抗病耐逆基因鉴定、智能设计育种、小麦

小麦是我国重要的粮食作物之一, 其高产、稳产对保障我国粮食安全至关重要。由布氏白粉病菌（Blumeria graminis f. sp. tritici, Bgt）引起的白粉病是威胁小麦安全生产的主要病害之一。当前, 小麦白粉病主要通过喷洒化学药剂和改善栽培措施进行防治, 与之相比, 发掘并利用小麦抗白粉病优异基因, 培育抗病品种是控制白粉病流行更为经济、环保和有效的措施。位于小麦5D染色体短臂上的抗白粉病基因Pm2编码一个CC-NBS-LRR蛋白, 其抗性表现优异, 载体材料综合农艺性状优良, 是小麦抗白粉病育种中应用最广泛的基因之一。本文从Pm2基因位点的发现与分子标记定位、等位基因的发掘与利用、基因克隆、功能标记的开发、单倍型分析、无毒基因的研究以及在育种上的应用等方面系统总结了Pm2相关的最新研究进展, 提出了: 1) Pm2不同等位基因抗谱存在差异可能是由遗传背景的不同和其他调控因子以及白粉菌高度杂合所致; 2) 在抗病育种中应当合理布局利用抗白粉病基因Pm2, 从而延长其使用寿命; 3) 深入发掘并利用新的抗病基因及优异等位变异, 加强种质创新, 是保证小麦持久抗性的根本手段。本文为小麦抗白粉病基因Pm2抗病机制的进一步解析和育种应用提供了理论依据。

To excavate the function of MYB transcription factor TaMYB70 in wheat, TaMYB70 gene was isolated using homology cloning strategy. The expression patterns of TaMYB70 under different stresses were examined by quantitative real-time PCR (qRT-PCR). The results showed that the TaMYB70 partial cDNA was 1 272bp and contained an open reading frame of 1 108bp, encoding 335 amino acids. TaMYB70 protein contained two Myb-type HTH DNA binding domains which were helix-turn-helix motifs. The homologous sequence alignment indicated that the TaMYB70 had higher homology with MYB44 from other plants, such as Aegilops tauschii and Brachypodium distachyum (L.). TaMYB70 belongs to the same branch as the 22nd members of the arabidopsis R2R3-MYB transcription factors. The expression of TaMYB70 was upregulated under ABA treatment, and downregulated under PEG and NaCl stresses, and which may be involved in stress response of wheat.

【Objective】 To identify and locate the molecular markers which were stable and significantly correlated to the traits of biomass and N efficiency under different N nutrition levels will help to provide reference for cloning and characterization of the related genes.【Method】A group of 134 wheat varieties (or lines) were used in a two-years (2013 and 2014) hydroponic experiments, in which three treatments applying normal level N, low level N and high level N were set up. Fourteen traits related to biomass and N efficiency were measured, as the respective average values of each treatment in one year and two years. Genome-wide association analysis using 90K SNP molecular markers was carried out for the tested traits by MLM+K+Q mixed linear model. 【Result】 Compared with normal nitrogen treatments, roots, shoots, and plant nitrogen content and nitrogen accumulation were significantly reduced in low nitrogen treatments, while root biomass and root and plant nitrogen efficiency were significantly increased. In high nitrogen treatments, almost all traits are significantly increased. The heritability of all the tested traits were above 40%. According to genome-wide association analysis on the 9 329 SNPs, a total of 838 molecular marker sites were identified associating with 14 traits significantly (P ≤0.001). These markers located on 21 chromosomes, among which 435 (51.91%) molecular marker sites were detected in only one environment, 403 and 8 environment stable sites were identified in at least two or three environments, two environmental stable SNP marker sites were identified in at least four environments. The two stable markers (Kukri_c65481_121 and tplb0025f09_1052) were significantly related to total nitrogen use efficiency of plant (TNUE) and root nitrogen use efficiency (RNUE), respectively. Five multi-trait co-location SNP marker sites which simultaneously associated with at least six traits were located on chromosomes 1A, 1B(2), and 2A(2). Furtherly, candidate gene prediction was conducted in the 214 kb genomic region of 5 SNP sites co-located with 6 traits (biomass and N efficiency traits) and 2 SNP sites associated with multiple environments (4 environments). According to the genome annotation and LD attenuation level, a total of 84 candidate genes were determined. Gene function annotations of these genes were performed using the coding protein types of known cloned nitrogen efficiency genes, candidate gene function annotation information and the use of plant comparative genomics resource library protein sequence homology analysis, 3 candidate genes were initially determined. 【Conclusion】 Different N treatments significantly affected the phenotypic traits of biomass, N efficiency and the expression of related QTLs at seedling stage of wheat. Most SNPs were detected in only one N environment, but there were some locations with relatively strong environmental stability. There was a significant correlation between biomass and N efficiency related traits, and they might be partly controlled by the same QTL/gene. The functions of related candidate genes related to N efficiency and biomass of wheat selected in this paper needed to be further verified.

