QTL For Resistance Research Articles

Association of Genome-Wide SNP Markers with Resistance to Common Scab of Potato

Common scab is a soilborne disease that occurs in potato worldwide. Scab is usually present superficially on potato tubers but nonetheless reduces marketability. A genome-wide association study for common scab resistance was performed using 13,002 genome-wide SNPs, with 165 genotypes mostly for chip-processing. We identified a novel QTL for common scab resistance that explained at most 14.7% of the total variance; this QTL was within the 640 kb interval between 0.43 Mb and 1.07 Mb on potato chromosome 1. Recessive homozygosity at this QTL increased levels of resistance. There is no agreement in terms of the locations of QTLs and their genetic modes between the results of previous studies and the present study or among any study. As such, common scab resistance is a highly complex trait, as the QTLs discovered to date are all minor-effect QTLs.

Fine mapping of a thrips resistance QTL in Capsicum and the role of diterpene glycosides in the underlying mechanism

Key messageA major thrips resistance QTL in Capsicum was fine-mapped to a region of 0.4 Mbp, and a multidisciplinary approach has been used to study putative underlying mechanisms.Resistance to thrips is an important trait for pepper growers. These insects can cause extensive damage to fruits, flowers and leaves on field and greenhouse grown plants worldwide. Two independent studies in Capsicum identified diterpene glycosides as metabolites that are correlated with thrips resistance. In this study, we fine-mapped a previously defined thrips resistance QTL on chromosome 6, to a region of 0.4 Mbp harbouring 15 genes. Two of these 15 candidate genes showed differences in gene expression upon thrips induction, when comparing plants carrying the resistance allele in homozygous state to plants with the susceptibility allele in homozygous state for the QTL region. Three genes, including the two genes that showed difference in gene expression, contained a SNP that was predicted to lead to changes in protein structure. Therefore, these three genes, i.e. an acid phosphatase 1 (APS1), an organic cation/carnitine transporter 7 (OCT7) and an uncharacterized locus LOC107874801, are the most likely candidates for playing a role in thrips resistance and are a first step in elucidating the genetic basis of thrips resistance in Capsicum. In addition, we show that the diterpene glycoside profiles did not differ between plants with the resistance and susceptibility allele for the chromosome 6 QTL, suggesting that these compounds do not play a role in the resistance conferred by the genes located in the major thrips resistance QTL studied.

Genome-wide association mapping of leaf rust and stripe rust resistance in wheat accessions using the 90K SNP array.

A genome-wide association analysis identified diverse loci for seedling and adult plant resistance to leaf rust and stripe rust. KASP markers were developed and validated for marker-assisted selection. Wheat leaf rust and stripe rust cause significant losses in many wheat producing regions worldwide. The objective of this study was to identify chromosome regions conferring resistance to both leaf rust and stripe rust at the seedling and adult plant stages. A diversity panel of 268 wheat lines, including 207 accessions from different wheat growing regions in China, and 61 accessions from foreign countries, were evaluated for leaf rust response at seedling stage using eight Chinese Puccinia triticina pathotypes, and also tested for leaf rust and stripe rust at adult plant stage in multiple field environments. The panel was genotyped with the Wheat 90K Illumina iSelect SNP array. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Twenty-two resistance loci including the known Lr genes, Lr1, Lr26, Lr3ka, LrZH22, and 18 potentially new loci were identified associated with seedling resistance, explaining 4.6 to 25.2% of the phenotypic variance. Twenty-two and 23 adult plant resistance (APR) QTL associated with leaf and stripe rust, respectively, were identified at adult stage, explaining 4.2-11.5% and 4.4-9.7% of the phenotypic variance. Among them, QLr-2BS was the potentially most valuable all-stage resistance gene. Seven and six consistent APR QTL were identified in multiple environments including best linear unbiased prediction (BLUP) data, respectively. Comparison with previously mapped resistance loci indicated that three of the seven leaf rust resistance APR QTL, and two of the six stripe rust resistance APR QTL were new. Four potentially pleiotropic APR QTL, including Lr46/Yr29, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1, were identified. Twelve associated SNPs were converted into kompetitive allele-specific PCR (KASP) markers and verified in bi-parental populations. The study reports genetic loci conferring resistance to both diseases, and the closely linked markers should be applicable for marker-assisted wheat breeding.

The Barley HvWRKY6 Transcription Factor Is Required for Resistance Against Pyrenophora teres f. teres.

