KPS1 × V4718, and 190 F_2:3 and 74 BC₁F_1:2 lines derived from CN60 × RUM5 and CN60 × (CN60 × RUM5), respectively, were evaluated for response to PM under field conditions. Multiple interval mapping identified a major QTL on linkage group (LG) 9 and two minor QTL on LG4 for the resistance in V4718, and detected two major QTL on LG6 and LG9 and one minor QTL on LG4 for the resistance in RUM5. Comparative linkage analysis of the QTL for PM resistance in this study and in previous reports suggests that the resistance QTL on LG9 in V4718, RUM5, ATF3640 and VC6468-11-1A are the same locus or linked. One QTL on LG4 is the same in three sources (V4718, RUM5 and VC1210A). Another QTL on LG6 is the same in two sources (RUM5 and VC6468-11-1A). In addition, one QTL in V4718 on LG4 appears to be a new resistance locus. These different resistance loci will be useful for breeding durably PM-resistant mungbean cultivars.     

Genetic factors and diet affect long-bone length in the F34 LG,SM advanced intercross

Previous studies on the LG,SM advanced intercross line have identified approximately 40 quantitative trait loci (QTL) for long -bone (humerus, ulna, femur, and tibia) lengths. In this study, long-bone-length QTL were fine-mapped in the F₃₄ generation (n?=?1424) of the LG,SM advanced intercross. Environmental effects were assessed by dividing the population by sex between high-fat and low-fat diets, producing eight sex/diet cohorts. We identified 145 individual bone-length QTL comprising 45 pleiotropic QTL; 69 replicated QTL from previous studies, 35 were new traits significant at previously identified loci, and 41 were novel QTL. Many QTL affected only a subset of the population based on sex and/or diet. Eight of ten known skeletal growth genes were upregulated in 3-week-old LG/J male proximal tibial growth plates relative to SM/J.The sequences of parental strains LG/J and SM/J indicated the presence of over half a million polymorphisms in the confidence intervals of these 45 QTL. We examined 526 polymorphisms and found that 97 represented radical changes to amino acid composition while 40 were predicted to be deleterious to protein function.Additional experimentation is required to understand how changes in gene regulation or protein function can alter the genetic architecture and interact with the environment to produce phenotypic variation.     

QTL Mapping for Resistance to Iridovirus in Asian Seabass Using Genotyping-by-Sequencing

Identifying quantitative trait loci (QTL) for viral disease resistance is of particular importance in selective breeding programs of fish species. Genetic markers linked to QTL can be useful in marker-assisted selection (MAS) for elites resistant to specific pathogens. Here, we conducted a genome scan for QTL associated with Singapore grouper iridovirus (SGIV) resistance in an Asian seabass (Lates calcarifer) family, using a high-density linkage map generated with genotyping-by-sequencing. One genome-wide significant and three suggestive QTL were detected at LG21, LG6, LG13, and LG15, respectively. The phenotypic variation explained (PVE) by the four QTL ranged from 7.5 to 15.6%. The position of the most significant QTL at LG21 was located between 31.88 and 36.81 cM. The SNP marker (SNP130416) nearest to the peak of this QTL was significantly associated with SGIV resistance in an unrelated multifamily population. One candidate gene, MECOM, close to the peak of this QTL region, was predicted. Evidence of alternative splicing was observed for MECOM and one specific category of splicing variants was differentially expressed at 5 days post-SGIV infection. The QTL detected in this study are valuable resources and can be used in the selective breeding programs of Asian seabass with regard to resistance to SGIV.     

