Analysis of the bread wheat genome using whole-genome shotgun sequencing

Impact of arbuscular mycorrhizal fungi (AMF) on gene expression of some cell wall and membrane elements of wheat (Triticum aestivum L.) under water deficit using transcriptome analysis

Mycorrhizal symbiotic relationship is one of the most common collaborations between plant roots and the arbuscular mycorrhizal fungi (AMF). The first barrier for establishing this symbiosis is plant cell wall which strongly provides protection against biotic and abiotic stresses. The aim of this study was to investigate the gene expression changes in cell wall of wheat root cv. Chamran after inoculation with AMF, Funneliformis mosseae under two different irrigation regimes. To carry out this investigation, total RNA was extracted from the roots of mycorrhizal and non-mycorrhizal plants, and analyzed using RNA-Seq in an Illumina Next-Seq 500 platform. The results showed that symbiotic association between wheat and AMF and irrigation not only affect transcription profile of the plant growth, but also cell wall and membrane components. Of the 114428 genes expressed in wheat roots, the most differentially expressed genes were related to symbiotic plants under water stress. The most differentially expressed genes were observed in carbohydrate metabolic process, lipid metabolic process, cellulose synthase activity, membrane transports, nitrogen compound metabolic process and chitinase activity related genes. Our results indicated alteration in cell wall and membrane composition due to mycorrhization and irrigation regimes might have a noteworthy effect on the plant tolerance to water deficit.

Understanding DNA Methylation Patterns in Wheat

The bread wheat genome is large (17 Gb), allohexaploid, and highly repetitive (80-90% of the genome), which makes genomic and epigenomic analyses expensive to conduct and a challenge to analyze. Here we provide an overview of recent bioinformatic and experimental methods that have been developed to understand DNA methylation patterns in the complex polyploid genome of wheat.

Comparing the Potential of Marker-Assisted Selection and Genomic Prediction for Improving Rust Resistance in Hybrid Wheat

Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with those of genome-wide prediction. The hybrid wheat population included 1,744 single crosses from 236 parental lines. The genotypes were fingerprinted using a 15k SNP array and evaluated for leaf rust and stripe rust resistance in multi-location field trials. We observed a high congruency of putative quantitative trait loci (QTL) for leaf rust resistance between both populations. This was not the case for stripe rust resistance. Accordingly, prediction accuracy of the detected QTL was moderate for leaf rust but low for stripe rust resistance. Genome-wide selection increased the prediction accuracy slightly for stripe rust albeit at a low level but not for leaf rust. Thus, our findings suggest that marker-assisted selection seems to be a robust and efficient tool to improve leaf rust resistance in European wheat hybrids.

Cloning, characterization of TaGS3 and identification of allelic variation associated with kernel traits in wheat (Triticum aestivum L.)

Background

Grain weight is an important yield component. Selection of advanced lines with heavy grains show high grain sink potentials and strong sink activity, which is an increasingly important objective in wheat breeding programs. Rice OsGS3 has been identified as a major quantitative trait locus for both grain weight and grain size. However, allelic variation of GS3 has not been characterized previously in hexaploid wheat.

Results

We cloned 2445, 2393, and 2409 bp sequences of the homologs TaGS3-4A, TaGS3-7A, and TaGS3-7D in wheat ‘Changzhi 6406’, a cultivar that shows high grain weight. The TaGS3 genes each contained five exons and four introns, and encoded a deduced protein of 170, 169, and 169 amino acids, respectively. Phylogenetic analysis of plant GS3 protein sequences revealed GS3 to be a monocotyledon-specific gene and the GS3 proteins were resolved into three classes. The length of the atypical Gγ domain and the cysteine-rich region was conserved within each class and not conserved between classes. A single-nucleotide polymorphism in the fifth exon (at position 1907) of TaGS3-7A leads to an amino acid change (ALA/THR) and showed different frequencies in two pools of Chinese wheat accessions representing extremes in grain weight. Association analysis indicated that the TaGS3-7A-A allele was associated with higher grain weight in the natural population. The TaGS3-7A-A allele was favoured in global modern wheat cultivars but the allelic frequency varied among different wheat-production regions of China, which indicated that this allele is of potential utility to improve wheat grain weight in certain wheat-production areas of China.

