Single Sequence Repeat Research Articles

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms.

Simple SummaryWe completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade.White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.

Determination of inheritance of aphid resistance in cowpea genotypes and identification of single sequence repeat markers linked to resistance genes

AbstractAn understanding of the mode of inheritance is fundamental to plant breeding. The choice of an appropriate selection method considers the number of genes involved and their modes of action. In plant breeding, markers can overcome the false resistance that may arise from greenhouse screening. The goal of this study was to facilitate the better use of cowpea genotypes resistant to aphids. Specifically, we sought to determine the number of genes involved in the ability of cowpeas to survive aphid infestation and identify single sequence repeat (SSR) markers linked to aphid resistance genes. Two pairs of parents (Tiligre × KVX295‐124‐2‐99 and Tiligre × IT97K556‐6) were used to generate two F2 populations. Each of these populations was screened with aphids to determine the mode of inheritance of resistance to aphids in cowpeas. SSR markers were used to screen parent, F1, and F2 individuals to locate polymorphic markers and markers linked to the genes involved in resistance to aphids. The results showed that the ability to survive under aphid infestation in KVX295‐2‐124‐99 and IT97K556‐6 is controlled by two nonallelic genes. The markers MA61 and MA70 were found linked to aphid resistance in cowpea.

Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.).

Proso millet (Panicum miliaceum L.) or broomcorn millet is among the most important food crops to be domesticated by humans; it is widely distributed in America, Europe, and Asia. In this study, we genotyped 578 accessions of P. miliaceum using 37 single-sequence repeat (SSR) markers, to study the genetic diversity and population structure of each accession. We also investigated total phenolic content (TPC) and superoxide dismutase (SOD) activity and performed association analysis using SSR markers. The results showed that genetic diversity and genetic distance were related to geographic location and the fixation index (Fst). Population structure analysis divided the population into three subpopulations. Based on 3 subpopulations, the population is divided into six clusters in consideration of geographical distribution characteristics and agronomic traits. Based on the genetic diversity, population structure, pairwise Fst, and gene flow analyses, we described the topological structure of the six proso millet subpopulations, and the geographic distribution and migration of each cluster. Comparison of the published cluster (cluster 1) with unique germplasms in Japan and South Korea suggested Turkey as a possible secondary center of origin and domestication (cluster 3) for the cluster. We also discovered a cluster domesticated in Nepal (cluster 6) that is adapted to high-latitude and high-altitude cultivation conditions. Differences in phenotypic characteristics, such as TPC, were observed between the clusters. The association analysis showed that TPC was associated with SSR-31, which explained 7.1% of the total variance, respectively. The development of markers associated with TPC and SOD will provide breeders with new tools to improve the quality of proso millet through marker-assisted selection.

High density genetic mapping of stripe rust resistance in a ‘Strongfield’ / ‘Blackbird’ durum wheat population

Resistance breeding is an effective strategy against wheat stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici (Pst). To identify and map quantitative trait loci (QTL) associated with stripe rust resistance, a durum wheat doubled haploid population (n = 87) derived from ‘Strongfield/Blackbird’ was evaluated for disease severity near Toluca, Mexico (2017–2019) and Lethbridge, Canada (2016–2019). The population was genotyped with the wheat 90 K Illumina iSelect single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers, and QTL analysis was performed with MapQTL 6. We identified stripe rust-resistance QTL contributed by ‘Blackbird’ on chromosomes 3A (2 loci, designated QYr.spa-3A.1, QYr.spa-3A.2) and 5B (QYr.spa-5B), and ‘Strongfield’ on 2B (QYr.spa-2B). All seem to represent QTL not reported previously. The QYr.spa-3A.2 was most consistently effective against Pst races across the Lethbridge and Toluca nurseries. With a LOD value of 4.9, QYr.spa-3A.2 explained a maximum phenotypic variation of 22.7% observed at the Toluca 2019 nursery. The QYr.spa-2B from ‘Strongfield’ and QYr.spa-3A.1 from ‘Blackbird’ expressed in multiple years at Toluca but were not detected at Lethbridge. QYr.spa-5B was identified in the Lethbridge 2016 environment. The identified QTL should be valuable in diversifying resistance genes used in breeding durum wheat cultivars with stripe rust resistance. ‘Blackbird’ was particularly useful for introducing the new QTL QYr.spa-3A.2 resistance that is effective in Canada and Mexico into traditional durum wheat germplasm. SNP markers associated with QTL will have application in marker-assisted breeding of resistance to Pst in durum wheat.

