Structural and functional partitioning of bread wheat chromosome 3B

Wheat genomics: genomes, pangenomes, and beyond

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.

Evolutionary History of the DD41D Family of Tc1/Mariner Transposons in Two Mayetiola Species

Tc1/mariner elements are ubiquitous in eukaryotic genomes including insects. They are diverse and divided into families and sub-families. The DD34D family including mauritiana and irritans subfamilies have already been identified in two closely related species of Cecidomyiids M. destructor and M. hordei. In the current study the de novo and similarity-based methods allowed the identification for the first time of seven consensuses in M. destructor and two consensuses in M. hordei belonging to DD41D family whereas the in vitro method allowed the amplification of two and three elements in these two species respectively. Most of identified elements accumulated different mutations and long deletions spanning the N-terminal region of the transposase. Phylogenetic analyses showed that the DD41D elements were clustered in two groups belonging to rosa and Long-TIR subfamilies. The age estimation of the last transposition events of the identified Tc1/mariner elements in M. destructor showed different evolutionary histories. Indeed, irritans elements have oscillated between periods of silencing and reappearance while rosa and mauritiana elements have shown regular activity with large recent bursts. The study of insertion sites showed that they are mostly intronic and that some recently transposed elements occurred in genes linked to putative DNA-binding domains and enzymes involved in metabolic chains. Thus, this study gave evidence of the existence of DD41D family in two Mayetiola species and an insight on their evolutionary history.

Harnessing landrace diversity empowers wheat breeding

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.

LEAFY and WAPO1 jointly regulate spikelet number per spike and floret development in wheat

In wheat, the transition of the inflorescence meristem to a terminal spikelet (IM→TS) determines the spikelet number per spike (SNS), an important yield component. In this study, we demonstrate that the plant-specific transcription factor LEAFY (LFY) physically and genetically interacts with WHEAT ORTHOLOG OF APO1 (WAPO1) to regulate SNS and floret development. Loss-of-function mutations in either or both genes result in significant and similar reductions in SNS, as a result of a reduction in the rate of spikelet meristem formation per day. SNS is also modulated by significant genetic interactions between LFY and the SQUAMOSA MADS-box genes VRN1 and FUL2, which promote the IM→TS transition. Single-molecule fluorescence in situ hybridization revealed a downregulation of LFY and upregulation of the SQUAMOSA MADS-box genes in the distal part of the developing spike during the IM→TS transition, supporting their opposite roles in the regulation of SNS in wheat. Concurrently, the overlap of LFY and WAPO1 transcription domains in the developing spikelets contributes to normal floret development. Understanding the genetic network regulating SNS is a necessary first step to engineer this important agronomic trait.

Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine

We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.

Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.

Cloning a novel reduced-height (Rht) gene TaOSCA1.4 from a QTL in wheat

Reducing plant height (PH) is one of the core contents of the "Green Revolution", which began in the 1960s in wheat. A number of 27 reduced-height (Rht) genes have been identified and a great number of quantitative trait loci (QTLs) for PH have been mapped on all 21 chromosomes. Nonetheless, only several genes regulated PH have been cloned. In this study, we found the interval of QTL QPh-1B included an EST-SSR marker swes1079. According to the sequence of swes1079, we cloned the TaOSCA1.4 gene. We developed a CAPS marker to analyze the variation across a natural population. The result showed that the PH was significantly different between the two haplotypes of TaOSCA1.4-1B under most of the 12 environments and the average values of irrigation and rainfed conditions. This result further demonstrated that TaOSCA1.4 was associated with PH. Then, we validated the TaOSCA1.4 via RNAi technology. The average PHs of the wild-type (WT), RNAi lines 1 (Ri-1) and 2 (Ri-2) were 94.6, 83.6 and 79.2 cm, respectively, with significant differences between the WT and Ri-1 and Ri-2. This result indicated that the TaOSCA1.4 gene controls PH. TaOSCA1.4 is a constitutively expressed gene and its protein localizes to the cell membrane. TaOSCA1.4 gene is a member of the OSCA gene family, which regulates intracellular Ca2+ concentration. We hypothesized that knock down mutants of TaOSCA1.4 gene reduced regulatory ability of Ca2+, thus reducing the PH. Furthermore, the cell lengths of the knock down mutants are not significantly different than that of WT. We speculate that TaOSCA1.4 gene is not directly associated with gibberellin (GA), which should be a novel mechanism for a wheat Rht gene.

An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.

