A genetic analysis of quantitative resistance to late blight in potato: towards marker-assisted selection

Late blight caused by the oomycete Phytophthora infestans is the most important fungal disease in potato cultivation worldwide. Resistance to late blight is controlled by a few major genes (R genes) which can be easily overcome by new races of P. infestans and/or by an unknown number of genes expressing a quantitative type of resistance which may be more durable. Quantitative resistance of foliage to late blight was evaluated in five F₁ hybrid families originating from crosses among seven different diploid potato clones. Tuber resistance was evaluated in four of the families. Two of the families were scored for both foliage maturity and vigour. The five families were genotyped with DNA-based markers and tested for linkage with the traits analysed. QTL (quantitative trait locus) analysis identified at least twelve segments on ten chromosomes of potato having genes that affect reproducibly foliage resistance. Two of those segments also have major R genes for resistance to late blight. The segments are tagged by 21 markers that can be analyzed based on PCR (polymerase chain reaction) with specific oligonucleotide primers. One QTL was detected for tuber resistance and one for foliage vigour. Two QTLs were mapped for foliage maturity. Major QTL effects on foliage and tuber resistance to late blight and on foliage maturity and vigour were all linked with marker GP179 on linkage group V of potato. Plants having alleles at this QTL, which increased foliage resistance, exhibited decreased tuber resistance, later maturity and more vigour.     

QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato.

Quantitative trait loci (QTLs) for resistance to Phytophthora infestans (late blight) were mapped in tomato. Reciprocal backcross populations derived from cultivated Lycopersicon esculentum x wild Lycopersicon hirsutum (BC-E, backcross to L. esculentum; BC-H, backcross to L. hirsutum) were phenotyped in three types of replicated disease assays (detached-leaflet, whole-plant, and field). Linkage maps were constructed for each BC population with RFLPs. Resistance QTLs were identified on all 12 tomato chromosomes using composite interval mapping. Six QTLs in BC-E (lb1a, lb2a, lb3, lb4, lb5b, and lb11b) and two QTLs in BC-H (lb5ab and lb6ab) were most consistently detected in replicated experiments or across assay methods. Lycopersicon hirsutum alleles conferred resistance at all QTLs except lb2a. Resistance QTLs coincided with QTLs for inoculum droplet dispersal on leaves, a trait in L. hirsutum that may contribute to resistance, and dispersal was mainly associated with leaf resistance. Some P. infestans resistance QTLs detected in tomato coincided with chromosomal locations of previously mapped R genes and QTLs for resistance to P. infestans in potato, suggesting functional conservation of resistance within the Solanaceae.     

Detection of QTLs controlling alpha-amylase activity in a diversity panel of 343 barley accessions

The α–amylase activity of cultivated barley is critically important to the brewing industry. Here, we surveyed variation in malt α–amylase activity in 343 cultivated barley accessions from around the world. Population structure analysis based on genotype data at 1536 SNPs clustered these accessions into two groups, one comprising South-East Asian and Ethiopian accessions and one group containing the other accessions. A genome-wide association study identified significant quantitative trait loci (QTLs) for α–amylase activity on all seven chromosomes of barley. Accessions showing high and low α–amylase activity were crossed with the high-quality Japanese malting barley cv. Harun Nijo to develop F₂ mapping populations. We identified two QTLs on chromosome 6H in a cross between Haruna Nijo (high activity) × Weal (highest activity). Single QTLs were identified each on 3H, 4H, and 5H from a cross between Haruna Nijo (high activity) × VLB-1 (low activity), indicating that the high α–amylase activity in Haruna Nijo might be derived from loci on these chromosomes. The addition of the high α–amylase activity QTL alleles from chromosome 6H in cv. Weal further increased the α–amylase activity conferred by alleles of Haruna Nijo. These results demonstrate that a target haplotype can be successfully improved using a strategy comprising diversity analysis of ex situ collections followed by introducing effective new alleles.     