Uncovering QTL for resistance and survival time to Philasterides dicentrarchi in turbot (Scophthalmus maximus)

Disease resistance‐related traits have received increasing importance in aquaculture breeding programs worldwide. Currently, genomic information offers new possibilities in breeding to address the improvement of this kind of traits. The turbot is one of the most promising European aquaculture species, and Philasterides dicentrarchi is a scuticociliate parasite causing fatal disease in farmed turbot. An appealing approach to fight against disease is to achieve a more robust broodstock, which could prevent or diminish the devastating effects of scuticociliatosis on farmed individuals. In the present study, a genome scan for quantitative trait loci (QTL) affecting resistance and survival time to P. dicentrarchi in four turbot families was carried out. The objectives were to identify QTL using different statistical approaches [linear regression (LR) and maximum likelihood (ML)] and to locate significantly associated markers for their application in genetic breeding strategies. Several genomic regions controlling resistance and survival time to P. dicentrarchi were detected. When analyzing each family separately, significant QTL for resistance were identified by the LR method in two linkage groups (LG1 and LG9) and for survival time in LG1, while the ML methodology identified QTL for resistance in LG9 and LG23 and for survival time in LG6 and LG23. The analysis of the total data set identified an additional significant QTL for resistance and survival time in LG3 with the LR method. Significant association between disease resistance‐related traits and genotypes was detected for several markers, a single one explaining up to 22% of the phenotypic variance. Obtained results will be essential to identify candidate genes for resistance and to apply them in marker‐assisted selection programs to improve turbot production.     

Mapping QTLs for Swimming Ability Related Traits in Cyprinus carpio L.

Body height (BH), head length (HL), snout length (SL), and tail length (TL) are important traits related with swimming ability of fish. Therefore, improving these traits will increase the production which is the basic goal of aquaculture breeding. To understand the genetic basis of swimming ability related traits in Cyprinus carpio L., a high-density linkage map spanning 3,301 cM in 50 linkage groups was utilized for quantitative trait locus (QTL) mapping. Mapping family comprised 190 offspring and 627 molecular markers were genotyped with average distance of 5.6 cM. A total of 15 QTLs including four (qBH13, qBH30, qBH33, qBH48) for BH, four (qHL10, qHL18, qHL29, qHL48) for HL, three (qSL24, qSL27, qSL45) for SL, and four (qTL15, qTL17, qTL18, qTL44) for TL were detected on 13 linkage groups LG10, LG13, LG15, LG17, LG18, LG24, LG27, LG29, LG30, LG33, LG44, LG45, and LG48. Each LG consisted on single QTL except LG18 and LG48. LG18 was found with two QTLs associated with HL and TL. While LG48 was comprised, the QTLs related with BH and HL. The phenotype variance was recorded from 12.6 to 40.6 %. Five QTLs, qHL48, qSL45, qTL15, qTL18, and qTL44, explained phenotype variance of >20 % with a significant levels of 0.047, 0.049, 0.037, 0.025, and 0.023, respectively. The neighbored loci of these QTLs were considered as main region of chromosomes controlling the traits. These identified genetic regions will be the main source of discovering gene(s) associated with swimming ability related traits in C. carpio L.     

Quantitative trait loci (QTL) mapping of blush skin and flowering time in a European pear (<Emphasis Type="Italic">Pyrus communis</Emphasis>) progeny of ‘Flamingo’ × ‘Abate Fetel’

Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored phenotypically over three seasons and flowering time was scored over two seasons. A total of 160 loci from 137 simple sequence repeat (SSR) markers were scored in the progeny and used to construct parental genetic linkage maps. Quantitative trait loci (QTL) analysis revealed two QTLs for blush skin, a major QTL on linkage group (LG) 5 in ‘Flamingo’, and a major QTL on LG9 in ‘Abate Fetel’. Two SSR markers, NB101a and SAmsCO865954, were closely linked with the major QTL on LG5 in ‘Flamingo’, with alleles 139 bp and 462 bp in coupling, respectively. These markers were present in approximately 90% of the seedlings scored as good blush (class 4) based on the average data set. These two markers were used to genotype other pear accessions to validate the QTL on LG5 with the view of marker-assisted selection. Two candidate genes, MYB86 and UDP-glucosyl transferase, were associated with the QTL on LG5 and MYB21 and MYB39 were associated with the QTL on LG9. QTL analysis for flowering time revealed a major QTL located on LG9 in both parents. Marker GD142 with allele 161 bp from ‘Flamingo’ was present in approximately 88% of the seedlings that flowered earlier than either parent, based on the average data set. The QTLs and linked markers will facilitate marker-assisted selection for the improvement of these complex traits.     

Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman)

Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex × Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0–9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R ² < 27%). The loci were within the intervals Satt632–A2D8 on linkage group (LG) A2 (chromosome 8); Satt583–Satt415 on LG B1 (11); Satt009–Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R ² < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R ² < 24%) between Satt632–A2D8 on LG A2 (8) and Sat_039–Satt160 on LG F (13); and a major locus effect (R ² = 54%) for antibiosis on LG D2 (17) between Satt464–Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).     

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.     

Mapping quantitative trait loci (QTL) for body weight, length and condition factor traits in backcross (BC1) family of Common carp (Cyprinus carpio L.)

Body weight and length are economical important traits in aquaculture species influenced by quantitative trait loci (QTL) and environmental factors. In this study, a backcross (BC1) common carp family, with 86 progeny, was utilized to construct genetic map for preliminary QTL mapping. The genetic map was constructed with 366 markers, including 191 SNP from gene, coverage 50 linkage groups with an average marker distance of 18.5 cM. A total of fourteen QTLs associated with body weight (BW), body length (BL) and condition factor (K) were detected on ten linkage groups (LGs). Among these QTLs detected, three (qBW8, qBL8 and qK8) were associated with BW, BL and K respectively, were mapped on LG8. qBW8 and qK8 were identified on similar interval neared locus HLJ2394 explained 14.9 and 20.9 % of the phenotype variance, while qBL8 was identified on separate nearby locus HLJ571 with 30.8 % of phenotype variance. Two QTLs, qBW13 and qK13, related with BW and K separately, were found on LG13 at different locus with phenotype variance of 25.3 and 20.9 %. Other two QTLs, qBW19 and qBL19, associated to BW and BL were mapped on same region near SNP0626 on LG19, and explained 10.3 and 15.6 % of phenotype variance. While other seven QTLs related with BW and BL were located on different LGs. Confidential interval was ranged from 1.1 to 10 cM in the present study. These markers, with lower QTL interval, have great influence on the body weight and length. Therefore, these QTLs will be helpful to find out the genes related with specific trait.     

Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F₂ mapping population derived by crossing the inbred lines ‘835’ (susceptible) and ‘B2’ (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.     

Integration of EST-SSR markers of Medicago truncatula into intraspecific linkage map of lentil and identification of QTL conferring resistance to ascochyta blight at seedling and pod stages

Microsatellite markers have been extensively utilised in the leguminosae for genome mapping and identifying major loci governing traits of interest for eventual marker-assisted selection (MAS). The lack of available lentil-specific microsatellite sequences and gene-based markers instigated the mining and transfer of expressed sequence tag simple sequence repeat (EST-SSR)/SSR sequences from the model genome Medicago truncatula, to enrich an existing intraspecific lentil genetic map. A total of 196 markers, including new 15 M. truncatula EST-SSR/SSR, were mapped using a population of 94 F₅ recombinant inbred lines produced from a cross between cv. Northfield (ILL5588)?×?cv. Digger (ILL5722) and clustered into 11 linkage groups (LG) covering 1156.4?cM. Subsequently, the size and effects of quantitative trait loci (QTL) conditioning Ascochyta lentis resistance at seedling and pod/maturity stages were characterised and compared. Three QTL were detected for seedling resistance on LG1 and LG9 and a further three were detected for pod/maturity resistance on LG1, LG4 and LG5. Together, these accounted for 34 and 61% of the total estimated phenotypic variation, respectively, and demonstrated that resistance at the different growth stages is potentially conditioned by different genomic regions. The flanking markers identified may be useful for MAS and for the future pyramiding of potentially different resistance genes into elite backgrounds that are resistant throughout the cropping season.     

Identification of quantitative trait loci for resistance to Verticillium wilt and yield parameters in hop (Humulus lupulus L.)

