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Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.

The population structure and evolution of basidiomycetes like rust fungi are influenced by complex reproductive cycles and dikaryotic life stages where two independent nuclear haplotypes are present in the cell. The ability to alternate between asexual (clonal) and sexual reproduction increases the evolutionary capacity in these species. Furthermore, exchange of intact nuclei (somatic hybridization) in rust fungi can allow for rapid generation of genetic variability outside of the sexual cycle. Puccinia coronata f. sp. avenae (Pca), the causal agent of oat crown rust, is a pathogen of global economic importance that is difficult to control due to rapid breakdown of host genetic resistance. The contribution of sexuality, clonality, and migration to virulence evolution varies across Pca populations. As such, the Pca pathosystem is ideal to address the role of mating type, recombination, mutation, and somatic hybridization in host adaptation. We expanded the existing resources for USA and South African populations by generating whole genome sequencing data of Taiwanese and Australian isolates. An atlas of 30 chromosome-level, fully-phased nuclear haplotypes from six USA isolates and nine Australian isolates was created to capture the genomic composition of key Pca lineages. At the haplotype level, we confirmed previous reports of genetic recombination in the USA population and additionally detected either sexual or cryptic recombination between Australian isolates, contrasting previous evaluations that suggested Pca populations in Australia to be purely clonal. We also identified somatic hybridization events in Pca that are not only associated with significant changes in fitness but also imply intercontinental migration of haplotypes, which provides further impetus for molecular monitoring of rust pathogen populations on a global scale. Author summary: Understanding the contribution of different processes to evolution in multinucleated fungi has been challenging due to the genome and life cycle complexity of these organisms. Rust fungi are pathogens of economically important crops and represent organisms in which the interplay between two independent nuclei impacts host adaptation. Recent advances in genomics in various fungal species including Puccinia coronata f. sp. avenae (Pca), the causal agent of oat crown rust, and the characterization of sizeable collections are allowing to finally dissect the contribution of clonality, sexuality, migration and nuclear exchanges to rust evolution. In this study, we generated 30 nuclear genome references for Pca isolates from USA and Australia to investigate the genetic diversity of this organism. We also explored the genetic relationship among Pca populations from USA, South Africa, Taiwan and Australia. Extensive genetic recombination in the Pca population from USA was confirmed and signatures of genetic recombination were also detected in Australian Pca isolates. We also found evidence that nuclear exchanges occur in Pca and that are associated with changes in host adaptation (virulence). Altogether, our findings make a strong case for monitoring of rust pathogens using molecular tools that allow tracking of individual nuclei. [ABSTRACT FROM AUTHOR]

Salinity stress has significant adverse effects on crop productivity and yield. The primary goal of this study was to quantitatively rank salt tolerance in wheat using hyperspectral imaging. Four wheat lines were assayed in a hydroponic system with control and salt treatments (0 and 200 mM NaCl). Hyperspectral images were captured one day after salt application when there were no visual symptoms. Subsequent to necessary preprocessing tasks, two endmembers, each representing one of the treatment, were identified in each image using successive volume maximization. To simplify image analysis and interpretation, similarity of all pixels to the salt endmember was calculated by a technique proposed in this study, referred to as vector-wise similarity measurement. Using this approach allowed high-dimensional hyperspectral images to be reduced to one-dimensional gray-scale images while retaining all relevant information. Two methods were then utilized to analyze the gray-scale images: minimum difference of pair assignments and Bayesian method. The rankings of both methods were similar and consistent with the expected ranking obtained by conventional phenotyping experiments and historical evidence of salt tolerance. This research highlights the application of machine learning in hyperspectral image analysis for phenotyping of plants in a quantitative, interpretable, and non-invasive manner.

Oat (Avena sativa L.) production worldwide is constrained by crown rust (caused by Puccinia coronata f. sp. avenae), which can cause significant yield losses. The disease is often controlled by spraying fungicides or planting resistant cultivars. Developing host resistance, however, is a challenge due to the high genetic variability of the pathogen. Race‐specific resistance usually succumbs to new races in just a few years. As such, the USDA‐ARS Cereal Disease Laboratory developed mapping populations to identify adult plant resistance (APR) loci from Avena sativa donors. Resistant lines from the mapping populations were selected and crossed with buckthorn (Rhamnus cathartica L.) nursery selection lines BT1020‐1‐1 and BT1021‐1‐1, which possess a different gene for crown rust resistance derived from Avena strigosa. From the crosses, CDL‐111 (Reg. no. GP‐122, PI 702639) and CDL‐167 (Reg. no. GP‐123, PI 702640), both containing three APR quantitative trait loci, were selected as germplasm for resistance breeding. High‐throughput markers for selection were developed and implemented in pyramiding the APR loci. Core Ideas: Oat crown rust is a devastating disease worldwide.Breeding for host resistance is economical and environmentally friendly.Race‐specific crown rust resistance is short lived in the field.Pyramiding APR loci may provide durable resistance to crown rust. [ABSTRACT FROM AUTHOR]

Abstract Background Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Results Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions.

Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop. [ABSTRACT FROM AUTHOR]

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. Key words: ATP6, mitochondria, wheat, rearrangement, duplication. Les mutations et les rearrangements chromosomiques sont les principaux moteurs de l'accroissement de la diversite genetique sur lesquels la selection naturelle peut agir et, ultimement, alimenter revolution. Bien que revolution du genome soit fonction de ces deux moteurs, il faut reconnaitre que l'importance de chacun peut varier parmi les differents genomes et au sein des diverses regions genomiques. On estime qu'au sein du genome mitochondrial les rearrangements joueraient un role plus important que les mutations ponctuelles, mais relativement peu de travaux ont porte sur cette question. Pour y repondre, les auteurs ont isole et sequence les genes ATP6-1 et ATP6-2 provenant de 46 lignees de ble euplasmiques ou alloplasmiques. Quatre orthologues d'ATP6-1 ont ete detectes, deux de ceux-ci etant rapportes pour la premiere fois. L'analyse de l'expression de ces genes a revele que les quatre orthologues sont transcrits. Les resultats ont aussi montre que les mutations ponctuelles et les rearrangements genomiques avaient tous deux joue un role dans revolution d'ATP6. Ce sont les rearrangements qui a cependant ete le principal moteur entrainant des changements majeurs. Les donnees indiquent egalement que la speciation des cultivars de ble domestiques s'est produite simultanement avec la duplication de ce gene. Ces resultats fournissent un appui direct a l'hypothese voulant que les rearrangements jouent un role significatif dans revolution du genome mitochondrial chez les plantes. [Traduit par la Redaction] Mots-cles: ATP6, mitochondries, ble, rearrangement, duplication., Introduction Mitochondria and chloroplast are semiautonomous organelles with their own genomes. They are thought to have originated from an α-proteobacterium and a cyanobacteria, respectively (Knoop 2004). However, after their acquisition [...]

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C = 17 000 Mb), repeat DNA accounts for ~90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RIM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome. Key words: wheat genome, genome-specific marker, repeat DNA junction, retrotransposon, genetic and physical mapping. Chez le ble hexaploide (Triticum aestivum L.) (AABBDD, C = 17 000 Mb), l'ADN repete compte pour ~90 % du genome et les elements transposables (TE) en constituent 60-80 %. En depit de l'evolution dynamique des TE, les travaux menes anterieurement par ces auteurs indiquent que la majorite des TE sont conserves et co-lineaires entre les chromosomes homeologues du ble sur la base de l'observation d'insertions identiques. Dans ce travail, les auteurs ont exploite l'abondance et le caractere unique des insertions chez l'Aegilops tauschii diploide pour developper chez le ble hexaploide des marqueurs specifiques des genomes sur la base des jonctions avec ces ADN repetes (marqueurs RJM pour << repeat DNA junction markers >>). Dans ce travail, tant des sequences terminales de clones BAC que des sequences aleatoires ont ete utilisees pour rechercher des RJM. Des 300 paires d'amorces RJM testees, 269 (90 %) ont amplifie des bandes uniques chez l'Ae. tauschii. De ces 269 paires d'amorces, 260 (97 %) ont amplifie chez le ble hexaploide alors que 3 % n'ont amplifie que chez l'Ae. tauschii. Parmi les amorces RJM qui ont amplifie chez le ble hexaploide, 88 % ont ete assignes avec succes a des chromosomes individuels du genome D. Parmi les 38 amorces RJM situees sur le chromosome 6D, 31 (82 %) ont ete assignees clairement e un segment du chromosome 6D e l'aide de diverses lignees portant des deletions. Ces resultats suggerent que les RJM uniques derives du genome D diploide permettront de faciliter la cartographie genetique, physique et de radiation du genome D chez le ble hexaploide. Mots-cles: genome du ble, marqueur specifique du genome, jonction avec un ADN repete, retrotransposon, cartographie genetique et physique. [Traduit par la Redaction], Introduction In most plants with complex genomes, transposable elements (TEs) and other repetitive sequences are the major identifiable non-genic DNA. TEs have been associated with evolution, specifically the structural and [...]