Strain-specific and recessive QTLs involved in the control of partial resistance to Fusarium oxysporum f. sp. melonis race 1.2 in a recombinant inbred line population of melon

Fusarium oxysporum f. sp. melonis (FOM) causes serious economic losses in melon (Cucumis melo L.). Two dominant resistance genes have been identified, Fom-1 and Fom-2, which provide resistance to races 0 and 2 and races 0 and 1, respectively, however FOM race 1.2 overcomes these resistance genes. A partial resistance to FOM race 1.2 that has been found in some Far East accessions is under polygenic control. A genetic map of melon was constructed to tag FOM race 1.2 resistance with DNA markers on a recombinant inbred line population derived from a cross between resistant (Isabelle) and susceptible (cv. Védrantais) lines. Artificial root inoculations on plantlets of this population using two strains, one that causes wilting (FOM 1.2w) and one that causes yellowing (FOM 1.2y), resulted in phenotypic and genotypic data that enabled the identification of nine quantitative trait loci (QTLs). These QTLs were detected on five linkage groups by composite interval mapping and explained between 41.9% and 66.4% of the total variation. Four digenic epistatic interactions involving seven loci were detected and increased the total phenotypic variation that was explained. Co-localizations between QTLs and resistance gene homologs or resistance genes, such as Fom-2 and Vat, were observed. A strain-specific QTL was detected, and some QTLs appeared to be recessive.     

Molecular markers locate genes for resistance to the Colorado potato beetle,Leptinotarsa decemlineata,in hybrid Solanum tuberosum x S. berthaultii potato progenies

The wild Bolivian potato, Solanum berthaultii Hawkes, has been used as a source of resistance to the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say, one of the most significant pests of potato. In this study, two reciprocal backcross S. tuberosum x S. berthaultii potato progenies, BCB and BCT, were mapped with RFLP markers and screened for resistance to CPB consumption, oviposition and defoliation. The genotypic and phenotypic data were combined and analysed to locate quantitative trait loci (QTLs) for resistance to CPB. Three QTLs on three chromosomes in BCB, and two QTLs on two chromosomes in BCT influenced resistance. The QTLs were generally additive but one instance of epistasis was noted. Each QTL accounted for 4–12% of the phenotypic variation observed in resistance. In the more resistant BCB population, a three QTL model explained ca. 20% of the variation in CPB oviposition. When alleles at the three QTLs were homozygous S. berthaultii, oviposition was reduced ca. 60% compared to the heterozygotes. The QTLs for resistance to CPB were compared to those previously identified for the type A and B glandular trichomes, which have been implicated in resistance in the same progenies. Generally, the QTLs for resistance to CPB coincided with loci associated with the glandular trichomes confirming the importance of the glandular trichomes in mediating resistance. However, a relatively strong and consistent QTL for insect resistance in both BCB and BCT on chromosome 1 was observed that was not associated with any trichome traits, suggesting the trichomes may not account for all of the resistance observed in these progenies.     

Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA

We used a well-characterized barley mapping population (BCD 47 × Baronesse) to determine if barley stripe rust (BSR) resistance quantitative trait loci (QTL) mapped in Mexico and the USA were effective against a reported new race in Peru. Essentially the same resistance QTL were detected using data from each of the three environments, indicating that these resistance alleles are effective against the spectrum of naturally occurring races at these sites. In addition to the mapping population, we evaluated a germplasm array consisting of lines with different numbers of mapped BSR resistance alleles. A higher BSR disease severity on CI10587, which has a single qualitative resistance gene, in Peru versus Mexico suggests there are differences in pathogen virulence between the two locations. Confirmation of a new race in Peru will require characterization using a standard set of differentials, an experiment that is underway. The highest levels of resistance in Peru were observed when the qualitative resistance gene was pyramided with quantitative resistance alleles. We also used the mapping population to locate QTL conferring resistance to barley leaf rust and barley powdery mildew. For mildew, we identified resistance QTL under field conditions in Peru that are distinct from the Mla resistance that we mapped using specific isolates under controlled conditions. These results demonstrate the long-term utility of a reference mapping population and a well-characterized germplasm array for locating and validating genes conferring quantitative and qualitative resistance to multiple pathogens.     

