Genetic Diversity among Wheat Accessions from the USDA National Small Grains Collection

Accessions of common wheat (Triticum aestivum L. subsp. aestivum) from the USDA–ARS National Small Grains Collection (NSGC) are a resource for wheat scientists worldwide. The genetic diversity of the wheat core subset, representing approximately 10% of the collection’s 42,138 T. aestivum accessions, was examined using 390 diversity arrays technology (DArT) markers, 4941 single nucleotide polymorphisms (SNPs), and descriptor data. The marker profiles revealed duplicates, which were excluded to form an informative core (iCore) of 3230 accessions. The iCore population structure and diversity within various subgroups were examined with analysis of molecular variance, principal coordinate analysis, cluster analysis, and by ranking the contribution of individual accessions to overall diversity. Accession groups based on molecular marker data corresponded well to their geographic origin, and population structure was accounted for primarily by differences between Iranian landrace accessions and the rest of the accessions. Accessions classified as breeding lines were overrepresented among those ranked as most diverse based on SNP data, whereas Iranian landraces were underrepresented. Although less diverse as a group, Iranian landrace accessions had a higher frequency of resistance to bunt diseases and Russian wheat aphid compared with the iCore as a whole. The present study provides support for establishing core subsets based on geographic origin of accessions and will be a basis for further study of diversity among NSGC wheats

Genomic targeting and mapping of a gametocidal gene in wheat

Doctor of PhilosophyDepartment of Plant PathologyBikram S. GillSegregation distortion describes the transmission of an allele or alleles of a heterozygous locus at a higher frequency than expected in a Mendelian ratio. From the organism's view, segregation distortion is the preferential retention of chromosomal blocks carrying genes beneficial to its fitness and reproductive viability. In wheat the best studied segregation distortes are those introduced from Aegilops species; these selfish genetic elements are named gametocidal (Gc) genes and the chromosomes carrying them are called Gc chromosomes. This genetic mechanism causes chromosome breakage in gametophytes lacking the Gc carrier chromosome, thus favoring its own retention in the genome. While the mode of action of the Gc genes is not yet known, they have been used extensively in wheat genetics for the development of deletion stocks, a key resource for elucidating the structure of physical regions containing important genes. The objective of this study was to develop the tools necessary to map the Gc2 gene derived from Ae. sharonensis and perform map-based cloning. Extensive physical and genetic mapping located the gametocidal gene on the distal 1% of the 4BL arm present in the T4BS[dot in middle of line]4BL-4S[sh superscript]#1L translocation chromosome. Comparative genomics using rice provided markers distal and proximal to the Gc2 locus; however, synteny broke down at the locus. The characterization of this chromosomal region has provided insight into its recombination frequency, synteny and composition; however, the dynamic architecture of the end of the chromosome has made comparative mapping of this region difficult

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici

Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving Pst population. Studying the pathogenicity mechanisms is critical for understanding how Pst virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. We re-sequenced 7 Pst isolates and included additional 7 previously sequenced isolates to represent balanced virulence/avirulence profiles for several avirulence loci in seretome analyses. We observed an uneven distribution of heterozygosity among the isolates. Secretome comparison of Pst with other rust fungi identified a large portion of species-specific secreted proteins, suggesting that they may have specific roles when interacting with the wheat host. Thirty-two effectors of Pst were identified from its secretome. We identified candidates for Avr genes corresponding to six Yr genes by correlating polymorphisms for effector genes to the virulence/avirulence profiles of the 14 Pst isolates. The putative AvYr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the candidate avirulence gene has produced races virulent to resistance gene Yr76. We conclude that incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate Avr genes in Pst. The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of Pst populations and the co-evolutionary arms race between Pst and wheat. The Avr candidates identified in this study will lead to cloning avirulence genes in Pst, which will enable us to understand molecular mechanisms underlying Pst-wheat interactions, to determine the effectiveness of resistance genes and further to develop durable resistance to stripe rust

Molecular Mechanisms of the Stripe Rust Interaction with Resistant and Susceptible Wheat Genotypes