Verticillium wilt (VW) can cause substantial yield loss in hop particularly with the outbreaks of the lethal strain of Verticillium albo-atrum. To elucidate genetic control of VW resistance in hop, an F₁ mapping population derived from a cross of cultivar Wye Target, with the predicted genetic basis of resistance, and susceptible male breeding line BL2/1 was developed to assess wilting symptoms and to perform QTL mapping. The genetic linkage map, constructed with 203 markers of various types using a pseudo-testcross strategy, formed ten major linkage groups (LG) of the maternal and paternal maps, covering 552.98 and 441.1 cM, respectively. A significant QTL for VW resistance was detected at LOD 7 on a single chromosomal region on LG03 of both parental maps, accounting for 24.2–26.0 % of the phenotypic variance. QTL analysis for alpha-acid content and yield parameters was also performed on this map. QTLs for these traits were also detected and confirmed our previously detected QTLs in a different pedigree and environment. The work provides the basis for exploration of QTL flanking markers for possible use in marker-assisted selection.     

Anther extrusion and plant height are associated with Type I resistance to Fusarium head blight in bread wheat line ‘Shanghai-3/Catbird’

Fusarium head blight (FHB) is a destructive wheat disease of global importance. Resistance breeding depends heavily on the Fhb1 gene. The CIMMYT line Shanghai-3/Catbird (SHA3/CBRD) is a promising source without this gene. A recombinant inbred line (RIL) population from the cross of SHA3/CBRD with the German spring wheat cv. Naxos was evaluated for FHB resistance and related traits in field trials using spray and spawn inoculation in Norway and point inoculation in China. After spray and spawn inoculation, FHB severities were negatively correlated with both anther extrusion (AE) and plant height (PH). The QTL analysis showed that the Rht-B1b dwarfing allele co-localized with a QTL for low AE and increased susceptibility after spawn and spray inoculation. In general, SHA3/CBRD contributed most of the favorable alleles for resistance to severity after spray and spawn inoculation, while Naxos contributed more favorable alleles for reduction in FDK and DON content and resistance to severity after point inoculation. SHA3/CBRD contributed a major resistance QTL close to the centromere on 2DLc affecting FHB severity and DON after all inoculation methods. This QTL was also associated with AE and PH, with high AE and tall alleles contributed by SHA3/CBRD. Several QTL for AE and PH were detected, and low AE or reduced PH was always associated with increased susceptibility after spawn and spray inoculation. Most of the other minor FHB resistance QTL from SHA3/CBRD were associated with AE or PH, while the QTL from Naxos were mostly not. After point inoculation, no other QTL for FHB traits was associated with AE or PH, except the 2DLc QTL which was common across all inoculation methods. Marker-assisted selection based on the 2DLc QTL from SHA3/CBRD combined with phenotypic selection for AE is recommended for resistance breeding based on this valuable source of resistance.     

Defense response genes co-localize with quantitative disease resistance loci in pepper

Functional bases of polygenically inherited disease resistance are still unknown. In recent years, molecular dissection of polygenic resistance has led to the identification and location of quantitative trait loci (QTLs) on many plant genetic linkage maps. This process is a pre-requisite for resistance QTL characterization at a molecular and functional level. Here, we report the use of a candidate gene approach based on the hypothesis that some resistance QTLs previously mapped in pepper may correspond to defense response (DR) genes. Degenerate oligonucleotide primers were designed for conserved regions of two DR gene families: pathogenesis-related proteins (PR) of class 2 (β-1,3-glucanase) and PR proteins of class 5 (antifungal activity). Cloned pepper PCR-products as well as other solanaceous DR gene families were used as RFLP probes for mapping in three intraspecific maps of the pepper genome. A total of 12 probes out of 23 were positioned and generated 16 loci. Some DR probes revealed multiple gene copies in the pepper genome (PR5, β-1,3-glucanase, chitinase and Glutathione S-transferase). Genes encoding acidic and basic β-1,3-glucanases were clustered on linkage group (LG) P1a, whereas genes encoding chitinases occurred on several LGs (P1b, P2a and P5). A class-III chitinase gene co-localized with a major-effect QTL controlling resistance to Phytophthora capsici on LG P5. PR4, PR2 and PR10 loci mapped within the region of resistance QTLs to P. capsici (LG P1b), Potato virus Y (LG P1a) and Potyvirus E (LG P3), respectively. A digenic interaction between a PR4 and a PR2 loci explained a large effect (35%) of the resistance to Potyvirus E.