Distinct growth patterns in seedling and tillering wheat plants suggests a developmentally restricted role of HYD2 in salt-stress response

KEY MESSAGE

Mutants lacking functional HYD2 homoeologs showed improved seedling growth, but comparable or increased susceptibility to salt stress in tillering plants, suggesting a developmentally restricted role of HYD2 in salt response. Salinity stress threatens global food security by reducing the yield of staple crops such as wheat (Triticum ssp.). Understanding how wheat responds to salinity stress is crucial for developing climate resilient varieties. In this study, we examined the interplay between carotenoid metabolism and the response to salt (NaCl) stress, a specific form of salinity stress, in tetraploid wheat plants with mutations in carotenoid β-hydroxylase 1 (HYD1) and HYD2. Our investigation encompassed both the vulnerable seedling stage and the more developed tillering stage of wheat plant growth. Mutant combinations lacking functional HYD2 homoeologs, including hyd-A2 hyd-B2, hyd-A1 hyd-A2 hyd-B2, hyd-B1 hyd-A2 hyd-B2, and hyd-A1 hyd-B1 hyd-A2 hyd-B2, had longer first true leaves and slightly enhanced root growth during germination under salt stress compared to the segregate wild-type (control) plants. Interestingly, these mutant seedlings also showed decreased levels of neoxanthin and violaxanthin (xanthophylls derived from β-carotene) and an increase in β-carotene in roots. However, tillering hyd mutant and segregate wild-type plants generally did not differ in their height, tiller count, and biomass production under acute or prolonged salt stress, except for decreases in these parameters observed in the hyd-A1 hyd-B1 hyd-A2 hyd-B2 mutant that indicate its heightened susceptibility to salt stress. Taken together, these findings suggest a significant, yet developmentally restricted role of HYD2 homoeologs in salt-stress response in tetraploid wheat. They also show that hyd-A2 hyd-B2 mutant plants, previously demonstrated for possessing enriched nutritional (β-carotene) content, maintain an unimpaired ability to withstand salt stress.

A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat

The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.

FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis

Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1-3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position. We analysed figl1 mutants and virus-induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid. FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1-fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals. Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding.

Investigation of two-pore K+ (TPK) channels in Triticum aestivum L. suggests their role in stress response

Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.

Bioinformatic Identification and Expression Analyses of the MAPK-MAP4K Gene Family Reveal a Putative Functional MAP4K10-MAP3K7/8-MAP2K1/11-MAPK3/6 Cascade in Wheat (Triticum aestivum L.)

The mitogen-activated protein kinase (MAPK) cascades act as crucial signaling modules that regulate plant growth and development, response to biotic/abiotic stresses, and plant immunity. MAP3Ks can be activated through MAP4K phosphorylation in non-plant systems, but this has not been reported in plants to date. Here, we identified a total of 234 putative TaMAPK family members in wheat (Triticum aestivum L.). They included 48 MAPKs, 17 MAP2Ks, 144 MAP3Ks, and 25 MAP4Ks. We conducted systematic analyses of the evolution, domain conservation, interaction networks, and expression profiles of these TaMAPK-TaMAP4K (representing TaMAPK, TaMAP2K, TaMAP3K, and TaMAP4K) kinase family members. The 234 TaMAPK-TaMAP4Ks are distributed on 21 chromosomes and one unknown linkage group (Un). Notably, 25 of these TaMAP4K family members possessed the conserved motifs of MAP4K genes, including glycine-rich motif, invariant lysine (K) motif, HRD motif, DFG motif, and signature motif. TaMAPK3 and 6, and TaMAP4K10/24 were shown to be strongly expressed not only throughout the growth and development stages but also in response to drought or heat stress. The bioinformatics analyses and qRT-PCR results suggested that wheat may activate the MAP4K10-MEKK7-MAP2K11-MAPK6 pathway to increase drought resistance in wheat, and the MAP4K10-MAP3K8-MAP2K1/11-MAPK3 pathway may be involved in plant growth. In general, our work identified members of the MAPK-MAP4K cascade in wheat and profiled their potential roles during their response to abiotic stresses and plant growth based on their expression pattern. The characterized cascades might be good candidates for future crop improvement and molecular breeding.

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics, influencing the overall distribution and frequency of crossovers. Here we show how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species with diffused centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is distally biased, in sharp contrast to the diffused distribution of hundreds of centromeric units and (epi)genomic features. Remarkably, we found that crossovers were abolished inside centromeric units but not in their proximity, indicating the absence of a canonical centromere effect. We further propose that telomere-led synapsis of homologues is the feature that best explains the observed recombination landscape. Our results hint at the primary influence of mechanistic features of meiotic pairing and synapsis rather than (epi)genomic features and centromere organization in determining the distally biased crossover distribution in R. breviuscula, whereas centromeres and (epi)genetic properties only affect crossover positioning locally.