Conclusions

The novel molecular information on wheat GS3 homologs and the KASP functional marker designed in this study may be useful in marker-assisted breeding for genetic improvement of wheat.

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

Background

Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences.

Results

We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture.

Conclusions

We show that a capture design employing an “island strategy” can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

BACKGROUND

The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.

RESULTS

To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains.

CONCLUSIONS

Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

Transcriptome-wide alternative splicing modulation during plant-pathogen interactions in wheat

Alternative splicing (AS) enhances the diversities of both transcripts and proteins in eukaryotes, which contribute to stress adaptation. To catalog wheat (Triticum aestivum L.) AS genes, we characterized 45 RNA-seq libraries from wheat seedlings infected by powdery mildew, Blumeria graminis f. sp. tritici (Bgt) or stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst). We discovered that 11.2% and 10.4% of the multiexon genes had AS transcripts during Bgt and Pst infections, respectively. In response to fungal infection, wheat modulated AS not only in disease resistance proteins, but also in splicing related factors. Apart from the stress induced or activated splicing variants by pathogen, the differential expression profiles were fold increased through changing the ratio of full spliced transcripts versus intron retention (IR) transcripts. Comparing AS transcripts produced by the same gene in Bgt with Pst stress, the spliced terminal exons and the stranded introns are independent and different. This demonstrated that differential induction of specific splice variants were activated against two fungal pathogens. The specific induced AS genes in the Pst-resistant plants were enriched in improving the membrane permeability and protein modification ability, whereas gene expression involved in protein translation and transport were strengthened in Pst-susceptible plants.

In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum)

Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.

Early Root Transcriptomic Changes in Wheat Seedlings Colonized by Trichoderma harzianum Under Different Inorganic Nitrogen Supplies

Wheat is one of the most important crops worldwide. The use of plant growth promoting microorganisms, such as those of the genus Trichoderma, constitutes an alternative to chemical fertilizers, since they are cheaper and are not detrimental to the environment. However, the interaction between Trichoderma and wheat plants has been scarcely studied, at least at a molecular level. In the present work, a microarray approach was used to study the early transcriptomic changes induced in wheat roots by Trichoderma harzianum, applied alone or in combination with different concentrations of calcium nitrate [Ca(NO₃)₂], which was last used as nitrogen (N) source. Our results show that T. harzianum causes larger transcriptomic changes than Ca(NO₃)₂ in wheat roots, and such changes are different when plants are challenged with Trichoderma alone or treated with a combination of T. harzianum and Ca(NO₃)₂. Overall, T. harzianum activates the expression of defense-related genes at early stages of the interaction with the roots, while this fungus reduces the expression of genes related to plant growth and development. Moreover, the current study in wheat roots, subjected to the different T. harzianum and Ca(NO₃)₂ combinations, reveals that the number of transcriptomic changes was higher when compared against those caused by the different Ca(NO₃)₂ concentrations than when it was compared against those caused by T. harzianum. N metabolism gene expression changes were in agreement with the levels of nitrate reductase activity measured in plants from Trichoderma plus Ca(NO₃)₂ conditions. Results were also concordant with plant phenotypes, which showed reduced growth at early interaction stages when inoculated with T. harzianum or with its combination with Ca(NO₃)₂ at the lowest dosage. These results were in a good agreement with the recognized role of Trichoderma as an inducer of plant defense.

