Molecular Mapping of Quantitative Trait Loci for Fusarium Head Blight Resistance in the Brazilian Spring Wheat Cultivar "Surpresa".

Fusarium head blight (FHB) is a devastating disease in wheat. The use of resistant germplasm from diverse sources can significantly improve resistance to the disease. "Surpresa" is a Brazilian spring wheat cultivar with moderate FHB resistance, different from currently used sources. In this study, we aimed to identify and map the genetic loci for FHB resistance in Surpresa. A mapping population consisting of 187 recombinant inbred lines (RILs) was developed from a cross between Surpresa and a susceptible spring wheat cultivar, "Wheaton." The population was evaluated for FHB by the point-inoculation method in three greenhouse experiments and four field trials between 2016 and 2018. Mean disease severity for Surpresa and Wheaton was 41.2 and 84.9% across the 3 years of experiments, ranging from 30.3 to 59.1% and 74.3 to 91.4%, respectively. The mean FHB severity of the NILs was 57%, with an overall range from 7 to 100%, suggesting transgressive segregation in the population. The population was genotyped using a two-enzyme genotyping-by-sequencing approach, and a genetic map was constructed with 5,431 single nucleotide polymorphism (SNP) markers. Four QTL for type II resistance were detected on chromosomes 3A, 5A, 6A, and 7A, explaining 10.4-14.4% of the total phenotypic variation. The largest effect QTL was mapped on chromosome 7A and explained 14.4% of the phenotypic variation; however, it co-localized with a QTL governing the days to anthesis trait. A QTL for mycotoxin accumulation was also detected on chromosome 1B, explaining 18.8% of the total phenotypic variation. The QTL for FHB resistance identified in the study may diversify the FHB resistance gene pool and increase overall resistance to the disease in wheat.

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.

QTL mapping of resistance to tan spot induced by race 2 of Pyrenophora tritici-repentis in tetraploid wheat.

KEY MESSAGE: A total of 12 QTL conferring resistance to tan spot induced by a race 2 isolate, 86-124, were identified in three tetraploid wheat mapping populations. Durum is a tetraploid species of wheat and an important food crop. Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is a major foliar disease of both tetraploid durum wheat and hexaploid bread wheat. Understanding the Ptr-wheat interaction and identifying major QTL can facilitate the development of resistant cultivars and effectively mitigate the negative effect of this disease. Over 100 QTL have already been discovered in hexaploid bread wheat, whereas few mapping studies have been conducted in durum wheat. Utilizing resistant resources and identifying novel resistant loci in tetraploid wheat will be beneficial for the development of tan spot-resistant durum varieties. In this study, we evaluated four interconnected tetraploid wheat populations for their reactions to the race 2 isolate 86-124, which produces Ptr ToxA. Tsn1, the wheat gene that confers sensitivity to Ptr ToxA, was not associated with tan spot severity in any of the four populations. We found a total of 12 tan spot-resistant QTL among the three mapping populations. The QTL located on chromosomes 3A and 5A were detected in multiple populations and co-localized with race-nonspecific QTL identified in other mapping studies. Together, these QTL can confer high levels of resistance and can be used for the improvement in tan spot resistance in both hexaploid bread and durum wheat breeding. Two QTL on chromosomes 1B and 7A, respectively, were found in one population when inoculated with a ToxA knockout strain 86-124ΔToxA only, indicating that their association with tan spot was induced by other unidentified necrotrophic effectors, but under the absence of Ptr ToxA. In addition to removal of the known dominant susceptibility genes, integrating major race-nonspecific resistance loci like the QTL identified on chromosome 3A and 5A in this study could confer high and stable tan spot resistance in durum wheat.

Genetic Mapping and Prediction Analysis of FHB Resistance in a Hard Red Spring Wheat Breeding Population.

Fusarium head blight (FHB) is one of the most destructive diseases in wheat worldwide. Breeding for FHB resistance is hampered by its complex genetic architecture, large genotype by environment interaction, and high cost of phenotype screening. Genomic selection (GS) is a powerful tool to enhance improvement of complex traits such as FHB resistance. The objectives of this study were to (1) investigate the genetic architecture of FHB resistance in a North Dakota State University (NDSU) hard red spring wheat breeding population, (2) test if the major QTL Fhb1 and Fhb5 play an important role in this breeding population; and (3) assess the potential of GS to enhance breeding efficiency of FHB resistance. A total of 439 elite spring wheat breeding lines from six breeding cycles were genotyped using genotyping-by-sequencing (GBS) and 102,147 SNP markers were obtained. Evaluation of FHB severity was conducted in 10 unbalanced field trials across multiple years and locations. One QTL for FHB resistance was identified and located on chromosome arm 1AL, explaining 5.3% of total phenotypic variation. The major type II resistance QTL Fhb1 only explained 3.1% of total phenotypic variation and the QTL Fhb5 was not significantly associated with FHB resistance in this breeding population. Our results suggest that integration of many genes with medium/minor effects in this breeding population should provide stable FHB resistance. Genomic prediction accuracies of 0.22-0.44 were obtained when predicting over breeding cycles in this study, indicating the potential of GS to enhance the improvement of FHB resistance.