TaRECQ4 contributes to maintain both homologous and homoeologous recombination during wheat meiosis

Introduction

Meiotic recombination (or crossover, CO) is essential for gamete fertility as well as for alleles and genes reshuffling that is at the heart of plant breeding. However, CO remains a limited event, which strongly hampers the rapid production of original and improved cultivars. RecQ4 is a gene encoding a helicase protein that, when mutated, contributes to improve recombination rate in all species where it has been evaluated so far.

Methods

In this study, we developed wheat (Triticum aestivum L.) triple mutant (TM) for the three homoeologous copies of TaRecQ4 as well as mutants for two copies and heterozygous for the last one (Htz-A, Htz-B, Htz-D).

Results

Phenotypic observation revealed a significant reduction of fertility and pollen viability in TM and Htz-B plants compared to wild type plants suggesting major defects during meiosis. Cytogenetic analyses of these plants showed that complete absence of TaRecQ4 as observed in TM plants, leads to chromosome fragmentation during the pachytene stage, resulting in problems in the segregation of chromosomes during meiosis. Htz-A and Htz-D mutants had an almost normal meiotic progression indicating that both TaRecQ4-A and TaRecQ4-D copies are functional and that there is no dosage effect for TaRecQ4 in bread wheat. On the contrary, the TaRecQ4-B copy seems knocked-out, probably because of a SNP leading to a Threonine>Alanine change at position 539 (T539A) of the protein, that occurs in the crucial helicase ATP bind/DEAD/ResIII domain which unwinds nucleic acids. Occurrence of numerous multivalents in TM plants suggests that TaRecQ4 could also play a role in the control of homoeologous recombination.

Discussion

These findings provide a foundation for further molecular investigations into wheat meiosis regulation to fully understand the underlying mechanisms of how TaRecQ4 affects chiasma formation, as well as to identify ways to mitigate these defects and enhance both homologous and homoeologous recombination efficiency in wheat.

Genome-wide identification and comprehensive analysis of the phytochrome-interacting factor (PIF) gene family in wheat

Phytochrome-interacting factors (PIFs) are essential transcription factors for plant growth, development, and stress responses. Although PIF genes have been extensively studied in many plant species, they have not been thoroughly investigated in wheat. Here, we identified 18 PIF genes in cultivated hexaploid wheat (Triticum aestivum L). Phylogenetic analysis, exon-intron structures, and motif compositions revealed the presence of four distinct groups of TaPIFs. Genome-wide collinearity analysis of PIF genes revealed the evolutionary history of PIFs in wheat, Oryza sativa, and Brachypodium distachyon. Cis-regulatory element analysis suggested that TaPIF genes indicated participated in plant development and stress responses. Subcellular localization assays indicated that TaPIF2-1B and TaPIF4-5B were transcriptionally active. Both were found to be localized to the nucleus. Gene expression analyses demonstrated that TaPIFs were primarily expressed in the leaves and were induced by various biotic and abiotic stresses and phytohormone treatments. This study provides new insights into PIF-mediated stress responses and lays a strong foundation for future investigation of PIF genes in wheat.

Dual RNA-sequencing of Fusarium head blight resistance in winter wheat

Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.

Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat

Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their clustering into three groups, which are also related to the subcellular localization in the peroxisome matrix, peroxisome membrane, and chloroplast. Each TaMDHAR protein consisted of two conserved domains; Pyr_redox and Pyr_redox_2 of the pyridine nucleotide disulfide oxidoreductase family. The occurrence of diverse groups of cis-regulatory elements in the promoter region and their interaction with numerous transcription factors suggest assorted functions of TaMDHARs in growth and development and in light, phytohormones, and stress responses. Expression analysis in various tissues further revealed their importance in vegetative and reproductive development. In addition, the differential gene expression and enhanced enzyme activity during drought, heat, and salt treatments exposed their role in abiotic stress response. Interaction of MDHARs with various antioxidant enzymes and biochemicals related to the ascorbate-glutathione cycle exposed their synchronized functioning. Interaction with auxin indicated the probability of cross-talk between antioxidants and auxin signaling. The miR168a, miR169, miR172 and others interaction with various TaMDHARs further directed their association with developmental processes and stress responses. The current study provides extensive information about the importance of TaMDHARs, moreover, the precise role of each gene needs to be established in future studies.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

Comparison of genomic-enabled cross selection criteria for the improvement of inbred line breeding populations