Genetic and molecular characterisation of subtropically adapted low-phytate genotypes for utilisation in mineral biofortification of maize (

Phytic acid (PA) is a major anti-nutritional factor in maize grains and significantly reduces the bioavailability of minerals such as iron and zinc in humans. Reduction of PA in maize (Zea mays L.) thus assumes great significance. Despite the availability of low phytic-acid (lpa) mutants in maize, their utilisation in breeding has been limited because of non-availability of well adapted lpa-based inbreds. A set of 24 subtropically adapted lpa1-1-based maize inbreds derived through molecular breeding was evaluated along with seven wild-type inbreds at multilocation. The lpa1-1 inbreds possessed 35.8% lower PA (1.68 mg/g) than the wild-type inbreds (2.61 mg/g). Mean proportion of PA was lower in the lpa1-1-based inbreds (62.8%) than in the wild-type inbreds (91.6%). The lpa1-1 inbreds showed similar performance for plant- and ear-height besides flowering behaviour as did wild types. Average grain yield among lpa1-1 inbreds (2735.9 kg/ha) was at par with the original versions (2907.3 kg/ha). Molecular profiling of these lpa1-1 inbreds using 60 genome-wide single-sequence repeats generated 172 alleles, with a mean of 2.87 alleles per locus. Mean polymorphism information content and mean gene diversity were 0.41 and 0.48 respectively. Genetic dissimilarity ranged from 0.23 to 0.81, with an average of 0.64. Cluster analyses grouped 24 lpa1-1 genotypes into three major clusters, and principal-coordinate analysis depicted the diverse nature of genotypes. The study also identified a set of potential hybrid combinations with low PA for their direct utilisation in biofortification program. This is the first study on comprehensive characterisation of lpa1-1-based inbreds adapted to subtropical conditions.

Comparative assessment of microsatellite and retrotransposon‐based markers for genetic characterization of commercial banana cultivars (Musa spp.)

AbstractBanana cultivars of agronomic interest have been genetically characterized using two different molecular markers. On the one hand, a panel of 14 trinucleotide single sequence repeats (SSRs or microsatellites) was optimized for homogeneous PCR conditions. It was tested with 50 individuals from seven cultivars, yielding 76 alleles and 5.4 ± 1.8 alleles per locus, while the presence of cultivar‐exclusive alleles allowed the discrimination of all cultivars. On the other hand, a retrotransposon‐based marker system named inter‐primer binding site (iPBS) was implemented for the first time in the Musa genus. A total of 120 bands were detected in eight different Musa cultivars, from which 65.8% were polymorphic and 23.3% were cultivar exclusive. Both techniques allowed a cut‐off identification of all cultivars studied, but overall, iPBS analysis was a more straightforward and economical choice. Despite the fact that we were unable to distinguish local banana varieties belonging to the same cultivar, new cultivar‐specific molecular markers have been developed for the Musa genus, which could be used to guide new breeding programmes and maintain high quality of Plátano de Canarias.

