Abstract: Interval mapping of quantitative trait loci (QTL) for resistance to late blight, height, and maturity was performed on a tetraploid full-sib family of potato comprising 227 clones froma cross between a susceptible parent, 12601ab1, and a resistant cultivar, Stirling, which were of similar height and main crop maturity. Thirty-eight AFLP primer combinations provided 585 informative markers, and 23 SSRs proved useful for identifying linkage groups (LGs). A simplex QTL allele was found on LGV of Stirling close to marker STM3179, which was associated with early maturity, short plants, and susceptibility to blight and explained 54.7, 26.5, 26.3, and 17.5% of the variation for maturity, height, tuber blight, and foliage blight. When the residuals from the regressions of foliage and tuber blight on maturity were analyzed, there was no significant effect of a QTL on LGV, but a duplex QTL allele for resistance was found on LGIV of Stirling, which explained 30.7 and 13.6% of the variation for foliage and tuber blight on an additive model. Partial dominance for resistance explained even more of the variation, up to 37.2% for foliage blight. A major gene for blight resistance in Stirling was also mapped to LGXI.
Abstract: Association or linkage disequilibrium (LD)-based mapping strategies are receiving increased attention for the identification of quantitative trait loci (QTL) in plants as an alternative to more traditional, purely linkage-based approaches. An attractive property of association approaches is that they do not require specially designed crosses between inbred parents, but can be applied to collections of genotypes with arbitrary and often unknown relationships between the genotypes. A less obvious additional attractive property is that association approaches offer possibilities for QTL identification in crops with hard to model segregation patterns. The availability of candidate genes and targeted marker systems facilitates association approaches, as will appropriate methods of analysis. We propose an association mapping approach based on mixed models with attention to the incorporation of the relationships between genotypes, whether induced by pedigree, population substructure, or otherwise. Furthermore, we emphasize the need to pay attention to the environmental features of the data as well, i.e., adequate representation of the relations among multiple observations on the same genotypes. We illustrate our modeling approach using 25 years of Dutch national variety list data on late blight resistance in the genetically complex crop of potato. As markers, we used nucleotide binding-site markers, a specific type of marker that targets resistance or resistance-analog genes. To assess the consistency of QTL identified by our mixed-model approach, a second independent data set was analyzed. Two markers were identified that are potentially useful in selection for late blight resistance in potato.
Abstract: Amplified fragment length polymorphism(AFLP) was conducted on a set of 92 Nicotiana tabacum L. accessions from diverse types (flue-cured, dark aircured, burley, oriental, and cigar wrapper) and breeding origins to identify markers associated with disease resistances. Eleven primer combinations were required to identify 33 polymorphic fragments. This allowed the identification of 92% of these accessions, and yielded suficient information for building a neighbor joining tree. Clusters of accessions with common traits or breeding origins were observed. An important part of this polymorphism could be related to interspecific introgressions from other Nicotiana species, performed
during the breeding history of N. tabacum to confer resistance to pathogens. Seven fragments were associated with three different resistances: two for the bluemold (Peronospora tabacina Adam) resistance derived from Nicotiana debneyi Domin, two for the Va gene (Potato Virus Y susceptibility), and three for the black root rot (Chalara elegans) resistance of N. debneyi origin. Some of these markers were converted into sequence characterized amplified region markers, and validated on recombinant inbred lines or doubled-haploid lines.
Abstract: Broad tolerance to phytophthora root rot (PRR) caused by Phytophthora sojae has become an important goal for the improvement of soybean
(Glycine max) because of the rapid spread of races that defeat the available resistance genes. The aim of this research was to identify the location of quantitative trait loci (QTL) in ‘Conrad’, a soybean cultivar with broad tolerance to many races of P. sojae. A PRR susceptible breeding line OX760-6-1 was crossed with Conrad. Through single-seed-descent, 112, F2 derived, F7 recombinant inbred lines (RILs) were advanced. A total of 39 random ampliWed polymorphic DNA bands (RAPDs) and 89 type 1 microsatellite (simple sequence repeat; SSR) markers were used to construct a genetic linkage map. In the greenhouse, RILs were inoculated with four P. sojae isolates (three from China and one from Canada). Disease was measured as the percent of dead plants 20 days after germination in P. sojae inoculated vermiculite in the greenhouse. Three QTLs (QGP1,QGP2,QGP3) for PRR tolerance in the greenhouse were detected using WinQTLCart 2.0 with a log-likelihood (LOD) score 27.14 acquired through permutations (1,000 at P · 0.05). QGP1 (near Satt509) was located at linkage group F and explained 13.2%, 5.9%, and 6.7% of the phenotypic variance for tolerance to the JiXi, JianSanJiang and ShuangYaShan isolates, respectively. QGP2 (near Satt334) was located in a different interval on linkage group F and explained 5.1% and 2.4% of the phenotypic variance for JiXi and ShuangYaShan isolates, respectively. QGP3 was located on linkage group D1b + W (near OPL18800/SCL18659) and explained 10.2% of the phenotypic variance for Woodslee isolate. QGP1 and QGP2 appeared to be associated with PRR tolerance across a range of isolates but QGP3 was active only against the Woodslee isolate. At Woodslee and Weaver (in Ontario) in 2000, the interval associated with QGP3 explained 21.6% and 16.7% of phenotypic variance in
resistance to PRR, respectively and was referred as QFP1. The identified QTLs would be beneficial for marker assistant selection of PRR tolerance varieties
against both China and North America P. sojae races.