A crucial step in inbred plant breeding is the choice of mating design to derive high-performing inbred varieties while also maintaining a competitive breeding population to secure sufficient genetic gain in future generations. In practice, the mating design usually relies on crosses involving the best parental inbred lines to ensure high mean progeny performance. This excludes crosses involving lower performing but more complementary parents in terms of favorable alleles. We predicted the ability of crosses to produce putative outstanding progenies (high mean and high variance progeny distribution) using genomic prediction models. This study compared the benefits and drawbacks of 7 genomic cross selection criteria (CSC) in terms of genetic gain for 1 trait and genetic diversity in the next generation. Six CSC were already published, and we propose an improved CSC that can estimate the proportion of progeny above a threshold defined for the whole mating plan. We simulated mating designs optimized using different CSC. The 835 elite parents came from a real breeding program and were evaluated between 2000 and 2016. We applied constraints on parental contributions and genetic similarities between selected parents according to usual breeder practices. Our results showed that CSC based on progeny variance estimation increased the genetic value of superior progenies by up to 5% in the next generation compared to CSC based on the progeny mean estimation (i.e. parental genetic values) alone. It also increased the genetic gain (up to 4%) and/or maintained more genetic diversity at QTLs (up to 4% more genic variance when the marker effects were perfectly estimated).

Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike

KEY MESSAGE

The wheat transcription factor bZIPC1 interacts with FT2 and affects spikelet and grain number per spike. We identified a natural allele with positive effects on these two economically important traits. Loss-of-function mutations and natural variation in the gene FLOWERING LOCUS T2 (FT2) in wheat have previously been shown to affect spikelet number per spike (SNS). However, while other FT-like wheat proteins interact with bZIP-containing transcription factors from the A-group, FT2 does not interact with any of them. In this study, we used a yeast-two-hybrid screen with FT2 as bait and identified a grass-specific bZIP-containing transcription factor from the C-group, designated here as bZIPC1. Within the C-group, we identified four clades including wheat proteins that show Y2H interactions with different sets of FT-like and CEN-like encoded proteins. bZIPC1 and FT2 expression partially overlap in the developing spike, including the inflorescence meristem. Combined loss-of-function mutations in bZIPC-A1 and bZIPC-B1 (bzipc1) in tetraploid wheat resulted in a drastic reduction in SNS with a limited effect on heading date. Analysis of natural variation in the bZIPC-B1 (TraesCS5B02G444100) region revealed three major haplotypes (H1-H3), with the H1 haplotype showing significantly higher SNS, grain number per spike and grain weight per spike than both the H2 and H3 haplotypes. The favorable effect of the H1 haplotype was also supported by its increased frequency from the ancestral cultivated tetraploids to the modern tetraploid and hexaploid wheat varieties. We developed markers for the two non-synonymous SNPs that differentiate the bZIPC-B1b allele in the H1 haplotype from the ancestral bZIPC-B1a allele present in all other haplotypes. These diagnostic markers are useful tools to accelerate the deployment of the favorable bZIPC-B1b allele in pasta and bread wheat breeding programs.

Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks

Analysis of eukaryotic genomes requires the detection and classification of transposable elements (TEs), a crucial but complex and time-consuming task. To improve the performance of tools that accomplish these tasks, Machine Learning approaches (ML) that leverage computer resources, such as GPUs (Graphical Processing Unit) and multiple CPU (Central Processing Unit) cores, have been adopted. However, until now, the use of ML techniques has mostly been limited to classification of TEs. Herein, a detection-classification strategy (named YORO) based on convolutional neural networks is adapted from computer vision (YOLO) to genomics. This approach enables the detection of genomic objects through the prediction of the position, length, and classification in large DNA sequences such as fully sequenced genomes. As a proof of concept, the internal protein-coding domains of LTR-retrotransposons are used to train the proposed neural network. Precision, recall, accuracy, F1-score, execution times and time ratios, as well as several graphical representations were used as metrics to measure performance. These promising results open the door for a new generation of Deep Learning tools for genomics. YORO architecture is available at https://github.com/simonorozcoarias/YORO.

Multi-target genome editing reduces polyphenol oxidase activity in wheat (Triticum aestivum L.) grains

Introduction

Polyphenol oxidases (PPO) are dual activity metalloenzymes that catalyse the production of quinones. In plants, PPO activity may contribute to biotic stress resistance and secondary metabolism but is undesirable for food producers because it causes the discolouration and changes in flavour profiles of products during post-harvest processing. In wheat (Triticum aestivum L.), PPO released from the aleurone layer of the grain during milling results in the discolouration of flour, dough, and end-use products, reducing their value. Loss-of-function mutations in the PPO1 and PPO2 paralogous genes on homoeologous group 2 chromosomes confer reduced PPO activity in the wheat grain. However, limited natural variation and the proximity of these genes complicates the selection of extremely low-PPO wheat varieties by recombination. The goal of the current study was to edit all copies of PPO1 and PPO2 to drive extreme reductions in PPO grain activity in elite wheat varieties.