Wheat yields have continued to increase globally at a steady pace over the past decade despite challenges faced by breeding programs from evolving and migrating races of rust and other wheat disease-inducing fungi. Additionally, pathogens are becoming tolerant to fungicides because of their injudicious use. We highlight the challenges in breeding and deploying resistant varieties and discuss global strategies to protect wheat from diseases. The continuous identification, utilization, and deployment of diverse resistance genes and quantitative trait loci for durable adult plant resistance, supported by precision phenotyping, marker-assisted and genomic selection, real-time pathogen diagnostics, and the rapid diffusion of resistant varieties, are helping to minimize crop losses while enhancing productivity. The potential for genetic engineering, including the introduction of resistance gene cassettes and precise genome editing of susceptibility or resistance genes, has also increased because of the recent acceptance of genetically modified wheat carrying the HB4® drought tolerance gene in some countries.

A rich past of generating and configuring genetic structures in wheat (Triticum aestivum) combined with advances in DNA sequencing, bioinformatics and genome engineering has transformed the field of wheat functional genomics. Cloning a gene from the large and complex wheat genome is no longer unattainable; in the past 5 years alone, the molecular identity of 33 wheat disease resistance genes has been elucidated. The next 15 years will see the cloning of most of the ∼460 known wheat resistance genes and their corresponding effectors. Coupled with mechanistic insights into how resistance genes, effectors and pathogenicity targets interact and are affected by different genetic backgrounds, this will drive systems biology and synthetic engineering studies towards the alluring goal of generating durable disease resistance in wheat.

Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.

Wheat is cultivated across diverse global environments, and its productivity is significantly impacted by various biotic stresses, most importantly but not limited to rust diseases, Fusarium head blight, wheat blast, and powdery mildew. The genetic diversity of modern cultivars has been eroded by domestication and selection, increasing their vulnerability to biotic stress due to uniformity. The rapid spread of new highly virulent and aggressive pathogen strains has exacerbated this situation. Three strategies can be used for enhancing disease resistance through genome editing: introducing resistance (R) gene-mediated resistance, engineering nucleotide-binding leucine-rich repeat receptors (NLRs), and manipulating susceptibility (S) genes to stop pathogens from exploiting these factors to support infection. Utilizing R gene-mediated resistance is the most common strategy for traditional breeding approaches, but the continuous evolution of pathogen effectors can eventually overcome this resistance. Moreover, modifying S genes can confer pleiotropic effects that hinder their use in agriculture. Enhancing disease resistance is paramount for sustainable wheat production and food security, and new tools and strategies are of great importance to the research community. The application of CRISPR-based genome editing provides promise to improve disease resistance, allowing access to a broader range of solutions beyond random mutagenesis or intraspecific variation, unlocking new ways to improve crops, and speeding up resistance breeding. Here, we first summarize the major disease resistance strategies in the context of important wheat diseases and their limitations. Next, we turn our attention to the powerful applications of genome editing technology in creating new wheat varieties against important wheat diseases.