Barley is an important cereal crop worldwide because of its use in the brewing and distilling industry. However, adequate supplies of quality malting barley are threatened by global climate change due to drought in some regions and excess precipitation in others, which facilitates epidemics caused by fungal pathogens. The disease net form net blotch caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt) has emerged as a global threat to barley production and diverse populations of Ptt have shown a capacity to overcome deployed genetic resistances. The barley line CI5791 exhibits remarkably effective resistance to diverse Ptt isolates from around the world that maps to two major QTL on chromosomes 3H and 6H. To identify genes involved in this effective resistance, CI5791 seed were γ-irradiated and two mutants, designated CI5791-γ3 and CI5791-γ8, with compromised Ptt resistance were identified from an M2 population. Phenotyping of CI5791-γ3 and -γ8 × Heartland F2 populations showed three resistant to one susceptible segregation ratios and CI5791-γ3 × -γ8 F1 individuals were susceptible, thus these independent mutants are in a single allelic gene. Thirty-four homozygous mutant (susceptible) CI5791-γ3 × Heartland F2 individuals, representing 68 recombinant gametes, were genotyped via PCR genotype by sequencing. The data were used for single marker regression mapping placing the mutation on chromosome 3H within an approximate 75 cM interval encompassing the 3H CI5791 resistance QTL. Sequencing of the mutants and wild-type (WT) CI5791 genomic DNA following exome capture identified independent mutations of the HvWRKY6 transcription factor located on chromosome 3H at ∼50.7 cM, within the genetically delimited region. Post transcriptional gene silencing of HvWRKY6 in barley line CI5791 resulted in Ptt susceptibility, confirming that it functions in NFNB resistance, validating it as the gene underlying the mutant phenotypes. Allele analysis and transcript regulation of HvWRKY6 from resistant and susceptible lines revealed sequence identity and upregulation upon pathogen challenge in all genotypes analyzed, suggesting a conserved transcription factor is involved in the defense against the necrotrophic pathogen. We hypothesize that HvWRKY6 functions as a conserved signaling component of defense mechanisms that restricts Ptt growth in barley.

Mapping and Validation of Stem Rust Resistance Loci in Spring Wheat Line CI 14275.

Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) remains a constraint to wheat production in East Africa. In this study, we characterized the genetics of stem rust resistance, identified QTLs, and described markers associated with stem rust resistance in the spring wheat line CI 14275. The 113 recombinant inbred lines, together with their parents, were evaluated at the seedling stage against Pgt races TTKSK, TRTTF, TPMKC, TTTTF, and RTQQC. Screening for resistance to Pgt races in the field was undertaken in Kenya, Ethiopia, and the United States in 2016, 2017, and 2018. One gene conferred seedling resistance to race TTTTF, likely Sr7a. Three QTL were identified that conferred field resistance. QTL QSr.cdl-2BS.2, that conferred resistance in Kenya and Ethiopia, was validated, and the marker Excalibur_c7963_1722 was shown to have potential to select for this QTL in marker-assisted selection. The QTL QSr.cdl-3B.2 is likely Sr12, and QSr.cdl-6A appears to be a new QTL. This is the first study to both detect and validate an adult plant stem rust resistance QTL on chromosome arm 2BS. The combination of field QTL QSr.cdl-2BS.2, QSr.cdl-3B.2, and QSr.cdl-6A has the potential to be used in wheat breeding to improve stem rust resistance of wheat varieties.

Mapping of Ug99 stem rust resistance in Canadian durum wheat

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), has potential to cause major yield losses in durum wheat. Development of durum cultivars with improved resistance to stem rust is a sustainable option for effective control of this disease. This study was conducted to identify genomic regions associated with resistance to Ug99-derived Pgt races using a doubled haploid (DH) mapping population produced from a cross between the resistant experimental line A9919-BY5C and the moderately susceptible cultivar ‘Strongfield’. The parents and DH lines were phenotyped for adult plant disease severity and infection response at Njoro, Kenya, for four years, and for seedling reaction to race TTKSK in a containment facility near Morden, Canada. Composite interval mapping using 612 SNP and DArT markers indicated four significant QTL for resistance to stem rust on chromosomes 1B, 4A, 5B, and 6A. A major and stable QTL from A9919-BY5C was identified on the short arm of chromosome 6A (6AS), which accounted for 71% of variation explained for seedling resistance and up to 46% for field resistance. This QTL mapped near the Sr8 locus and may be Sr8155B1, or a novel gene at the same location. Another QTL for adult plant resistance from A9919-BY5C was mapped on chromosome 1B that explained up to 14% of the phenotypic variation and likely is Sr14. Two minor QTL were identified in ‘Strongfield’ on chromosomes 4A and 5B that were inconsistent over years. Markers associated with the 6AS and 1B QTL can be used to proactively stack resistance to Ug99-derived races of Pgt into Canadian durum wheat.

Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Barley stripe rust, Puccinia striiformis f. sp. hordei, (PSH) occurs worldwide and is one of the major barley diseases of South Asia and North Africa. The aim of this study was to identify and map rust resistance loci at the seedling and the adult plant stages in 336 barley genotypes assembled at ICARDA as AM-2014. The seedling resistance to PSH was evaluated in the greenhouse individually for six virulent races originated from India. The adult stage resistance to PSH was evaluated in field located at Durgapura, Rajasthan, India. The AM-2014 panel was genotyped with infinium iSelect 9K barley SNP markers and genome-wide association studies were carried out using mixed linear model accounting for population structure (PCA) and kinship (K) as covariates. Eleven barley genotypes were identified resistant to all six PSH races at the seedling stage while these genotypes were also resistant at adult plant stage in the field. The most effective SNP markers (at least one for each QTL) associated with rust resistance was also identified using stepwise regression. A total of 17 and 25 resistance QTL to six races of PSH were identified in two- and six-rowed barley at the seedling stage, respectively. While, six and seven resistance QTL to PSH were detected at the adult stage in two- and six-rowed barley, respectively. The novel PSH resistant QTL detected at the seedling and adult stages are important for barley breeding programs globally.

Identification of QTL for resistance to leaf blast in foxtail millet by genome re-sequencing analysis.

Three QTL for resistance to leaf blast were identified on chromosomes 1, 2, and 8 of the foxtail millet cultivar Yugu 5. Leaf blast disease of foxtail millet (Setaria italica) is caused by Pyricularia spp., can infect all the aboveground parts of plants, and is the most frequently observed blast disease in China. Lack of information on genetic control of disease resistance impedes developing leaf blast-resistant cultivars. An F6 recombinant inbred line (RIL) population from the cross Yugu 5 × Jigu 31 was phenotyped for its reactions to leaf blast in six field trials in the naturally diseased nurseries. An ultra-density genetic linkage map was constructed using 35,065 single nucleotide polymorphism (SNP) markers generated by sequencing of the RIL population. Three QTL, QLB-czas1, QLB-czas2, and QLB-cazas8, were detected in the genomic intervals of 276.6kb, 1.62Mb, and 1.75Mb on chromosomes 1, 2, and 8 of Yugu 5, which explained 14-17% (2 environments), 9% (5 environments), and 12-20% (6 environments) of the phenotypic variations. Bulked segregant analysis (BSA) and RNA sequencing (BSR-Seq) method identified common SNPs that fell in the genomic region of QLB-czas8, providing additional evidence of localization of this QTL. Three and 19 predicted genes were annotated to be associated with disease resistance in the genomic intervals for QLB-czas2 and QLB-czas8. Due to their unique positions, these QTL appear to be new loci conferring resistance to leaf blast. The identification of these new resistance QTL will be useful in cultivar development and the study of the genetic control of blast resistance in foxtail millet.

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight

Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.

ALELOS ASOCIADOS AL ÍNDICE DE SEVERIDAD DE LA ENFERMEDAD MAL DE RÍO CUARTO EN GERMOPLASMA EXÓTICO DE MAÍZ

Mal de Río Cuarto (MRC) is one of the most important viral diseases of maize in Argentina. The disease severity index (DSI) allows to combine the incidence and severity of a disease in a single metric. The genotypic reaction to MRC has been extensively studied in biparental populations. However, this complex trait has not been analyzed by genome-wide association studies (GWAS). The aim of this work is to identify new resistance alleles associated with DSI of MRC in an exotic germplasm from the International Maize and Wheat Improvement Center (CIMMYT). A population of maize lines from CIMMYT was phenotypically evaluated in environments in the area where the disease is endemic. The predictors of genetic effects (BLUP, best linear unbiased predictor) and 78,376 SNP markers (Single Nucleotide Polymorphism) were used to perform the GWAS in 186 maize lines. The values of variance components and mean-basis heritability suggest a wide genotypic variability in the population. The GWAS allowed to identify 11 putative QTL of resistance to MRC. The incorporation of exotic germplasm into local maize breeding programs could contribute favorably to the creation of hybrids with a higher level of resistance to MRC. The predictive ability of associated markers with MRC resistance indicates that marker-assisted selection is an advisable tool for selecting MRC resistant genotypes. Key words: Disease severity index; genome-wide association study; QTL; SNP