Results

A CRISPR/Cas9 construct with one single guide RNA (sgRNA) targeting a conserved copper binding domain was used to edit all seven PPO1 and PPO2 genes in the spring wheat cultivar 'Fielder'. Five of the seven edited T1 lines exhibited significant reductions in PPO activity, and T2 lines had PPO activity up to 86.7% lower than wild-type. The same construct was transformed into the elite winter wheat cultivars 'Guardian' and 'Steamboat', which have five PPO1 and PPO2 genes. In these varieties PPO activity was reduced by >90% in both T1 and T2 lines. In all three varieties, dough samples from edited lines exhibited reduced browning.

Discussion

This study demonstrates that multi-target editing at late stages of variety development could complement selection for beneficial alleles in crop breeding programs by inducing novel variation in loci inaccessible to recombination.

Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.

Triticeae crop genome biology: an endless frontier

Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.

QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat

Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of "TN18 × LM6" (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait.

Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei

BACKGROUND

The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however, cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification.

RESULTS

In this work we developed a transgenic INTACT [isolation of nuclei tagged in specific cell types] system in tetraploid wheat for nuclei purifications. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing [ATAC-seq] to identify open chromatin regions in wheat root tip samples. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Importantly, we observed overlap between ATAC-seq peaks and cis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels.

CONCLUSIONS

We have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome.

Identification and validation of two major QTLs for spikelet number per spike in wheat (Triticum aestivum L.)

The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019-2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43-47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97-34.43 Mb), explained 13.97%-45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis-exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.

Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism

At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.

Fine mapping of meiotic crossovers in Brassica oleracea reveals patterns and variations depending on direction and combination of crosses

Meiotic recombination is crucial for assuring proper segregation of parental chromosomes and generation of novel allelic combinations. As this process is tightly regulated, identifying factors influencing rate, and distribution of meiotic crossovers (COs) is of major importance, notably for plant breeding programs. However, high-resolution recombination maps are sparse in most crops including the Brassica genus and knowledge about intraspecific variation and sex differences is lacking. Here, we report fine-scale resolution recombination landscapes for 10 female and 10 male crosses in Brassica oleracea, by analyzing progenies of five large four-way-cross populations from two reciprocally crossed F1s per population. Parents are highly diverse inbred lines representing major crops, including broccoli, cauliflower, cabbage, kohlrabi, and kale. We produced approximately 4.56T Illumina data from 1248 progenies and identified 15 353 CO across the 10 reciprocal crosses, 51.13% of which being mapped to <10 kb. We revealed fairly similar Mb-scale recombination landscapes among all cross combinations and between the sexes, and provided evidence that these landscapes are largely independent of sequence divergence. We evidenced strong influence of gene density and large structural variations on CO formation in B. oleracea. Moreover, we found extensive variations in CO number depending on the direction and combination of the initial parents crossed with, for the first time, a striking interdependency between these factors. These data improve our current knowledge on meiotic recombination and are important for Brassica breeders.

Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat

Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.

Identification, characterization, and rescue of CRISPR/Cas9 generated wheat SPO11-1 mutants

Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage-drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage-drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis-specific DNA double-strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11-1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11-1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11-1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild-type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11-1 with the TaSPO11-1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop.

Transcriptome Profiling of Gossypium anomalum Seedlings Reveals Key Regulators and Metabolic Pathways in Response to Drought Stress