Genome-Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations.

Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. The aim of this study was to identify major quality trait quantitative trait loci (QTL) for marker-assisted selection (MAS) and to explore potential application of genomic selection (GS) in a durum wheat breeding program. In this study, genome-wide association mapping was conducted for five quality traits using 1184 lines from the North Dakota State University (NDSU) durum wheat breeding program. Several QTL associated with test weight, semolina color, and gluten strength were identified. Genomic selection models were developed and forward prediction accuracies of 0.27 to 0.66 were obtained for the five quality traits. Our results show the potential for grain and semolina quality traits to be selected more efficiently through MAS and GS with further refinement. Considerable opportunity exists to extend these techniques to other traits such as grain yield and agronomic characteristics, further improving breeding efficiency in durum cultivar development.

Dissecting Plant Chromosomes by the Use of Ionizing Radiation.

Radiation treatment of genomes is used to generate chromosome breaks for numerous applications. This protocol describes the preparation of seeds and the determination of the optimal level of irradiation dosage for the creation of a radiation hybrid (RH) population. These RH lines can be used to generate high-resolution physical maps for the assembly of sequenced genomes as well as the fine mapping of genes. This procedure can also be used for mutation breeding and forward/reverse genetics.

Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants.

Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines.

Infestation and Quantification of Ochratoxigenic Fungi in Barley and Wheat Naturally Contaminated with Ochratoxin A.

Cereal grains are a significant source of ochratoxin A (OTA) in the human diet. Multiple ochratoxigenic Aspergillus and Penicillium spp. have been reported as contaminants on various cereal grains around the world, although relatively few species dominate in any given location. Efforts to mitigate the risk of fungal contamination and OTA accumulation can be made pre- and postharvest. Still, a rapid and reliable screening method is sought that can be used to predict the OTA level of a sample and to inform risk assessments prior to processing. In this study, we assessed the efficacy of two OTA-related indices for OTA level prediction. Infestation rates were determined by direct plating for freshly harvested and stored barley, durum, and hard red spring wheat samples (n = 139) with known OTA levels. Presumptive ochratoxigenic isolates were tested for their ability to produce OTA. The nonribosomal peptide synthase (otanpsPN) involved in OTA biosynthesis was used to quantify ochratoxigenic fungi in barley and wheat. Viable Penicillium verrucosum was present in 45% of the samples. In total, 62.7% (n = 110) of the P. verrucosum isolates tested produced OTA on dichloran yeast extract sucrose 18% glycerol agar. Both OTA level and infestation rate (r = 0.30), as well as OTA level and otanpsPN concentration (r = 0.56), were weakly correlated. Neither infestation rate nor otanpsPN concentration is a reliable predictor of OTA level in a sample.

Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent.

In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.

Analysis of ATP6 sequence diversity in the Triticum-Aegilops species group reveals the crucial role of rearrangement in mitochondrial genome evolution.

Mutation and chromosomal rearrangements are the two main forces of increasing genetic diversity for natural selection to act upon, and ultimately drive the evolutionary process. Although genome evolution is a function of both forces, simultaneously, the ratio of each can be varied among different genomes and genomic regions. It is believed that in plant mitochondrial genome, rearrangements play a more important role than point mutations, but relatively few studies have directly addressed this phenomenon. To address this issue, we isolated and sequenced the ATP6-1 and ATP6-2 genes from 46 different euplasmic and alloplasmic wheat lines. Four different ATP6-1 orthologs were detected, two of them reported for the first time. Expression analysis revealed that all four orthologs are transcriptionally active. Results also indicated that both point mutation and genomic rearrangement are involved in the evolution of ATP6. However, rearrangement is the predominant force that triggers drastic variation. Data also indicated that speciation of domesticated wheat cultivars were simultaneous with the duplication of this gene. These results directly support the notion that rearrangement plays a significant role in driving plant mitochondrial genome evolution.