Fitness benefits of loss of heterozygosity in Saccharomyces hybrids

With two genomes in the same organism, interspecific hybrids have unique fitness opportunities and costs. In both plants and yeasts, wild, pathogenic, and domesticated hybrids may eliminate portions of one parental genome, a phenomenon known as loss of heterozygosity (LOH). Laboratory evolution of hybrid yeast recapitulates these results, with LOH occurring in just a few hundred generations of propagation. In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness effects of hemizygosity are dependent on the species context, the selective environment, and the species origin of the deleted allele. Further, we found that hybrids have a wider distribution of fitness consequences versus matched S. cerevisiae hemizygous diploids. Our results suggest that LOH can be a successful strategy for adaptation of hybrids to new environments, and we identify candidate loci that drive the chromosomal rearrangements observed in evolution of yeast hybrids.

Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes

Centromeres mediate the pairing of homologous chromosomes during meiosis; this pairing is particularly challenging for polyploid plants such as hexaploid bread wheat (Triticum aestivum), as their meiotic machinery must differentiate homologs from similar homoeologs. However, the sequence compositions (especially functional centromeric satellites) and evolutionary history of wheat centromeres are largely unknown. Here, we mapped T. aestivum centromeres by chromatin immunoprecipitation sequencing using antibodies to the centromeric-specific histone H3 variant (CENH3); this identified two types of functional centromeric satellites that are abundant in two of the three subgenomes. These centromeric satellites had unit sizes greater than 500 bp and contained specific sites with highly phased binding to CENH3 nucleosomes. Phylogenetic analysis revealed that the satellites have diverged in the three T. aestivum subgenomes, and the more homogeneous satellite arrays are associated with CENH3. Satellite signals decreased and the degree of satellites variation increased from diploid to hexaploid wheat. Moreover, several T. aestivum centromeres lack satellite repeats. Rearrangements, including local expansion and satellite variations, inversions, and changes in gene expression, occurred during the evolution from diploid to tetraploid and hexaploid wheat. These results reveal the asymmetry in centromere organization among the wheat subgenomes, which may play a role in proper homolog pairing during meiosis.

Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.

Signatures of differential selection in chloroplast genome between japonica and indica

BACKGROUND

The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice.

RESULTS

A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F_ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice.

CONCLUSIONS

Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.

CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome

Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.

Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

BACKGROUND

As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip.

RESULTS

A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport.

CONCLUSIONS

QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.

Genome-wide identification, phylogenetic and expression analysis of the heat shock transcription factor family in bread wheat (Triticum aestivum L.)

Background

Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of Cd in edible tissues, which poses a major hazard to human health. It has been reported that heat shock transcription factor A 4a (HsfA4a) of wheat and rice conferred Cd tolerance by upregulating metallothionein gene expression. However, genome-wide identification, classification, and comparative analysis of the Hsf family in wheat is lacking. Further, because of the promising role of Hsf genes in Cd tolerance, there is need for an understanding of the expression of this family and their functions on wheat under Cd stress. Therefore, here we identify the wheat TaHsf family and to begin to understand the molecular mechanisms mediated by the Hsf family under Cd stress.

Results

We first identified 78 putative Hsf homologs using the latest available wheat genome information, of which 38 belonged to class A, 16 to class B and 24 to class C subfamily. Then, we determined chromosome localizations, gene structures, conserved protein motifs, and phylogenetic relationships of these TaHsfs. Using RNA sequencing data over the course of development, we surveyed expression profiles of these TaHsfs during development and under different abiotic stresses to characterise the regulatory network of this family. Finally, we selected 13 TaHsf genes for expression level verification under Cd stress using qRT-PCR.

Conclusions

To our knowledge, this is the first report of the genome organization, evolutionary features and expression profiles of the wheat Hsf gene family. This work therefore lays the foundation for targeted functional analysis of wheat Hsf genes, and contributes to a better understanding of the roles and regulatory mechanism of wheat Hsfs under Cd stress.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5876-x) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Homoeologous Expression Analysis of PP2C Genes in Wheat (Triticum aestivum L.)