Drought stress is a key limiting factor for cotton (Gossypium spp.) growth, production, development, and production worldwide. Some wild diploid cotton species are remarkably tolerant of water deficit and constitute an important reservoir for understanding the molecular mechanisms of Gossypium spp. drought tolerance and improving cultivated upland cotton. Here, we utilized RNA-Seq technology to characterize the leaf transcriptomes of a wild African diploid cotton species, Gossypium anomalum, under drought stress. A total of 12,322 differentially expressed genes (DEGs) were identified after mapping valid clean reads to the reference genome of G. anomalum, of which 1243 were commonly differentially expressed at all stages of drought stress. These genes were significantly enriched for molecular functions Gene Ontology terms related to cytoskeleton, hydrolase activity, cellular redox, and binding. Additionally, a substantial proportion of enriched biological process terms concerned cell or subcellular processes, while most in the cellular components category concerned membrane function and photosynthesis. An enrichment analysis against the Kyoto Encyclopedia of Genes and Genomes showed the top significantly enriched pathways to be photosynthesis-antenna proteins, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, MAPK signaling pathway, glutathione metabolism, and plant hormone signal transduction. The DEGs also exhibited interestingly significant enrichments for drought stress-induced tandemly repeated genes involved in iron ion binding, oxidoreductase activity, heme binding, and other biological processes. A large number of genes encoding transcription factors, such as MYB, bHLH, ERF, NAC, WRKY, and bZIP, were identified as playing key roles in acclimatizing to drought stress. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in Gossypium spp.

Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Triticum aestivum L.)

Calmodulin (CaM) and calmodulin-like (CML) genes are widely involved in plant growth and development and mediating plant stress tolerance. However, the whole genome scale studies about CaM and CML gene families have not been done in wheat, and the possible functions of most wheat CaM/CML gene members are still unknown. In this study, a total of 18 TaCaM and 230 TaCML gene members were identified in wheat genome. Among these genes, 28 TaCaM/CML gene members have 74 duplicated copies, while 21 genes have 48 transcript variants, resulting in 321 putative TaCaM/CML transcripts totally. Phylogenetic tree analysis showed that they can be classified into 7 subfamilies. Similar gene structures and protein domains can be found in members of the same gene cluster. The TaCaM/CML genes were spread among all 21 chromosomes with unbalanced distributions, while most of the gene clusters contained 3 homoeologous genes located in the same homoeologous chromosome group. Synteny analysis showed that most of TaCaM/CMLs gene members can be found with 1-4 paralogous genes in T. turgidum and Ae. Tauschii. High numbers of cis-acting elements related to plant hormones and stress responses can be observed in the promoters of TaCaM/CMLs. The spatiotemporal expression patterns showed that most of the TaCaM/TaCML genes can be detected in at least one tissue. The expression levels of TaCML17, 21, 30, 50, 59 and 75 in the root or shoot can be up-regulated by abiotic stresses, suggesting that TaCML17, 21, 30, 50, 59 and 75 may be related with responses to abiotic stresses in wheat. The spatiotemporal expression patterns of TaCaM/CML genes indicated they may be involved widely in wheat growth and development. Our results provide important clues for exploring functions of TaCaMs/CMLs in growth and development as well as responses to abiotic stresses in wheat in the future.

Genome-wide analysis of the laccase gene family in wheat and relationship with arbuscular mycorrhizal colonization

We identified 156 laccase genes belonging to 11 subfamilies in the wheat genome, and the natural variation of laccase genes significantly affected the development of wheat-arbuscular mycorrhizal symbiosis. Laccases (LACs) have a variety of functions in plant lignification, cell elongation and stress responses. This study aimed to reveal the phylogeny, chromosomal spatial distribution, coexpression and evolution of LAC genes in the wheat genome and to investigate the possible roles of LAC genes during arbuscular mycorrhizal (AM) symbiosis. The genomic characteristics of LAC genes were analyzed by using bioinformatics analysis methods, and the polymorphisms of LAC genes were analyzed by using a diverse wheat panel composed of 289 wheat cultivars. We identified 156 LAC genes belonging to 11 subfamilies in the wheat genome, and segmental duplication dominated the amplification of the LAC gene family in the wheat genome. LACs are dominantly located in the R2 region of wheat chromosomes. Some LACs are collinear with the characterized LACs in Arabidopsis thaliana or rice. A number of genes encoding transcription factors, kinases, and phosphatases were coexpressed with LAC genes in wheat. TaLACs may be potential targets for some miRNAs. Most TaLACs are mainly expressed in the roots and stems of plants. The expression of TaLACs could be regulated by the inoculation of Fusarium graminearum or AM fungi. The polymorphisms of TaLACs mainly accumulate by random drift instead of by selection. Through candidate gene association analysis, we found that the natural variations in TaLACs significantly affected root colonization by AM fungi. The present study provides useful information for further study of the biological functions of LAC genes in wheat, especially the roles of LAC genes during the development of AM symbiosis.

OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response

The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca²⁺-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.