Genetic diversity of common bean (Phaseolus vulgaris L.) germplasm from Serbia, as revealed by single sequence repeats (SSR)

Genetic diversity and structure of common bean (Phaseolus vulgaris L.) germplasm from Serbia, comprising 118 landraces and 18 cultivars, was assessed with the application of 27 Single Sequence Repeats (SSR) markers. Thirteen accessions from Agricultural Institute of Slovenia were used as references for gene pool determination. Main parameters of genetic diversity were calculated for each SSR loci, i.e. number of different and rare alleles, number of effective alleles, Shannon's information index, observed and expected heterozygosity and polymorphic information content. A total of 445 allelic variants, with 16.5 alleles per locus on average, were detected. Mean gene diversity (He = 0.79) indicated sufficient reservoir of genetic variation preserved in studied bean germplasm. Landraces displayed higher variability compared to cultivars (405 in relation to 233 allelic variants). Genetic structure and relatedness of accessions was assessed by model-based method and hierarchical clustering method in combination with genetic distance calculation. The Bayesian clustering model implemented in STRUCTURE software, on the primary level (K = 2), revealed clear separation of accessions into two groups, corresponding to gene pool affiliation. Mesoamerican gene pool (M) was represented with 23.5% of accessions, while Andean (A) was larger, composed of 68.4% of studied germplasm. Small group (8.1%) showed admixed genetic structure between two gene pools. Additional variation in respect to two recognized gene pools was revealed (K = 3), whose basis was acknowledged to be within Andean gene pool. Further subdivision of accessions (K = 8), mainly according to the seed forms, was observed. Genetic distance analysis associated with Neighbour-joining clustering method revealed grouping pattern of landraces and cultivars corresponding to the gene pool and their seed phenotypes. Classification and structuring of the bean accessions according to and beyond the gene pool of origin should facilitate conservation strategies and breeding of this material. Combining the information of phenotypic variation obtained in previous research and molecular data reveled in this study will assist in selection of parental components for breeding, or in the choice of smaller sample in order to further acknowledge their breeding value. In addition, obtained results of this work should serve as an additional information on common bean germplasm variation in Western Balkans and beyond, in Europe.

QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time.

Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.

Deconstructing molecular phylogenetic relationship among cultivated and wild Brassica species

Brassica represents an agriculturally important and diverse group of oilseed crops with a long evolutionary history. Molecular markers played an important role in understanding origin and evolution of Brassica species. In the present research, both Single Nucleotide Polymorphisms (SNPs) and Simple Sequence Repeats (SSRs) developed from Brassica juncea L. Czern. were used to find out the phylogenetic relationship between different cultivated and wild Brassica species. A total of 88 SSR and 58 SNP markers were found to be functional across 38 genotypes belonging to ten different taxon groups. The polymorphic markers were able to group the genotypes into three different clusters and showed relatedness among different genomes based on genetic distances. The transferability of these markers serve the purpose of their quick use in cultivar identification, diversity and phylogenetic analysis in those orphan crops species where no or less genomic information is available.

Transfer of fusarium head blight resistance from Thinopyrum elongatum to bread wheat cultivar Chinese Spring

The diploid form of tall wheatgrass, Thinopyrum elongatum (Host) D.R. Dewey (2n = 2x = 14, EE genome), has a high level of resistance to fusarium head blight. The symptoms did not spread beyond the inoculated florets following point inoculation. Using a series of E-genome chromosome additions in a bread wheat cultivar Chinese Spring (CS) background, the resistance was found to be localized to the long arm of chromosome 7E. The CS mutant ph1b was used to induce recombination between chromosome 7E, present in the 7E(7D) substitution and homoeologous wheat chromosomes. Multivalent chromosome associations were detected in the BC1 hybrids, confirming the effectiveness of the ph1b mutant. Genetic markers specific for chromosome 7E were used to estimate the size of the 7E introgression in the wheat genome. Using single sequence repeat (SSR) markers specific for homoeologous wheat chromosome 7, introgressions were detected on wheat chromosomes 7A, 7B, and 7D. Some of the introgression lines were resistant to fusarium head blight.

Nutritional analysis and molecular characterization of hybrid mushrooms developed through intergeneric protoplast fusion between Pleurotus sajor-caju and Calocybe indica with the purpose to achieve improved strains.