Identification of novel tan spot resistance loci beyond the known host-selective toxin insensitivity genes in wheat

Tan spot, caused by Pyrenophora tritici-repentis, is a destructive foliar disease of wheat causing significant yield reduction in major wheat growing areas throughout the world. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to tan spot in the synthetic hexaploid wheat (SHW) line TA4152-60. A doubled haploid (DH) mapping population derived from TA4152-60 × ND495 was inoculated with conidia produced by isolates of each of four virulent races of P. tritici-repentis found in North America. QTL analysis revealed a total of five genomic regions significantly associated with tan spot resistance, all of which were contributed by the SHW line. Among them, two novel QTLs located on chromosome arms 2AS and 5BL conferred resistance to all isolates tested. Another novel QTL on chromosome arm 5AL conferred resistance to isolates of races 1, 2 and 5, and a QTL specific to a race 3 isolate was detected on chromosome arm 4AL. None of these QTLs corresponded to known host selective toxin (HST) insensitivity loci, but a second QTL on chromosome arm 5BL conferred resistance to the Ptr ToxA producing isolates of races 1 and 2 and corresponded to the Tsn1 (Ptr ToxA sensitivity) locus. This indicates that the wheat-P. tritici-repentis pathosystem is much more complex than previously thought and that selecting for toxin insensitivity alone will not necessarily lead to tan spot resistance. The markers associated with the QTLs identified in this work will be useful for deploying the SHW line as a tan spot resistance source in wheat breeding. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum) background

Phytophthora infestans causes an economically important disease of potato called late blight. The epidemic is controlled chemically but resistant potatoes can become an environment-friendly and financially justified alternative solution. The use of diploid Solanum tuberosum derived from European tetraploid cultivars enabled the introgression of novel genes encoding foliage resistance and tuber resistance from other species into the modern cultivated potato gene pool. This study evaluated the resistance of the obtained hybrids, its quality, expression in leaflets and tubers and its relation to the length of vegetation period. We also identified genetic loci involved in late blight resistance and the length of vegetation period. A family of 156 individuals segregating for resistance to late blight was assessed by three laboratory methods: detached leaflet, tuber slice and whole tuber test, repeatedly over 5 years. Length of vegetation period was estimated by a field test over 2 years. The phenotypic distributions of all traits were close to normal. Using sequence-specific PCR markers of known chromosomal position on the potato genetic map, six quantitative trait loci (QTLs) for resistance and length of vegetation period were identified. The most significant and robust QTL were located on chromosomes III (explaining 17.3% of variance observed in whole tuber tests), IV (15.5% of variance observed in slice tests), X (15.6% of variance observed in leaflet tests) and V (19.9% of variance observed in length of vegetation period). Genetic characterization of these novel resistance sources can be valuable for potato breeders and the knowledge that the most prominent QTLs for resistance and vegetation period length do not overlap in this material is promising with respect to breeding early potatoes resistant to P. infestans. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763

Soybean cyst nematode (SCN) is a major soybean pest throughout the soybean growing regions in the world, including the USA. Soybean PI 90763 is an important SCN resistance source. It is resistant to several SCN populations including races 2, 3 and 5. But its genetics of resistance is not well known. The objectives of this study were to: (1) confirm quantitative trait loci (QTLs) for resistance to SCN race 3 in PI 90763 and (2) identify QTLs for resistance to SCN races 2 and 5. QTLs were searched in Hamilton × PI 90763 F_2:3populations using 193 polymorphic simple sequence repeats (SSRs) covering 20 linkage groups (LGs). QTLs for resistance to SCN were identified on LGs A2, B1, E, G, J and L. The same QTL was suggested for resistance to different SCN races where their 1-LOD support intervals of QTL positions highly overlapped. The QTL on LG G was associated with resistance to races 2, 3 and 5. The QTL on LG B1 was associated with resistance to races 2 and 5. The QTL on LG J was associated with resistance to races 2 and 3. The QTLs on LGs A2 and L were associated with resistance to race 3. The QTL on LG E was associated with resistance to race 5. We conclude that LGs A2 and B1 may represent an important distinction between resistance to SCN race 3 and resistance to SCN races 2 and 5 in soybean.     