Wheat productivity is threatened by global climate change. In several parts of NW Europe it will get warmer and dryer during the main crop growing period. The resulting likely lower realized on-farm crop yields must be kept by breeding for resistance against already existing and emerging diseases among other measures. Multi-disease resistance will get especially crucial. In this review, we focus on disease resistance breeding approaches in wheat, especially related to rust diseases and Fusarium head blight, because simulation studies of potential future disease risk have shown that these diseases will be increasingly relevant in the future. The long-term changes in disease occurrence must inevitably lead to adjustments of future resistance breeding strategies, whereby stability and durability of disease resistance under heat and water stress will be important in the future. In general, it would be important to focus on non-temperature sensitive resistance genes/QTLs. To conclude, research on the effects of heat and drought stress on disease resistance reactions must be given special attention in the future.

We investigated the genetic variability in wheat for dual-nutrient stress (DNS) tolerance in field conditions due to soil deficiencies in essential nutrients like nitrogen (N) and phosphorus (P). Most studies focus on model plants in controlled environments, but our research addresses DNS tolerance at both field and controlled conditions. Seventy wheat genotypes were evaluated in field under low nutrient conditions (two years each for N and P). Data were subjected to principal component analysis and genotypes clustering by Ward’s method. In selected genotypes, the DNS tolerance mechanisms at morpho-physiological and molecular level were studied under different N and P treatment combinations. Field evaluation under low N and P demonstrated decreased total biomass and grain yield while nutrient use efficiency increased in comparison to their respective controls. The principal component analysis (PCA; PC1 + PC2) accounted for 54.1% (low N) and 56.1% (low P) genetic variability. Among genotypes, the traits like biomass, N and P uptake, root morphology, N assimilation, and acid phosphatase activity were superior in HD2781, while inferior in C306 thereby, confirming the pattern obtained in the field. The expression of candidate genes involved in N and P transport, N assimilation, internal P remobilization, and transcription factors was significantly higher in HD2781 in comparison to C306. Differential gene expression in wheat, particularly in HD2781, enhanced nutrient uptake, assimilation, and internal nutrient reutilization, contributing to dual-nutrient stress tolerance. Recognizing resilient genotypes like HD2781 is crucial for sustaining wheat productivity in low-fertility soils.

Abstract Wheat is a major staple food in the human diet, but its production under current climate scenarios is problematic given the predicted extent of land salinization and the fact that wheat is highly sensitive to soil salinity. This work aims to critically assess previous breeding efforts and the pros and cons of targeting Salt Overly Sensitive 1 (SOS1) and High-affinity K+ Transporter 1 (HKT1) genes to improve salinity stress tolerance in wheat. We argue that overexpressing SOS1 genes encoding Na+/H+ exchangers for Na+ removal from root to the rhizosphere may come with the caveat of increased loading of Na+ into the xylem and its delivery to the shoot, as well as numerous pleiotropic effects. Similarly, targeting HKT1 transporters for removing Na+ from the shoot comes with significant yield penalties due to the high carbon cost of osmotic adjustment; this strategy is also limited by the relatively small capacity of the root to store excessive Na+ without experiencing toxicity symptoms. We suggest that targeting tissue tolerance traits such as K+ retention in mesophyll and vacuolar Na+ sequestration in the shoot will be able to deliver better outcomes. We also call for a better understanding of the structure–function relationships of various isoforms of key proteins involved in maintenance of Na+ and K+ homeostasis and a need for more in-depth physiological studies of wheat species with the DD genome, a key contributor to tissue tolerance traits. Our arguments are supported by a bioinformatic analysis of the number of orthologs for some key genes between hexaploid (AABBDD) and tetraploid (AABB) wheats and their structural differences.