Two edible mushrooms Calocybe indica and Pleurotus sajor-caju were chosen as parent strains in this study to approach the concept of hybridization through theprotoplast fusion technique. Protoplast fusion in presence of polyethylene glycol (PEG) was conducted between the parent strains and by further double selection screening method, six somatic hybrid lines were developed. Those fruit bodies of the hybrid lines showed phenotypic resemblance with Pleurotus sajor-caju when grown on paddy straw under favorable conditions. The hybridity of the newly developed somatic hybrid strains was established by barrage reaction, morphological traits, fruitbody parameter and, inter single sequence repeat (ISSR) profiling. One-way analysis of variance (ANOVA) was used for the analysis of phenotypic data of hybrid lines and parents. Five ISSR primers were used to generate 51 amplified DNA fragments ranged between 250 and 3000bp in size in six hybrids and two parents with 90.19% polymorphism. Some of the hybrids contain some non-parental bands whichindicate that recombination might happen in thehybrid genome hence confirming the hybridity of newly developed strains. The dendrogram was created using theAverage Linkage (Between Groups) method based on ISSR profiling and genetic distance between parent-hybrids and hybrid-hybrid was analyzed by Jaccard's proximity matrix. A definite improvement in nutritional properties and biological activity was observed in the study. Due to ease in their cultivation, it can play a significant role in the rural economic development.

Combining ability and genetic divergence among tropical maize inbred lines using SSR markers

Our objectives were to evaluate general and specific combining ability (SCA) and genetic divergence among tropical maize inbred lines using single sequence repeat (SSR) markers. Thirteen inbred lines were crossed based on a complete diallel scheme. Hybrids and three checks were evaluated in a lattice experimental design. Silk and anthesis flowering, average plant height, average ear height, white spot (Pantoea ananatis) and gray leaf spot (Cercospora zeae-maydis) severity, and grain yield were evaluated. Significant differences (p < 0.05) for general and specific combining abilities were observed for all traits. Based on additive effects, inbred lines 1 (Flash) and 12 (SG 6015) were selected to reduce the flowering period and plant and ear height. Inbred lines 2 (CD 303) and 3 (AG 8080) were selected to reduce disease severity. For the simultaneous increase in grain yield and reduced severity of diseases, line 11 (AG 9090) as a parent or tester in topcross schemes is recommended. According to non-additive effects, crosses 2 (CD 303) × 13 (DKB 747) and 11 (AG 9090) × 12 (SG 6015) were selected for grain yield and future breeding programs. Six groups were identified using SSR markers; a major group contained six inbred lines. Because of the minor relationship between genetic divergence and SCA effects on grain yield limits, the use of the groups for future divergent crosses is recommended.

Genomics‐assisted lentil breeding: Current status and future strategies

AbstractGenomics‐assisted breeding has become a powerful tool to develop high‐yielding climate‐resilient varieties for adaptation to adverse environmental conditions such as heat and drought stresses. Previously, efforts have been made to develop genomic resources in lentil, leading to the development of many trait‐specific mapping populations, cores and mini‐cores, and single nucleotide polymorphism and simple sequence repeat markers. Molecular markers have been used in genetic diversity analyses and to clarify genetic relationships in lentil. However, availability of cost‐effective next‐generation sequencing and genotyping‐by‐sequencing technologies has provided unprecedented opportunities for advancing genetics research and breeding applications. For instance, it has become possible to assemble the large and complex genome, develop high‐density genetic maps for high‐resolution QTL mapping, and deploy genome‐wide association study in lentil. Furthermore, a range of cost‐effective marker genotyping platforms have been developed. These developments offer ample opportunities to modernize current breeding programs in lentil for accelerating genetic gains. This review discusses the current status and future possibilities of genomics‐assisted breeding to develop and deploy lentil cultivars suitable for changing climatic conditions.