Genetic Overlap in the Quantitative Resistance of Rice at the Seedling and Adult Stages to <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis>

The genetic components responsible for the qualitative and quantitative resistance of rice to three Chinese races (C2, C4, and C5) of Xanthomonas oryzae pv. oryzae (Xoo) were investigated at the seedling and adult stages in two successive years in set of Lemont/Teqing cross introgression lines (ILs) in a Teqing background, to create a complete linkage map using 160 well-distributed SSR markers. Teqing was resistant to C2 and C4, but moderately susceptible to C5, whereas Lemont was susceptible to all three races. Highly significant correlations were detected among the resistance to different races at different developmental stages. A major gene (Xa4), 14 main-effect QTLs (M-QTLs), and 18 epistatic QTLs were identified in the two developmental stages over 2 years, and were largely responsible for the segregation of resistance in the ILs. In 2007, the Lemont alleles at all loci in the seedling stage, except QBbr10 to C4, increased lesion length (LL) or decreased resistance. The Teqing allele at the Xa4 locus acted as a resistance gene against C2 and C4, but acted as a M-QTL when its resistance was overcome by the virulent race C5. M-QTLs showed a degree of race specificity and had a cumulative effect on resistance. Most M-QTLs (94%) consistently expressed resistance to the same race at the seedling and adult stages, indicating that a high degree of genetic overlap exists between Xoo resistance at both developmental stages in rice. Among the digenic interactions, most co-introgressed Lemont alleles at the two epistatic loci lead to significantly smaller LL with all three races, compared to other types of interacting alleles at both development stages. The results indicate that a high level of resistance may be achieved by the cumulative effect of multiple M-QTLs, including the residual effects of “defeated” major resistance genes and the epistatic effects of co-introgression from diverse susceptible varieties.     

Lactuca saligna,a non-host for lettuce downy mildew ( Bremia lactucae), harbors a new race-specific Dm gene and three QTLs for resistance

Lactuca sativa (lettuce) is susceptible to Bremia lactucae (downy mildew). In cultivated and wild Lactuca species, Dm genes have been identified that confer race-specific resistance. However, these genes were soon rendered ineffective by adaptation of the pathogen. Lactuca saligna (wild lettuce) is resistant to all downy mildew races and can be considered as a non-host. Therefore, L. saligna might be an alternative source for a more-durable resistance to downy mildew in lettuce. In order to analyze this resistance, we have developed an F(2) population based on a resistant L. saligna x susceptible L. sativa cross. This F(2) population was fingerprinted with AFLP markers and tested for resistance to two Bremia races NL14 and NL16. The F(2) population showed a wide and continuous range of resistance levels from completely resistant to completely susceptible. By comparison of disease tests, we observed a quantitative resistance against both Bremia races as well as a race-specific resistance to Bremia race NL16 and not to NL14. QTL mapping revealed a qualitative gene ( R39) involved in the race-specific resistance and three QTLs ( RBQ1, RBQ2 and RBQ3) involved in the quantitative resistance. The qualitative gene R39 is a dominant gene that gives nearly complete resistance to race NL16 in L. saligna CGN 5271 and therefore it showed features similar to Dm genes. The three QTLs explained 51% of the quantitative resistance against NL14, which indicated that probably only the major QTLs have been detected in this F(2) population. The perspectives for breeding for durable resistance are discussed.     

Can the QTL for late blight resistance on potato chromosome 5 be attributed to foliage maturity type?