Abstract:Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F2 individuals from a cross between Capsicum annuum CM334 and C. annuum Chilsungcho. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot
and damping-oV resistance was performed in F2:3 originated from a cross between resistant Mexican landrace C. annuum CM334 and susceptible Korean landrace C. annuum Chilsungcho using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-oV resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artiWcial chromosome (BAC) library from C. annuum CM334 was
screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two
SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.
Abstract: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 cul-
tivated potato gene pool. This study evaluated the resistance of the obtained hybrids, its quality, expression in leaXets 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 leaXet, tuber slice and whole tuber test, repeatedly over 5 years. Length of vegetation period was estimated by a Weld 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 leaXet 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.
Abstract: Clusters of Resistance-like genes (RLGs) have been identified from a variety of plant species. In soybean, RLG-specific primers and BAC-fingerprinting were used to develop a contig of overlapping BACs for a cluster of RLGs on soybean linkage group J. The resistance genes Rps2 (Phytophthora stem and root rot) and Rmd-c (powdery mildew) and the ineffective nodulation gene Rj2 were previously mapped to this region of linkage group J. PCR hybridization was used to place two TIR/NBD/LRR cDNAs on overlapping BACs from this contig. Both of the cDNAs were present on BAC 34P7. Fingerprinting of this BAC suggested as many as twelve different RLGs were present. Given the high nucleotide identity shared between cDNAs LM6 and MG13 (>90%), direct sequencing of this region would be difficult. More sequence information was needed about the RLGs within this region before sequencing could be undertaken. By comparing the genomic sequences of cDNAs LM6 and MG13 we identified conserved regions from which oligonucleotide primers specific to BAC 34P7 RLGs could be designed. The nine primer pairs spanned the genomic sequence of LM6 and produced overlapping RLG products upon amplification of BAC 34P7. Amplification products from 12 different RLGs were identified. On average, nucleotide identity between RLG sequences was greater than 95%. Examination of RLG sequences also revealed evidence of additions, deletions and duplications within targeted regions of these genes. Using previously mapped cDNAs we were able to quickly and inexpensively access multiple RLGs within a single specific cluster.
Abstract:Phytophthora sojae, an important yield limiting pathogen of soybean, causes seed, seedling,root, and stem rots. Losses caused by P. sojae can be controlled by both major gene and partial resistance. Early maturity group (MG) soybeans are an increasingly important crop in northwestern Minnesota and
eastern North Dakota. Early MG plant introductions (PIs) from the USDA Soybean Germplasm Collection and early MG public and private cultivars were evaluated for resistance and partial resistance to P. sojae. Of the 113 PIs, PI438445, and PI438454 exhibited resistance to P. sojae races 4, 7, 17, and 28 indicating they may possess either Rps1c, Rps1k, previously unidentified or multiple resistance gene to Phytophthora sojae (Rps) genes. Because they exhibited partial resistance equal to or greater than the standard check cultivar Conrad, three early MG soybean cultivars (MN0902, MN0302, and 91B53)were selected as standard checks to evaluate early MG PIs for partial resistance. Sixty-nine PIs were evaluated for partial resistance to P. sojae races 7 and 25 using the inoculum layer method. Of this group of
PIs, 22 had the same level of partial resistance as Conrad to P. sojae race 7 while 19 had the same degree of partial resistance to race 25. Twelve PIs had same level of partial resistance as Conrad to both P.sojae races 7 and 25. The PIs and cultivars identified in this study will be of great value in developing early MG soybean cultivars suitable for planting in Canada and the northern United States.
Abstract: Transgenic plants expressing the bacterio-opsin (bO) gene can spontaneously activate programmed cell death (pcd) and may enhance broad-spectrum pathogen resistance by activating an intrinsic defense pathway in plant species such as tobacco and potato. In this work, we produced transgenic Rangpur lime plants with the bO gene, via Agrobacterium tumefaciens-mediated transformation, and evaluated these plants for Phytophthora nicotianae resistance. Two transgenic lines were successfully regenerated and transformation was confirmed by GUS activity assay, PCR analysis, Southern, Northern and Western blot analyses, in addition to detecting the expressed bO protein by an immunological approach. Evaluation for Phytophthora nicotianae resistance was carried out by plant inoculations with the pathogen and quantification of the affected area. One of the two transgenic lines showed greater tolerance to the fungal pathogen as compared to the control, with significantly smaller stem lesions after pathogen challenge. This increase in pathogen tolerance is correlated with a significantly higher level of transgene expression in this line when compared with the other transgenic line. This is the first report of the introduction of a potentially important gene into Rangpur lime to provide novel pathogen tolerance.
Abstract: Bulked segregant analysis (BSA) was used to identify seven random amplified polymorphic DNA (RAPD) markers linked to the Rpf1 gene. Rpf1 confers resistance to Phytophthora fragariae var. fragariae, the
causal agent of red stele root rot in Fragaria spp. The bulked DNAs represented subsets of a F1 population obtained fromthe crossMd683]Senga Sengana which consisted of 60 plants and segregated in a 1:1 ratio for resistance or susceptibility to race 2.3.4 isolate NS2 of P. fragariae. Seven markers were shown to be linked to Rpf 1 and were generated from four primers; five of these markers were in coupling phase and two in repulsion phase with respect to the gene. A linkage map of this resistance gene region was generated using JoinMap 2.0. The manner in which Rpf1 and the linked markers co-segregated indicated that they are inherited in a disomic fashion. These markers could enable gene pyramiding and marker-assisted selection of resistance genes in strawberry breeding programmes.
Abstract