… wheat varieties with new alleles contributing to terminal heat stress tolerance is a top focus in wheat … a detailed understanding of the genetics of heat stress responsive characteristics. …

… key genes and molecular markers associated with iWUE through δ 13 C in wheat; (II) identify drought-adapted wheat lines for breeding applications; and (III) explore genetic diversity …

Salt and drought are the main abiotic stresses that restrict the yield of crops. Peroxidases (PRXs) are involved in various abiotic stress responses. Furthermore, only few wheat PRXs have been characterized in the mechanism of the abiotic stress response. In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III PRX gene family, was cloned and its response to salt stress was characterized. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model for TaPRX-2A, suggesting that occurrence of some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. Quantitative reverse transcription–polymerase chain reaction (qRT–PCR) results showed that TaPRX-2A exhibited relatively higher expression levels in root tissue than those exhibited in leaf and stem tissues. TaPRX-2A expression was also induced by abiotic stresses and hormone treatments such as polyethylene glycol 6000, NaCl, hydrogen peroxide (H2O2), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild-type (WT) plants. Confocal microscopy revealed that TaPRX-2A-eGFP was mainly localized in cell nuclei. Survival rate, relative water content, and shoot length were higher in TaPRX-2A-overexpressing wheat than in the WT wheat, whereas root length was not significantly different. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A-overexpressing wheat compared with those in the WT wheat, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. The expression levels of downstream stress-related genes showed that RD22, TLP4, ABAI, GST22, FeSOD, and CAT exhibited higher expressions in TaPRX-2A-overexpressing wheat than in WT under salt stress. The results show that TaPRX-2A plays a positive role in the response to salt stress by scavenging ROS and regulating stress-related genes.

… However, a more detailed study is required in polyploidy genomes such as wheat, where the control on the gene dosage between three sub-genomes could be checked through …

… In this investigation, the TaNAC22 NAC transcription factor gene was cloned from wheat. … that Cd stress induces a wheat NAC TF gene, TaNAC22. Overexpression of TaNAC22 in wheat …

… and MTA64 significantly reduced wheat spike exsertion length … forest model was optimal for genome selection. Additionally, the … reliable molecular markers for wheat breeding programs. …

… in wheat breeding will help to transform its production and breeding methodologies in coming years. In this article, we highlight the genomic selection … for wheat in the post-genomics era …

Selection for wheat (Triticum aestivum L.) grain quality is often costly and time-consuming since it requires extensive phenotyping in the last phases of development of new lines and cultivars. The development of high-throughput genotyping in the last decade enabled reliable and rapid predictions of breeding values based only on marker information. Genomic selection (GS) is a method that enables the prediction of breeding values of individuals by simultaneously incorporating all available marker information into a model. The success of GS depends on the obtained prediction accuracy, which is influenced by various molecular, genetic, and phenotypic factors, as well as the factors of the selected statistical model. The objectives of this article are to review research on GS for wheat quality done so far and to highlight the key factors affecting prediction accuracy, in order to suggest the most applicable approach in GS for wheat quality traits.

The goal of wheat breeding is the development of superior cultivars tailored to specific environments, and the identification of promising crosses is crucial for the success of breeding programs. Although genomic estimated breeding values were developed to estimate additive effects of genotypes before testing as parents, application has focused on predicting performance of candidate lines, ignoring nonadditive genetic effects. However, nonadditive genetic effects are hypothesized to be especially important in allopolyploid species due to the interaction between homeologous genes. The objectives of this study were to model additive and additive-by-additive epistatic effects to better delineate the genetic architecture of grain yield in wheat and to improve the accuracy of genome-wide predictions. The data set utilized consisted of 3,740 F5:6 experimental lines tested in the K-State wheat breeding program across the years 2016 and 2018. Covariance matrices were calculated based on whole- and sub-genome marker data, and the natural and orthogonal interaction approach was used to estimate variance components for additive and additive-by-additive epistatic effects. Incorporating epistatic effects in additive models resulted in nonorthogonal partitioning of genetic effects but increased total genetic variance and reduced deviance information criteria. Estimation of sub-genome effects indicated that genotypes with the greatest whole-genome effects often combine sub-genomes with intermediate to high effects, suggesting potential for crossing parental lines that have complementary sub-genome effects. Modeling epistasis in either whole-genome or sub-genome models led to a marginal (3%) improvement in genomic prediction accuracy, which could result in significant genetic gains across multiple cycles of breeding.