Plant protein phosphatase 2Cs (PP2Cs) play crucial roles in phytohormone signaling, developmental processes, and both biotic and abiotic stress responses. However, little research has been conducted on the PP2C gene family in hexaploid wheat (Triticum aestivum L.), which is an important cereal crop. In this study, a genome-wide investigation of TaPP2C gene family was performed. A total of 257 homoeologs of 95 TaPP2C genes were identified, of which 80% of genes had all the three homoeologs across A, B, and D subgenomes. Domain analysis indicated that all the TaPP2C homoeologs harbored the type 2C phosphatase domains. Based on the phylogenetic analysis, TaPP2Cs were divided into 13 groups (A-M) and 4 single branches, which corresponded to the results of gene structure and protein motif analyses. Results of chromosomal location and synteny relationship analysis of TaPP2C homoeologs revealed that known chromosome translocation events and pericentromeric inversions were responsible for the formation of TaPP2C gene family. Expression patterns of TaPP2C homoeologs in various tissues and under diverse stress conditions were analyzed using publicly available RNA-seq data. The results suggested that TaPP2C genes regulate wheat developmental processes and stress responses. Homoeologous expression patterns of TaPP2C triad homoeologs from A, B, and D subgenomes, revealed expression bias within triads under the normal condition, and variability in expression under different stress treatments. Quantitative real-time PCR (qRT-PCR) analysis of eight TaPP2C genes in group A revealed that they were all up-regulated after abscisic acid treatment. Some genes in group A also responded to other phytohormones such as methyl jasmonate and gibberellin. Yeast two-hybrid assays showed that group A TaPP2Cs also interacted with TaSnRK2.1 and TaSnRK2.2 from subclass II, besides with subclass III TaSnRK2s. TaPP2C135 in group A was transformed into Arabidopsis and germination assay revealed that ectopic expression of TaPP2C135 in Arabidopsis enhanced its tolerance to ABA. Overall, these results enhance our understanding of the function of TaPP2Cs in wheat, and provide novel insights into the roles of group A TaPP2Cs. This information will be useful for in-depth functional analysis of TaPP2Cs in future studies and for wheat breeding.

Cas Endonuclease Technology-A Quantum Leap in the Advancement of Barley and Wheat Genetic Engineering

Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or mutagenic chemicals facilitated dramatically increased mutation rates, which remarkably extended the genetic diversity of crop plants. However, a major drawback of conventionally induced mutagenesis is that genetic alterations occur simultaneously across the whole genome and at very high numbers per individual plant. By contrast, the newly emerging Cas endonuclease technology allows for the induction of mutations at user-defined positions in the plant genome. In fundamental and breeding-oriented research, this opens up unprecedented opportunities for the elucidation of gene functions and the targeted improvement of plant performance. This review covers historical aspects of the development of customizable endonucleases, information on the mechanisms of targeted genome modification, as well as hitherto reported applications of Cas endonuclease technology in barley and wheat that are the agronomically most important members of the temperate cereals. Finally, current trends in the further development of this technology and some ensuing future opportunities for research and biotechnological application are presented.

iTRAQ-Based Quantitative Analysis of Responsive Proteins Under PEG-Induced Drought Stress in Wheat Leaves

Drought is an important abiotic stress that seriously restricts crop productivity. An understanding of drought tolerance mechanisms offers guidance for cultivar improvement. In order to understand how a well-known wheat genotype Jinmai 47 responds to drought, we adopted the iTRAQ and LC/MS approaches and conducted proteomics analysis of leaves after exposure to 20% of polyethylene glycol-6000 (PEG)-induced stress for 4 days. The study identified 176 differentially expressed proteins (DEPs), with 65 (36.5%) of them being up-regulated, and 111 (63.5%) down-regulated. DEPs, located in cellular membranes and cytosol mainly, were involved in stress and redox regulation (51), carbohydrate and energy metabolism (36), amino acid metabolism (24), and biosynthesis of other secondary metabolites (20) primarily. Under drought stress, TCA cycle related proteins were up-regulated. Antioxidant system, signaling system, and nucleic acid metabolism etc. were relatively weakened. In comparison, the metabolism pathways that function in plasma dehydration protection and protein structure protection were strongly enhanced, as indicated by the improved biosynthesis of 2 osmolytes, sucrose and Proline, and strongly up-regulated protective proteins, LEA proteins and chaperones. SUS4, P5CSs, OAT, Rab protein, and Lea14-A were considered to be important candidate proteins, which deserve to be further investigated.