EVALUATION GENETIC DIVERSITY AND A BOTTLENECK OF Cinnamomum balansae H. Lecomte POPULATIONS IN PHU THO PROVINCE BY MICROSATELITE (SSR) MARKERS

Cinnamomum balansae Lecomte (Lauraceae) is considered as an endemic to Vietnam and is assessed as endangered. This species an ecologically and economically important tree species. To conserve the species in tropical forests, genetic diversity was investigated on the basis of ten microsatellites (single sequence repeat, SSR). In all, fifty-two C. balansae individuals of four populations in Phu Tho (Doan Hung, Thanh Son, Ha Hoa and Viet Tri city) were analyzed in thisstudy. A total of 27 alelles were observed across the studied loci. The polymorphic information content (PIC) averaged 0.43 and indicated a high polymorphic value. Other values including discrimination power (PD = 0.58), resolving power (Rp = 2.57) and Marker index (MI = 1.08) were revealed. Genetic diversity in population level was higher (Ne = 2.68; Ho = 0.47 and He = 0.37) and positive inbreeding value (Fis = 0.16). Bottleneck tests had not found of four populations. This study also showed the importance of conserving the genetic resources of C. balansae species in Phu Tho province.

Analysis of Intraspecific Diversity in Two Green Capsuled Accessions of Bixa orellana L., a FoodDye Plant by Single Sequence Repeat (SSR) Markers

Analysis of Intraspecific Diversity in Two Green Capsuled Accessions of Bixa orellana L., a FoodDye Plant by Single Sequence Repeat (SSR) Markers

SSR Marker based Molecular Screening of Blast Resistant Genes in selected Rice genotypes

Rice blast caused by Magnaporthe oryzae is one of the most devastating disease causing major yield losses worldwide in every year. Use of resistant rice varieties is one of the most effective ways to control the disease and reduce yield loss. Molecular screening and allelic diversity of major rice blast resistant genes were determined in forty-eight (48) genotypes of rice germplasms of Bangladesh with ten (10) previously synthesized gene based SSR (Single Sequence Repeats) markers [RM 541, RM 224, RM21, RM527, RM 208, RM 247,RM 72, RM 259, RM 246 & RM 206]. The genetic frequencies of ten (10) major blast resistance genes (Pi-9, Pi-1, Pi-5(t), Piz-5, Pi-b, Pi-b, Pi-ta, Pi-33, Pi27(t), Pitp(t) and Pi-kh) were ranged from 2% to 93%. The blast resistance gene Pi-kh was widely (93%) and Pi5 (2%) was sparsely distributed among the studied genotypes. Nine (9) genotypes sonaanjana, jabedshail, karaja, pajon, IR-09, BAU 39, binni, katiabagdad and kataribhug, had maximum eight (8) blast resistance genes and only one BRRIdhan 46 had minimum two (2) blast resistance genes. Twelve genotypes possessed seven, twelve had six, seven had five and five had four resistant genes. Out of forty-eight (48) genotypes, forty-five (45) genotypes occupied at least five (5) positive fragments of expected product size. Allelic diversity was also found among the rice genotypes for different blast resistance genes.

Research Article Development and transferability of microsatellite loci for <i>Spondias</i> <i>tuberosa</i> (Anacardiaceae: Sapindales), a species endemic to the Brazilian semi-arid region

The umbu tree (Spondias tuberosa) is one of the best known plants of the Brazilian semi-arid region; it has great potential for the fruit market due to excellent consumer acceptance. This tree is not presently cultivated; fruit commercialization is based on extrativism. Consequently, there has been little research on the genetics of this species. Our objective was to develop, evaluate and transfer single sequence repeat (SSR) loci to S. tuberosa to support work on genetic resources and agronomic improvement of this species. SSR loci for the umbu tree were developed from a new enriched genomic library and evaluated by PCR. Fourteen SSR loci developed for S. radlkoferi were evaluated for use in S. tuberosa, as well as 18 SSR loci previously identified for this species. DNA was extracted from leaf tissue of eight umbu trees available that are part of a germplasm collection located in Petrolina, PE, Brazil. Of the 14 pairs of primers that were tested, six yielded amplicons, and two showed polymorphism in the genotyped samples. All SSR loci of S. radlkoferi transferred to the umbu tree species, yielding amplicons; however, only four were polymorphic in this sample. Among the eighteen available species-specific SSR loci, six were polymorphic for these eight trees. Among the 38 loci that we evaluated, 12 were polymorphic in the sample, including two new loci for S. tuberosa. The number of alleles ranged from 2 to 12, and 10 of them were moderately to highly informative (PIC>0.50), while nine had heterozygosity greater than 0.50. The six new SSR loci and the 14 SSR loci transferred from S. radlkoferi increase the number of available loci for population studies, germplasm collection and resource management for the development of new umbu tree cultivars.

Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant Lagenaria siceraria

<i>Lagenaria siceraria</i> (Molina) Standley has unique biological characteristics with high nutritional and medicinal values. It is an important pharmaceutical plant with various biologically active ingredients. Genetic improvement and deeper genomic studies require a rich resource of molecular markers. The application of next-generation sequencing technology, especially for transcriptome profiling, has greatly facilitated high throughput single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) discovery. In this study, we sequenced the transcriptome of three major cultivars of <i>L. siceraria</i> and obtained 64.88 GB of clean data. The assembled high-quality reads were clustered into 89,347 unigenes, which were annotated by non-redundant protein database, Swiss-Port, Eukaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes, and gene ontology databases. A total of 8,891 SSR and 35,873 SNP markers were predicted from unigenes by MISA and SAM tools, respectively. Characterization of the predicted markers in <i>L. siceraria</i> showed that the SSR and SNP densities were 60 and 243 markers per Mb of genome, respectively, and the estimated ratio of transition to transversion of SNP was 2.016. These markers will be very useful for genetic studies in <i>L. siceraria</i>, especially for the high-density linkage map construction and genome-wide association studies. Further genomic studies based on these results will facilitate the identification of novel genes or alleles of pharmaceutical importance.

Integration of meta-QTL discovery with omics: Towards a molecular breeding platform for improving wheat resistance to Fusarium head blight

Fusarium head blight (FHB) is a global wheat disease that devastates wheat production. Resistance to FHB spread within a wheat spike (type II resistance) and to mycotoxin accumulation in infected kernel (type III resistance) are the two main types of resistance. Of hundreds of QTL that have been reported, only a few can be used in wheat breeding because most show minor and/or inconsistent effects in different genetic backgrounds. We describe a new strategy for identifying robust and reliable meta-QTL (mQTL) that can be used for improvement of wheat FHB resistance. It involves integration of mQTL analysis with mQTL physical mapping and identification of single-copy markers and candidate genes. Using meta-analysis, we consolidated 625 original QTL from 113 publications into 118 genetic map-based mQTL (gmQTL). These gmQTL were further located on the Chinese Spring reference sequence map. Finally, 77 high-confidence mQTL (hcmQTL) were selected from the reference sequence-based mQTL (smQTL). Locus-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers and 17 genes responsive to FHB were then identified in the hcmQTL intervals by combined analysis of transcriptomic and proteomic data. This work may lead to a comprehensive molecular breeding platform for improving wheat resistance to FHB.

Population Structure of Phytophthora infestans from a Single Location in Poland Over a Long Period of Time in Context of Weather Conditions

Phytophthora infestans (Mont.) de Bary is a destructive potato pathogen. Changing weather conditions are among the factors that influence the pathogen population structure. In this study, 237 P. infestans isolates were collected from a single unprotected experimental field in an area with high late-blight pressure located in Boguchwała in the southeastern part of Poland during 15 growing seasons (2000–2014). The isolates were assessed for mating type, mitochondrial haplotype, resistance to metalaxyl, virulence, and polymorphism of 14 single-sequence repeat markers (SSRs). The results revealed 89 unique genotypes among the 237 P. infestans isolates. Eighty-seven isolates belonged to genotype 34_A1, which was detected in all the years of research except 2012. Isolates of P. infestans from individual years were very similar to each other, as shown by Nei’s genetic identity based on 14 SSR markers. The obtained results on isolate characteristics were analyzed in terms of meteorological data (air temperature and precipitation) and indicated that frost, long winters, and hot, dry summers did not directly affect the P. infestans population structure. We described the variability in metalaxyl resistance and virulence among isolates of the P. infestans genotype 34_A1.