… rAMP-seq for genomic selection in bread wheat. rAMP-seq is … of genotyped lines in a genomic selection strategy. The high … In addition to genomic selection, wheat rAMP-seq may be …

Conventional wheat-breeding programs involve crossing parental lines and subsequent selfing of the offspring for several generations to obtain inbred lines. Such a breeding program takes more than 8 years to develop a variety. Although wheat-breeding programs have been running for many years, genetic gain has been limited. However, the use of genomic information as selection criterion can increase selection accuracy and that would contribute to increased genetic gain. The main objective of this study was to quantify the increase in genetic gain by implementing genomic selection in traditional wheat-breeding programs. In addition, we investigated the effect of genetic correlation between different traits on genetic gain. A stochastic simulation was used to evaluate wheat-breeding programs that run simultaneously for 25 years with phenotypic or genomic selection. Genetic gain and genetic variance of wheat-breeding program based on phenotypes was compared to the one with genomic selection. Genetic gain from the wheat-breeding program based on genomic estimated breeding values (GEBVs) has tripled compared to phenotypic selection. Genomic selection is a promising strategy for improving genetic gain in wheat-breeding programs.

Diseases are among the most important limiting factors for wheat production. Breeding for fungal diseases of wheat, primarily for rusts and Fusarium head blight (FHB), are major resource consuming activities in most breeding programs which prevent breeders from focusing entirely on improving yield. Breeding for these diseases is challenging because resistance is inherited mostly in a quantitative fashion and is greatly influenced by weather conditions. Recent advances in genomics, phenomics and big-data analysis provide opportunities for accelerating the development of low-cost and efficient selection methods for such complex traits. Genomic selection (GS) may provide opportunities for reducing the time and cost of making selections. By appropriately integrating GS in the breeding workflow, it is possible to select new parents purely based on genomic estimated breeding values before breeding materials are entered into nurseries and field trials. Due to reduced selection cycle time, annual genetic gain for GS is predicted to be two to threefold greater than for a conventional phenotypic selection program. In this paper, we review the recent GS studies focusing on the prediction of resistance to rusts and FHB including those that benefits from modeling multiple phenological traits correlated with the resistance. In addition, we discuss the potential of integrating phenomics and machine learning for evaluating plant disease and the integration of multiple “omics” data in genomic prediction to improve the applicability of GS for disease resistance breeding in wheat.

… The methods outlined previously in this section are based on single-trait genomic selection (STGS… In such cases, multi-trait genomic selection (MTGS)-based methods may provide more …

… selection is a promising alternative or complement to genomic selection in wheat breeding. … (PS) is a recent breeding approach similar to genomic selection (GS) except that genotyping …

There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years.

Background Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63  from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection. Results YR63  exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS _ YR63  and sunCS_67 , positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63  locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63  is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63  within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63  and validated on a panel of Australian bread wheat, durum and triticale cultivars. Conclusions This study highlights YR63  as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63  into elite cultivars through marker-assisted selection. The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.

The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.

Tetraploid wheat (Triticum turgidum L., BBAA), a key pasta crop, serves as an untapped genetic resource with rich genomic diversity for hexaploid bread wheat improvement. Here we de novo assembled 12 genomes spanning all 10 recognized tetraploid wheat (genome BBAA) subspecies, and a graph-based pangenome was constructed. Chromosome rearrangements drove subgenome asymmetry and shaped genomic divergence, with an average of 0.25 million structural variations per accession, predominantly attributable to transposon activity. Using 736 globally distributed tetraploid wheat accessions, we identified locally adapted subgroups with untapped breeding potential and discovered a novel retrotransposon‑induced loss‑of‑function Btr1-A allele responsible for convergent adaptation of non-brittle rachis. Genome-wide association studies identified 287 loci associated with 32 traits. A homeodomain-leucine zipper transcription factor HAT14-B that enhances both spikelet number and grain size was identified. This subspecies-wide pangenome enriches Triticeae AB subgenome resources and facilitates the discovery and application of agronomically important genetic variations. A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning 10 subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.