Mapping Solanum berthaultii-based Late Blight (Phytophthora infestans) Resistance in a Diploid Population

Late blight, caused by the oomycete Phytophthora infestans (Mont) de Bary, is the most important disease of cultivated potato (Solanum tuberosum L.). An efficient long-term strategy for controlling late blight infection involves integration of host plant resistance to disease management programs. In this study, a diploid potato population segregating for late blight resistance was generated from an interspecific cross (MSX902) between S. tuberosum x S. chacoense hybrid (84SD22) and a late blight resistant Solanum berthaultii hybrid (Ber83). A total of 129 progeny and two parents were tested for foliar resistance against the US-23 P. infestans genotype using detached-leaf bioassays and inoculated field trials (2014 and 2015). Distribution of foliar late blight resistance and susceptibility was bimodal in both types of phenotype evaluation, suggesting a major R-gene may be associated with the resistance. A major QTL for late blight resistance on chromosome 10 was detected using both detached leaf bioassay and field trial data. The SNP marker solcap_snp_c1_15219 (26.5 cM) was at the peak of the QTL. Additionally, a minor QTL on chromosomes 5 was linked to SNPs solcap_snp_c1_3793. These SNP markers closely linked to the late blight resistance QTL can be used for marker-assisted breeding.

Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance

Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран- тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред- ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не- матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля- ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со- временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды. К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до- стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую- щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде- ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов и подходов. Представлены результаты изучения структурной и функциональной организации генов устойчиво- сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле- кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых сортов, в том числе с групповой устойчивостью.

Comparative mapping and validation of multiple disease resistance QTL for simultaneously controlling common and dwarf bunt in bread wheat

Key messageResistance QTL on chromosomes 1AL and 7AL are effective against common and dwarf bunt, QTL on 1BS affects common bunt and QTL on 7DS affects dwarf bunt in bread wheat.Common bunt, caused by Tilletia caries and T. laevis, and dwarf bunt, caused by T. controversa, negatively affect grain yield and quality of wheat and are particularly destructive in low-input and organic production systems. Two recombinant inbred line (RIL) populations derived by crossing the highly and durably resistant cultivars ‘Blizzard’ and ‘Bonneville’ to the susceptible cultivar ‘Rainer’ were evaluated for their resistance to common and dwarf bunt in artificially inoculated field and greenhouse trials over two growing seasons and genotyped with a 15 K SNP array. Bunt resistance QTL were mapped to chromosomes 1AL, 1BS, 7AL and 7DS. Common bunt resistance was regulated by the major QTL QBt.ifa-1BS and QBt.ifa-1AL together with the moderate effect QTL QBt.ifa-7AL. Dwarf bunt resistance was on the other hand regulated by the QTL QBt.ifa-1AL, QBt.ifa-7AL and QBt.ifa-7DS. Common bunt resistance QTL exhibited pronounced epistatic effects, while epistatic effects were of smaller magnitude for dwarf bunt QTL. Kompetitive Allele-Specific PCR (KASP) markers were developed from SNPs associated with bunt resistance QTL and successfully used for QTL validation in an independent set of RILs. These KASP markers have the potential to support targeted introgression of QTL into elite wheat germplasm and accelerate breeding for enhanced bunt resistance. Durable protection against both common and dwarf bunt can be achieved by combining multiple resistance genes in the same genetic background.

A maizewin protein confers enhanced antiinsect and antifungal resistance when the gene is transgenically expressed in maize callus

Maize is a crop of worldwide importance, but insects and plant pathogens limit sustainable production. The development of maize varieties with improved resistance will be facilitated by identification of relevant resistance alleles through appropriate biological assays. A barwin-like gene (which we call maizewin) located in a QTL for Fusarium resistance annotated such that potential glucanase and chitinase activity could occur in the translated protein, was cloned from an ear rot resistant inbred and transgenically expressed in maize callus. Although limited increases in insect resistance occurred in the transgenic callus material containing the maizewin gene compared to a GUS control gene, resistance to Fusarium pathogens was common and associated with increased glucanase activity. The gene appeared to produce a protein with glucanase and chitosanase activity, consistent with an antifungal role. The allele that produces the functional resistant protein may be relatively uncommon in maize germplasm. Incorporation of a functional maizewin allele into susceptible germplasm should help increase production by contributing to control of both insect pests and plant pathogens.