We investigated the association between late blight resistance and foliage maturity type in potato by means of molecular markers. Two QTLs were detected for foliage resistance against Phytophthora infestans (on chromosomes 3 and 5) and one for foliage maturity type (on chromosome 5). The QTL for resistance to late blight and the QTL for foliage maturity type on chromosome 5 appeared to be mapped on indistinguishable positions. We were interested whether this genetic linkage was due to closely linked but different genes, or due to one (or more) gene(s) with pleiotropic effects. We therefore developed an approach to detect QTLs, in which resistance to late blight was adjusted for foliage maturity type. This analysis revealed the same two QTLs for resistance against P. infestans, but the effect of the locus on chromosome 5 was reduced to only half the original effect. This is a strong indication that the two indistinguishable QTLs for foliage maturity type and for late blight resistance on chromosome 5 may actually be one gene with a pleiotropic effect on both traits. However, there was still a significant effect on resistance against P. infestans on the locus on chromosome 5 after adjusting for foliage maturity type. Therefore we cannot rule out the presence of two closely linked QTLs on chromosome 5: one with a pleiotropic effect on both late blight resistance and foliage maturity type, and another with merely an effect on resistance. In addition, the two QTLs for resistance to late blight showed an important epistatic interaction, suggesting that QTLs for resistance affect each other's expression.     

QTLs for resistance to Setosphaeria turcica in an early maturing Dent×Flint maize population

Quantitative trait loci (QTLs) for resistance to the fungal pathogen Setosphaeria turcica, the cause of northern corn leaf blight (NCLB), were mapped in a population of 220 F₃ families derived from a cross between two moderately resistant European inbred lines, D32 (dent) and D145 (flint). The population was genotyped with 87 RFLP and 7 SSR markers. Trials were conducted in the field in Switzerland, and in the greenhouse with selected F₃ families in Germany. The F₃ population segregated widely for resistance with transgression of the parents. By composite interval mapping, a total of 13 QTLs were detected with two disease ratings (0 and 3 weeks after flowering). Together these QTLs explained 48% and 62% of the phenotypic variation. Gene action at most QTLs was partially dominant. Eight out of the 13 QTL alleles for resistance were contributed by the more-resistant parent, D145. On chromosomes 3, 5 and 8, QTLs were located in the same chromosomal regions as QTLs in tropical and U.S. Corn Belt germplasm. Some QTLs affected NCLB, head smut and common rust at the same time, with alleles at these loci acting isodirectionally. Received: 25 January 1999 / Accepted: 20 Februar 1999     

QTL clusters reflect character associations in wild and cultivated rice

The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs). Major evolutionary trends in cultivated rice of Asiatic origin (Oryza sativa) and its wild progenitor (O. rufipogon) are: (1) differentiation from wild to domesticated types (domestication), (2) ecotype differentiation between the perennial and annual types in wild races, and (3) the Indica versus Japonica type differentiation in cultivated races. Using 125 recombinant inbred lines (RILs) derived from a cross between an Indica cultivar of O. sativa and a strain of O. rufipogon carrying some Japonica-like characteristics, we mapped 147 markers, mostly RFLPs, on 12 chromosomes. Thirty-seven morphological and physiological quantitative traits were evaluated, and QTLs for 24 traits were detected. The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits. QTLs for perennial/annual type differences did not cluster. This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits. Further, it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor(s) controlling various traits through diverse metabolic pathways. Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected. This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs.     

QTL analysis of late blight resistance in a diploid potato family of Solanum phureja × S. stenotomum

Field resistance to Phytophthora infestans (Mont.) de Bary, the causal agent of late blight in potatoes, has been characterized in a potato segregating family of 230 full-sib progenies derived from a cross between two hybrid Solanum phureja × S. stenotomum clones. The distribution of area under the disease progress curve values, measured in different years and locations, was consistent with the inheritance of multigenic resistance. Relatively high levels of resistance and transgressive segregations were also observed within this family. A genetic linkage map of this population was constructed with the intent of mapping quantitative trait loci (QTLs) associated with this late blight field resistance. A total of 132 clones from this family were genotyped based on 162 restriction fragment length polymorphism (RFLP) markers. The genome coverage by the map (855.2 cM) is estimated to be at least 70% and includes 112 segregating RFLP markers and two phenotypic markers, with an average distance of 7.7 cM between two markers. Two methods were employed to determine trait–marker association, the non-parametric Kruskal–Wallis test and interval mapping analysis. Three major QTLs were detected on linkage group III, V, and XI, explaining 23, 17, and 10%, respectively, of the total phenotypic variation. The present study revealed the presence of potentially new genetic loci in this diploid potato family contributing to general resistance against late blight. The identification of these QTLs represents the first step toward their introgression into cultivated tetraploid potato cultivars through marker-assisted selection.     

Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding

In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.     

Mapping of loci involved in quantitatively inherited resistance to the potato cyst-nematode Globodera rostochiensis pathotype Ro1

We report the identification and mapping of two quantitative trait loci (QTLs) of Solanum spegazzinii BGRC, accession 8218-15, involved in resistance to the potato cyst-nematode Globodera rostochiensis pathotype Ro1, by means of restriction fragment length polymorphisms (RFLPs). For this purpose we crossed a susceptible diploid S. tuberosum with the resistant S. spegazzinii, and tested the F₁ population for resistance to the Ro1 pathotype. Since the F₁ segregated for the resistance, the S. spegazzinii parent was concluded to be heterozygous at the nematode resistance loci. For the mapping of the resistance loci we made use of RFLP markers segregating for S. spegazzinii alleles in the F₁. One hundred and seven RFLP markers were tested in combination with four different restriction enzymes; 29 of these displayed a heterozygous RFLP pattern within S. spegazzinii and were used for mapping. Analysis of variance (ANOVA) was applied to test the association of the RFLP patterns of these markers with nematode resistance. Two QTLs involved in disease resistance to Globodera rostochiensis pathotype Ro1 were identified and mapped to chromosomes 10 and 11 respectively.     

Mapping quantitative trait loci controlling common bunt resistance in a doubled haploid population derived from the spring wheat cross RL4452 × AC Domain

Wheat resistance to common bunt is a highly desirable trait for environmentally friendly grain grade protection. Valuable breeding achievements have been made to develop wheat varieties with enhanced resistance to the disease, and mapping of race-specific resistance genes has been reported. However, less is known of the chromosomal regions that control non-race specific resistance to common bunt. In this study, we have characterized a segregating population of 185 doubled haploid spring wheat lines derived from the cross RL4452 × AC Domain. Reactions to a mixture of common bunt races were assessed under field simulated spring-sown conditions in greenhouses in two locations over 2 years. A total 369 polymorphic maker loci including 356 microsatellite loci, five expressed sequences tag (ESTs), and eight genes were used to develop a linkage map. Quantitative trait loci (QTL) analysis using composite interval mapping detected three QTLs associated with common bunt resistance, of which two were located on chromosome 1B and one on chromosome 7A. AC Domain alleles contributed the common bunt resistance at all three QTLs. Usefulness of gene tagging within the identified chromosomal regions for common bunt resistance breeding is discussed.     

Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs

An earlier study identified quantitative trait loci (QTLs) lb4, lb5b, and lb11b for quantitative resistance to Phytophthora infestans (late blight) in a backcross population derived from crossing susceptible cultivated tomato (Lycopersicon esculentum) with resistant L. hirsutum. The QTLs were located in intervals spanning 28–47 cM. Subsequently, near-isogenic lines (NILs) were developed for lb4, lb5b, and lb11b by marker-assisted backcrossing to L. esculentum. Sub-NILs containing overlapping L. hirsutum segments across each QTL region were selected and used to validate the QTL effects, fine-map QTLs, and evaluate potential linkage drag between resistance QTLs and QTLs for horticultural traits. The NILs and sub-NILs were evaluated for disease resistance and eight horticultural traits at three field locations. Resistance QTLs were detected in all three sets of NIL lines, confirming the BC₁ mapping results. Lb4 mapped near TG609, and between TG182 and CT194, on chromosome 4, a 6.9-cM interval; lb5b mapped to an 8.8-cM interval between TG69a and TG413 on chromosome 5, with the most likely position near TG23; and lb11b mapped to a 15.1-cM interval on chromosome 11 between TG194 and TG400, with the peak centered between CT182 and TG147. Most QTLs for horticultural traits were identified in intervals adjacent to those containing the late blight resistance QTLs. Fine mapping of these QTLs permits the use of marker-assisted selection for the precise introgression of L. hirsutum segments containing late blight resistance alleles separately from those containing deleterious alleles at horticulturally important QTLs.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by D.B. Neale     

Allelic analysis of sheath blight resistance with association mapping in rice

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = −0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.