… stem-resistance gene Sr2 into the wheat cultivar ‘Marquis’ using the landrace ‘Yaroslav 50 … Here, we present a bread wheat pangenome to identify genes lost during modern breeding. …

The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog of the Viviparous-1 (VP-1) gene of maize and was reported to confer resistance to pre-harvest sprouting (PHS) in wheat. In this study, the structure of the TaVP1-B gene was analyzed using the wheat pan-genome consisting of 20 released cultivars (19 wheat are from China), and 3 single nucleotide polymorphisms (SNPs), which were identified at the 496 bp, 524 bp, and 1548 bp of the TaVP1-B CDS region, respectively. Haplotypes analysis showed that these SNPs were in complete linkage disequilibrium and that only two haplotypes designated as hap1 (TGG) and hap2 (GAA) were present. Association analysis between TaVP1-B haplotypes and PHS resistance of the 20 wheat cultivars in four experiment environments revealed that the average PHS resistance of accessions with hap1 was significantly better than that of accessions with hap2, which infers the effects of TaVP1-B on wheat PHS resistance. To further investigate the impacts of alleles at the TaVP1-B locus on PHS resistance, the SNP at 1548 bp of the TaVP1-B CDS region was converted to a KASP marker, which was used for genotyping 304 Chinese wheat cultivars, whose PHS resistance was evaluated in three environments. The average sprouting rates (SRs) of 135 wheat cultivars with the hap1 were significantly lower than the 169 cultivars with the hap2, validating the impacts of TaVP1-B on PHS resistance in Chinese wheat. The present study provided the breeding-friendly marker for functional variants in the TaVP1-B gene, which can be used for genetic improvement of PHS resistance in wheat.

… pangenome paper, more disease-resistance genes [13–15] and other functional genes such as the male sterility gene Ms2 [16,17] and preharvest-sprouting resistance gene MYB10 [18…

Disease resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterise a few handfuls of R genes, but to do so at a scale that would facilitate the breeding and deployment of crops that can recognise the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and pathogen through biparental mapping, mutational genomics and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavour presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. We utilise both the newly constructed gene-based wheat pan-genome and pan-transcriptome, demonstrating variation in the prolamin superfamily and immune-reactive proteins across cultivars. Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

… 5c,d), indicating the highly dynamic PAV of NLR genes due to rapid evolution… genes in the pan-genome, indicating the potential to discover novel disease-resistant genes in future wheat…

… The pan-genome represents the entire set of genes within a … , disease resistance genes are among the 4,873 genes in … worsen, these pools of genetic diversity in the dispensable …

Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. LncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only few model fungi have well-documented inventories of lncRNA. In this study, we apply a machine-learning based pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyzed genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host signals, such as those responses to oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling molecular genetics and functional analyses in an important pathogen. Impact statement Long non-coding RNAs (lncRNAs) serve distinct roles from messenger RNA. Despite not encoding proteins, lncRNAs can control important cellular processes such as growth and response to stress. In fungal pathogens, lncRNAs are particularly interesting because they can influence how pathogens infect and harm their hosts. Yet, only very few fungal pathogens have high-quality repertoires of lncRNA established. Here, we used machine learning to identify lncRNA in the major wheat pathogen Zymoseptoria tritici. We found that lncRNAs are highly active during the early stages of infection, before the pathogen switches to necrotrophic growth. These lncRNAs are mainly located in regions of the genome associated with pathogenicity. The repertoire of expressed lncRNAs varies substantially among individuals highlighting the potential for pathogen adaptation based on variation in lncRNAs. By expanding our knowledge of lncRNAs in important pathogen models, we enable research to comprehensively investigating their roles across fungi.

Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the qPBR1 locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The qPBR1, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.

Summary Pigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers in India and Africa. Here, we present the first pigeon pea pangenome based on 89 accessions mainly from India and the Philippines, showing that there is significant genetic diversity in Philippine individuals that is not present in Indian individuals. Annotation of variable genes suggests that they are associated with self‐fertilization and response to disease. We identified 225 SNPs associated with nine agronomically important traits over three locations and two different time points, with SNPs associated with genes for transcription factors and kinases. These results will lead the way to an improved pigeon pea breeding programme.