Intercontinental trials reveal stable QTL for Northern corn leaf blight resistance in Europe and in Brazil

Key messageNCLB is the most devastating leaf disease in European maize, and the introduction of Brazilian resistance donors can efficiently increase the resistance levels of European maize germplasm.Northern corn leaf blight (NCLB) is one of the most devastating leaf pathogens in maize (Zea mays L.). Maize cultivars need to be equipped with broad and stable NCLB resistance to cope with production intensification and climate change. Brazilian germplasm is a great source to increase low NCLB resistance levels in European materials, but little is known about their effect in European environments. To investigate the usefulness of Brazilian germplasm as NCLB resistance donors, we conducted multi-parent QTL mapping, evaluated the potential of marker-assisted selection as well as genome-wide selection of 742 F1-derived DH lines. The line per se performance was evaluated in one location in Brazil and six location-by-year combinations (= environments) in Europe, while testcrosses were assessed in two locations in Brazil and further 10 environments in Europe. Jointly, we identified 17 QTL for NCLB resistance explaining 3.57–30.98% of the genotypic variance each. Two of these QTL were detected in both Brazilian and European environments indicating the stability of these QTL in contrasting ecosystems. We observed moderate to high genomic prediction accuracies between 0.58 and 0.83 depending on population and continent. Collectively, our study illustrates the potential use of tropical resistance sources to increase NCLB resistance level in applied European maize breeding programs.

Genetic mapping of Fusarium wilt resistance in a wild banana Musa acuminata ssp. malaccensis accession

Banana is an important fruit and food crop, but is threatened by Fusarium wilt, one of the most devastating soil-borne fungal diseases. Only host resistance facilitates banana cultivation in infested soils around the world, but the genetic basis of Fusarium wilt of banana (FWB) is unknown. We selfed a heterozygous wild banana accession Musa acuminata ssp. malaccensis (Mam, AA, 2n = 22) to generate a mapping population and to investigate the inheritance of resistance to Race 1 and tropical race 4 (TR4) that cause FWB. Phenotyping (N = 217) revealed segregation for resistance, and genotyping by sequencing resulted in 2802 high-quality single-nucleotide polymorphic markers (SNPs) that were used for genetic mapping. Combined analyses of these data showed that a single dominant resistance locus controls resistance to Race 1 and maps near the distal part of chromosome 10. Recombinants, together with the position of the putative resistance gene, were further analysed using graphical genotyping, which retrieved markers flanking a 360 kb genetic region that associates with Race 1 resistance. The region contains 165 putative genes on the reference genome, including 19 leucine-rich repeat receptor-like kinase-like genes. At the same position and phase, we also identified a QTL for TR4 resistance, showing that the locus for resistance against Race 1 provided partial resistance to TR4. However, this effect was far less significant and hence not included in the mapping. These data support the breeding of new banana varieties with resistance to Fusarium wilt.

MiRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection.

Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 “high viral load responding” miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect their target genes differently throughout disease progression. This shows that miRNAs are sensitive to VL and disease progression, and may act as fine-tuners of both immediate immune response activation and the later inflammatory processes.

Optical Sorter-Based Selection Effectively Identifies Soft Red Winter Wheat Breeding Lines With Fhb1 and Enhances FHB Resistance in Lines With and Without Fhb1

