Etienne Paux

The agronomical interest of hybrid wheat has long been a matter of debate. Compared to maize where hybrids have been successfully grown for decades, the mixed results obtained in wheat have been attributed at least partially to the lack of heterotic groups. The wheat genome is known to be strongly partitioned and characterized by numerous presence/absence variations and alien introgressions which have not been thoroughly considered in hybrid breeding. The objective was to investigate the relationships between hybrid performance and genomic diversity. For this, we characterized a set of 124 hybrids as well as their 19 female and 16 male parents. Phenotyping for yield and yield components was conducted during two years in three locations. Parental lines were genotyped using a 410 K SNP array as well as through sequence capture of roughly 200,000 loci. This led to the identification of 180 structural variations including presence-absence variations and alien introgressions. Twenty-six of them were associated to hybrid performance through either additivity or dominance effects. While no correlation was observed at the whole genome level, the genetic distance for 25 genomic regions resulting from the structural and functional partitioning of the chromosomes shown positive or negative correlation with agronomic traits including yield. Large introgressions, like the Aegilops ventricosa 2NS-2AS translocation, can correspond to entire chromosomal regions, such as the R1 region, with an impact on yield. Our results suggest hybrid breeding should consider both structural variations and chromosome partitioning rather than maximizing whole-genome genetic distance, and according to genomic regions to combine homozygosity and heterozygosity.

Key message: A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including thePm2agene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

Wheat yellow mosaic virus (WYMV) is a pathogen transmitted into its host’s roots by the soil-borne vector Polymyxa graminis . Ym1 and Ym2 genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that Ym1 and Ym2 act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of Ym1 reduced viral infection incidence, rather than viral titer, while that of Ym2 was ineffective in the leaf. To understand the basis of the root specificity of the Ym2 product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host’s disease response. Ym2 (B37500) and its paralog (B35800) are found in the near-relatives, respectively, Aegilops sharonensi s and Aegilops speltoides (a close relative of the donor of bread wheat’s B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species . Structural diversity in Ym2 has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the Ym2 region has evolved during the polyploidization events leading to the creation of cultivated wheat.

As genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat ( Triticum L.) and other Triticeae species. The core target space includes sequences from two Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.1) and regions of open chromatin identified with ATAC-seq from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of BLASTN searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species.

The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker–trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.

To meet the challenge of feeding almost 10 billion people by 2050, wheat yield has to double by 2050. However, over the past 20 years, yield increase has slowed down and even stagnated in the main producing countries. Following the example of maize, hybrids have been suggested as a solution to overcome yield stagnation in wheat. However, wheat heterosis is still limited and poorly understood. Gaining a better understanding of hybrid vigor holds the key to breed for better varieties. To this aim, we have developed and phenotyped for physiological and agronomic traits an incomplete factorial design consisting of 91 hybrids and their nineteen female and sixteen male parents. Monitoring the plant development with normalized difference vegetation index revealed that 89% of the hybrids including the five higher yielding hybrids had a longer grain filling phase with a delayed senescence that results in larger grain size. This average increase of 7.7% in thousand kernel weight translated to a positive mid-parent heterosis for grain yield for 86% of hybrids. In addition, hybrids displayed a positive grain protein deviation leading to a +4.7% heterosis in protein yield. These results shed light on the physiological bases underlying yield heterosis in wheat, paving new ways to breed for better wheat hybrids.

High-resolution melting analysis (HRM) is a resolutive technique, using PCR amplification and in-tube detection, which is based on the PCR product’s melting analysis. It is a promising technique for breeding analysis, as it does not require dedicated sequencing equipment. It can be performed using QRT-PCR equipment that can be available in small-medium molecular biology laboratories or locally by the breeders, and it does not require an electrophoretic step to analyze the amplified DNA fragments. To develop effective HRM assays, the search for highly polymorphic sites amenable to PCR amplification is a prerequisite, which is not an easy task in wheat due to its genome complexity. The insertion site-based polymorphism markers (ISBPs) are PCR markers designed based on the knowledge of the sequence flanking transposable element (TE) sequences. The two PCR primers are designed with one in the transposable element and the other in the flanking DNA sequence. TEs are very abundant and nested in the wheat genome, with unique (genome-specific) insertion sites that are highly polymorphic. In this work, we analyze the available HRM-ISBP assays for wheat 3B and 4A chromosomes, and update their applications in wheat diversity at drought and heat MQTL loci.

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so‐called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post‐polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat. Core ideas: Only one half of hexaploid wheat genes are in triads, i.e . in a 1:1:1 ratio across subgenomes Triads are likely part of the core genome; dyads and tetrads belong to the dispensable genome Subgenome dominance and biased fractionation are absent in hexaploid wheat Subgenome differences are related to two successive waves of post-polyploid diploidization