Tuning of meristem maturation rate increases yield in multiple Triticum aestivum cultivars

Breeding programs aim to improve crop yield and environmental stability for enhanced food security. The principal methodology in breeding for stable yield gain relies on the indirect selection of beneficial genetics by yield evaluation across diverse environmental conditions. This methodology requires substantial resources while delivering a slow pace of yield gain and environmental adaptation. Alternative methods are required to accelerate gain and adaptation, becoming even more imperative in a changing climate. New molecular tools and approaches can enable accelerated creation and deployment of multiple alleles of genes identified to control key traits. With the advent of tools that enable breeding by targeted allelic selection, identifying gene targets associated with an improved crop performance ideotype will become crucial. Previous studies have shown that altered photoperiod regimes increase yield in wheat (Triticum aestivum). In the current study, we have employed such treatments to study the resulting yield ideotype in five spring wheat cultivars. We found that the photoperiod treatment creates a yield ideotype arising from delayed spike establishment rates that are accompanied by increased early shoot expression of TARGET OF EAT1 (TaTOE1) genes. Genes identified in this way could be used for ideotype-based improve crop performance through targeted allele creation and selection in relevant environments.

MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress

Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.

Transcriptional signatures of wheat inflorescence development

In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.

Brachypodium: 20 years as a grass biology model system; the way forward?

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.

The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication

The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number

Understanding meiotic crossover (CO) variation in crops like bread wheat (Triticum aestivum L.) is necessary as COs are essential to create new, original and powerful combinations of genes for traits of agronomical interest. We cytogenetically characterized a set of wheat aneuploid lines missing part or all of chromosome 3B to identify the most influential regions for chiasma formation located on this chromosome. We showed that deletion of the short arm did not change the total number of chiasmata genome-wide, whereas this latter was reduced by ~35% while deleting the long arm. Contrary to what was hypothesized in a previous study, deletion of the long arm does not disturb the initiation of the synaptonemal complex (SC) in early meiotic stages. However, progression of the SC is abnormal, and we never observed its completion when the long arm is deleted. By studying six different deletion lines (missing different parts of the long arm), we revealed that at least two genes located in both the proximal (C-3BL2-0.22) and distal (3BL7-0.63-1.00) deletion bins are involved in the control of chiasmata, each deletion reducing the number of chiasmata by ~15%. We combined sequence analyses of deletion bins with RNA-Seq data derived from meiotic tissues and identified a set of genes for which at least the homoeologous copy on chromosome 3B is expressed and which are involved in DNA processing. Among these genes, eight (CAP-E1/E2, DUO1, MLH1, MPK4, MUS81, RTEL1, SYN4, ZIP4) are known to be involved in the recombination pathway.

TaNAC020 homoeologous genes are associated with higher thousand kernel weight and kernel length in Chinese wheat

NAC proteins constitute one of the largest plant-specific transcription factor (TF) families and play significant roles in plant growth and development. In the present study, three TaNAC020 homoeologous genes located on chromosomes 7A, 7B, and 7D were isolated from wheat (Triticum aestivum L.). TaNAC020s were predominantly expressed in developing grains. The developed transgenic rice lines for TaNAC020-B showed higher starch density and lower amylose contents than those of the wild type (WT). Sequence polymorphism studies showed seven and eight SNPs in TaNAC020-A/B, making three and two haplotypes, respectively. No sequence polymorphism was identified in TaNAC020-D. Association analysis revealed that HAP-2 of TaNAC020-A and TaNAC020-B was the favored haplotype for higher thousand kernel weight and length. Geographic distribution and allelic frequency showed that our favored haplotype experienced strong selection in China, and likewise, diversity increased in TaNAC020s during wheat polyploidization. The results obtained in this study demonstrate that TaNAC020s positively influence starch synthesis and accumulation and are one of the key regulators of the kernel (seed) size and kernel number and have the potential for utilization in wheat breeding to improve grain yield. Molecular markers developed in this study stand instrumental in marker-assisted selection for genetic improvement and germplasm enhancement in wheat.

Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat

Two homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.

Unravelling mechanisms that govern meiotic crossover formation in wheat

Wheat is a major cereal crop that possesses a large allopolyploid genome formed through hybridisation of tetraploid and diploid progenitors. During meiosis, crossovers (COs) are constrained in number to 1–3 per chromosome pair that are predominantly located towards the chromosome ends. This reduces the probability of advantageous traits recombining onto the same chromosome, thus limiting breeding. Therefore, understanding the underlying factors controlling meiotic recombination may provide strategies to unlock the genetic potential in wheat. In this mini-review, we will discuss the factors associated with restricted CO formation in wheat, such as timing of meiotic events, chromatin organisation, pre-meiotic DNA replication and dosage of CO genes, as a means to modulate recombination.