Previous results from our lab have shown that using an optical sorter to identify Fusarium head blight (FHB) resistant breeding lines was effective at reducing the toxin deoxynivalenol (DON) and FHB-associated kernel damage. In this paper we quantified the proportion of desirable genotypes at FHB resistance QTL in lines from three selection cycles of optical sorting. Breeding lines were genotyped at loci on chromosomes 3BS, 2DL, and 5A using the following DNA markers: TaHRC, CFD233, and GWM304. TaHRC is a KASP marker for Fhb1, a major FHB resistance QTL on chromosome 3BS. CFD233 is an SSR marker for Qfhs.nau-2DL on chromosome 2DL. GWM304 is an SSR marker for Qfhs.ifa-5A on chromosome 5A. Sorter selection was effective at identifying lines that had the resistant genotype at TaHRC; in other words, the sorter was able to identify lines with resistance alleles at Fhb1. The sorter was less effective at selecting for the resistant genotype at CFD233 and GWM304. However, the proportion of lines with resistant genotypes at GWM304 did increase with additional sorter selection, just not to the degree that was observed for the Fhb1-associated marker. The proportion of lines with resistant alleles at CFD233 did not show a consistent trend. In addition to increasing the proportion of lines with Fhb1 and Qfhs.ifa-5A each selection cycle, optical sorter-based mass selection enhanced FHB resistance in different marker genotype combinations evaluated in this study. For example, there were net reductions in DON and kernel damage after two cycles of sorter selection in 15X110601S07002, a line with Fhb1, with Qfhs.nau-2DL, and with Qfhs.ifa-5A; final C3 DON levels were 63% of the resistant check (KY02C-3005-25). Kernel damage was also reduced in 15X110601A08221 a line without Fhb1, without Qfhs.nau-2DL, and without Qfhs.ifa-5A. Our findings suggest the increased resistance observed in different marker genotype combinations was conferred by QTL other than Fhb1, QFhs.nau-2DL, and Qfhs.ifa-5, and validate our previous results that the optical sorter is effective at selecting FHB-resistant breeding material.

QTL mapping for stripe rust and powdery mildew resistance in Triticum durum–Aegilops speltoides backcross introgression lines

AbstractWheat, a major food crop, faces significant yield constraints due to losses caused by various diseases, especially rusts and powdery mildew. Since the causal organisms are always evolving, there is a never-ending hunt for new genes/quantitative trait loci (QTLs) for resistance to control the damage. For this purpose, Triticum durum–Aegilops speltoides backcross introgression lines (DS-BILs) developed in our wide hybridization programme were screened against stripe rust and powdery mildew at both seedling and adult plant stages. DS-BILs showed complete to moderate resistance at the adult plant stage while varying resistance and susceptibility at the seedling stage. A total of 1095 single-nucleotide polymorphisms (SNPs) identified on 14 chromosomes of T. durum, using genotyping by sequencing, were used for QTL mapping. Eleven unique QTLs, across six chromosomes (chr1B, chr2A, chr2B, chr3B, chr6B and chr7B) were identified for resistance, four QTLs for field mixture of stripe rust pathotypes, two QTLs for stripe rust pathotype 78S84 and five QTLs for field mixture of powdery mildew pathotypes using stepwise regression-based likelihood ratio test for additive effect of markers and single-marker analysis. Eleven DS-BILs carrying multiple QTLs were identified which will serve as a useful resource to transfer the respective resistance to susceptible cultivars to develop all stage resistant elite cultivars where QTL for stripe rust resistance QYrAs.pau-2A.1 (LOD 3.8, PVE 24.51 linked to SNP S2A_16016633) and QTL for powdery mildew resistance QPmAs.pau-6B (logarithm of the odds (LOD) 3.2, phenotypic variation explained (PVE) 17.75 linked to SNP S6B_26793381) are major targets of the transfer.

QTL mapping of resistance to Ug99 and other stem rust pathogen races in bread wheat

Most wheat cultivars planted worldwide are susceptible to the stem rust Ug99 race group. To prepare for the potential spread of these races into South America, we aimed to identify genomic regions responsible for resistance to Ug99 race group in germplasm adapted to South America. Two RIL populations from a cross between a stem rust susceptible parent “Baguette 13” and resistant local parents “INIA Tero” and “BR23//CEP19/PF85490” were developed. Phenotypical evaluation was completed at the seedling stage in Uruguay and under field conditions in Uruguay and Kenya. Both RIL populations were genotyped using the GBS approach. Besides Sr24, three other resistance loci in “INIA Tero” were detected on chromosomes 2B, 6A, and 7B. All four QTL were effective to local races, whereas only the QTL on chromosome 2B was effective against the Ug99 race group. Besides Sr31, “BR23//CEP19/PF85490” also carries two other stem rust resistance loci on chromosomes 2B and 6A. All three explained the resistance in Uruguay, while only the QTL on 2B was effective to Ug99 in Kenya. The physical location suggested that the QTL identified on chromosome 2B in both populations may correspond to Sr28, which was confirmed using specific molecular markers. Further studies are needed to determine the relationship between QTL for resistance to local races identified on chromosomes 6A and 7B and previously reported resistance genes and QTL. The results of this study are highly relevant for breeding wheat cultivars with diverse and durable resistance to stem rust.