Rust fungi cause significant damage to wheat production worldwide. In order to mitigate disease impact and improve food security via durable resistance, it is important to understand the molecular basis of host–pathogen interactions. Despite a long history of research and high agricultural importance, still little is known about the interactions between the stripe rust fungus and wheat host on the gene expression level. Here, we present analysis of the molecular interactions between a major wheat pathogen—Puccinia striiformis f. sp. tritici (Pst)—in resistant and susceptible host backgrounds. Using plants with durable nonrace-specific resistance along with fully susceptible ones allowed us to show how gene expression patterns shift in compatible versus incompatible interactions. The pathogen showed significantly greater number and fold changes of overexpressed genes on the resistant host than the susceptible host. Stress-related pathways including MAPK, oxidation–reduction, osmotic stress, and stress granule formation were, almost exclusively, upregulated in the resistant host background, suggesting the requirement of the resistance-countermeasure mechanism facilitated by Pst. In contrast, the susceptible host background allowed for broad overrepresentation of the nutrient uptake pathways. This is the first study focused on the stripe rust pathogen–wheat interactions, on the whole transcriptome level, from the pathogen side. It lays a foundation for the better understanding of the resistant/susceptible hosts versus pathogenic fungus interaction in a broader sense

Molecular Characterization of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Collections from Nine Countries

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. To understand the worldwide distribution of its molecular groups, as well as the diversity, differentiation, and migration of the Pst populations, 567 isolates collected from nine countries (China, Pakistan, Italy, Egypt, Ethiopia, Canada, Mexico, Ecuador, and the U.S.) in 2010–2018 were genotyped using 14 codominant simple sequence repeat markers. A total of 433, including 333 new multi-locus genotypes (MLGs), were identified, which were clustered into ten molecular groups (MGs). The MGs and country-wise populations differed in genetic diversity, heterozygosity, and correlation coefficient between the marker and virulence data. Many isolates from different countries, especially the isolates from Mexico, Ecuador, and the U.S., were found to be identical or closely related MLGs, and some of the MGs were present in all countries, indicating Pst migrations among different countries. The analysis of molecular variance revealed 78% variation among isolates, 12% variation among countries, and 10% variation within countries. Only low levels of differentiation were found by the pairwise comparisons of country populations. Of the 10 MGs, 5 were found to be involved in sexual and/or somatic recombination. Identical and closely related MLGs identified from different countries indicated international migrations. The study provides information on the distributions of various Pst genetic groups in different countries and evidence for the global migrations, which should be useful in understanding the pathogen evolution and in stressing the need for continual monitoring of the disease and pathogen populations at the global scale

Genetic Diversity of Clinal Freezing Tolerance Variation in Winter Wheat Landraces

Wheat (Triticumaestivum L.) is a major cereal crop grown across a wide range of environments, but its productivity around the world is challenged by various biotic and abiotic factors. Wheat landraces from around the world are a source of unexploited genetic diversity that can be essential for modern wheat-breeding programs in search of resistance to abiotic stresses like freezing tolerance. This genetic diversity study of 553 winter wheat landraces based on single-nucleotide polymorphisms (SNPs) revealed separate clusters of landraces related to the latitude of origin. Linkage block analysis revealed genomic regions with specific alleles skewed towards landraces from higher latitudes, suggesting that migration to higher latitudes resulted in the fixing of specific alleles. Electrolyte leakage was used to measure the tolerance of freezing to −14 °C, −16 °C, and −18 °C of 192 landraces. There was a significant negative correlation between latitude and electrolyte leakage, with an R2 value of 0.14, (p < 0.0001), in a regression analysis indicating greater freezing tolerance in landraces from higher latitudes. Genome-wide association studies identified regions in chromosomes 4A and 6A associated with higher latitudes and freezing tolerance, respectively. Landraces with freezing tolerance may be useful in developing new germplasm as novel sources of greater cold hardiness

Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions. •We developed the first set of SNP markers of Puccinia striiformis f. sp. tritici based on secreted protein genes.•We detected significant differences between the eastern and western US P. striiformis f. sp. tritici populations.•We identified high heterozygosity in the pathogen populations with significant differences among epidemiological regions.•We demonstrated the usefulness of SNPs in studying population genetics of wheat stripe rust fungi