Transcription factor retention through multiple polyploidization steps in wheat

Whole-genome duplication is widespread in plant evolutionary history and is followed by nonrandom gene loss to return to a diploid state. Across multiple angiosperm species, the retained genes tend to be dosage-sensitive regulatory genes such as transcription factors, yet data for younger polyploid species is sparse. Here, we analyzed the retention, expression, and genetic variation in transcription factors in the recent allohexaploid bread wheat (Triticum aestivum L.). By comparing diploid, tetraploid, and hexaploid wheat, we found that, following each of two hybridization and whole-genome duplication events, the proportion of transcription factors in the genome increased. Transcription factors were preferentially retained over other genes as homoeologous groups in tetraploid and hexaploid wheat. Across cultivars, transcription factor homoeologs contained fewer deleterious missense mutations than nontranscription factors, suggesting that transcription factors are maintained as three functional homoeologs in hexaploid wheat populations. Transcription factor homoeologs were more strongly coexpressed than nontranscription factors, indicating conservation of function between homoeologs. We found that the B3, MADS-M-type, and NAC transcription factor families were less likely to have three homoeologs present than other families, which was associated with low expression levels and high levels of tandem duplication. Together, our results show that transcription factors are preferentially retained in polyploid wheat genomes although there is variation between families. Knocking out one transcription factor homoeolog to alter gene dosage, using TILLING or CRISPR, could generate new phenotypes for wheat breeding.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

Pentaploidization Enriches the Genetic Diversity of Wheat by Enhancing the Recombination of AB Genomes

Allohexaploidization and continuous introgression play a key role in the origin and evolution of bread wheat. The genetic bottleneck of bread wheat resulting from limited germplasms involved in the origin and modern breeding may be compensated by gene flow from tetraploid wheat through introgressive hybridization. The inter-ploidy hybridization between hexaploid and tetraploid wheat generates pentaploid hybrids first, which absorbed genetic variations both from hexaploid and tetraploid wheat and have great potential for re-evolution and improvement in bread wheat. Therefore, understanding the effects of the pentaploid hybrid is of apparent significance in our understanding of the historic introgression and in informing breeding. In the current study, two sets of F2 populations of synthetic pentaploid wheat (SPW1 and SPW2) and synthetic hexaploid wheat (SHW1 and SHW2) were created to analyze differences in recombination frequency (RF) of AB genomes and distorted segregation of polymorphic SNP markers through SNP genotyping. Results suggested that (1) the recombination of AB genomes in the SPW populations was about 3- to 4-fold higher than that in the SHW populations, resulting from the significantly (P < 0.01) increased RF between adjacent and linked SNP loci, especially the variations that occurred in a pericentromeric region which would further enrich genetic diversity; (2) the crosses of hexaploid × tetraploid wheat could be an efficient way to produce pentaploid derivatives than the crosses of tetraploid × hexaploid wheat according to the higher germination rate found in the former crosses; (3) the high proportion of distorted segregation loci that skewed in favor of the female parent genotype/allele in the SPW populations might associate with the fitness and survival of the offspring. Based on the presented data, we propose that pentaploid hybrids should increasingly be used in wheat breeding. In addition, the contribution of gene flow from tetraploid wheat to bread wheat mediated by pentaploid introgressive hybridization also was discussed in the re-evolution of bread wheat.

FANCM promotes class I interfering crossovers and suppresses class II non-interfering crossovers in wheat meiosis

FANCM suppresses crossovers in plants by unwinding recombination intermediates. In wheat, crossovers are skewed toward the chromosome ends, thus limiting generation of novel allelic combinations. Here, we observe that FANCM maintains the obligate crossover in tetraploid and hexaploid wheat, thus ensuring that every chromosome pair exhibits at least one crossover, by localizing class I crossover protein HEI10 at pachytene. FANCM also suppresses class II crossovers that increased 2.6-fold in fancm msh5 quadruple mutants. These data are consistent with a role for FANCM in second-end capture of class I designated crossover sites, whilst FANCM is also required to promote formation of non-crossovers. In hexaploid wheat, genetic mapping reveals that crossovers increase by 31% in fancm compared to wild type, indicating that fancm could be an effective tool to accelerate breeding. Crossover rate differences in fancm correlate with wild type crossover distributions, suggesting that chromatin may influence the recombination landscape in similar ways in both wild type and fancm.

The FANCM helicase functions in limiting crossovers (COs) by unwinding inter-homolog repair intermediates. Here, the authors generate null mutants of fancm in tetraploid and hexaploid wheat and show that FANCM promotes class I interfering COs and suppresses class II noninterfering COs in wheat meiosis.