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88-98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.

Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence

A high-resolution genetic linkage map was constructed using the comparative genomics analysis approach and the wheat reference genome, which placed wheat powdery mildew resistance gene Pm52 in a 0.21-cM genetic interval on chromosome arm 2BL. The gene Pm52 confers resistance to powdery mildew and has been previously mapped on chromosome arm 2BL in winter wheat cultivar Liangxing 99. Because of its effectiveness against the disease, this study was initiated to finely map Pm52 using the comparative genomics analysis approach and the wheat reference genomic sequence. Based on the EST sequences that were located in the chromosome region flanking Pm52, four EST-SSR markers were developed, and another nine SSR markers were developed using the comparative genomics technology. These thirteen markers were integrated into a genetic linkage map using an F_2:3 subpopulation of the Liangxing 99 × Zhongzuo 9504 cross. Pm52 was mapped within a 3.2-cM genetic interval in the subpopulation that corresponded to a ~40-Mb genomic interval on chromosome arm 2BL of the Chinese Spring reference genome. The Pm52-flanking markers Xicsl163 and Xicsl62 identified 344 recombinant individuals from 8820 F₂ plants. Nine SSR markers generated from the Chinese Spring genomic interval were incorporated into a high-resolution genetic linkage map, which placed Pm52 in a 0.21-cM genetic interval corresponding to 5.6-Mb genomic region. The constructed high-resolution genetic linkage map will facilitate the map-based cloning of Pm52 and its marker-assisted selection.

Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS

Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders' 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.

A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples

Diverse invertebrate taxa including all 200,000 species of Hymenoptera (ants, bees, wasps and sawflies) have a haplodiploid sex determination system, where females are diploid and males are haploid. Thus, hymenopteran genome projects can make use of DNA from a single haploid male sample, which is assumed advantageous for genome assembly. For the purpose of gene annotation, transcriptome sequencing is usually conducted using RNA from a pool of individuals. We conducted a comparative analysis of genome and transcriptome assembly and annotation methods, using genetic sources of different ploidy: (1) DNA from a haploid male or a diploid female (2) RNA from the same haploid male or a pool of individuals. We predicted that the use of a haploid male as opposed to a diploid female will simplify the genome assembly and gene annotation thanks to the lack of heterozygosity. Using DNA and RNA from the same haploid individual is expected to provide better confidence in transcript-to-genome alignment, and improve the annotation of gene structure in terms of the exon/intron boundaries. The haploid genome assemblies proved to be more contiguous, with both contig and scaffold N50 size at least threefold greater than their diploid counterparts. Completeness evaluation showed mixed results. The SOAPdenovo2 diploid assembly was missing more genes than the haploid assembly. The SPAdes diploid assembly had more complete genes, but a higher level of duplicates, and a greatly overestimated genome size. When aligning the two transcriptomes against the male genome, the male transcriptome gave 2–3% more complete transcripts than the pool transcriptome for genes with comparable expression levels in both transcriptomes. However, this advantage disappears in the final results of the gene annotation pipeline that incorporates evidence from homologous proteins. The RNA pool is still required to obtain the full transcriptome with genes that are expressed in other life stages and castes. In conclusion, the use of a haploid source material for a de novo genome project provides a substantial advantage to the quality of the genome draft and the use of RNA from the same haploid individual for transcriptome to genome alignment provides a minor advantage for genes that are expressed in the adult male.

Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

BACKGROUND

Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations.

RESULTS

We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis.

CONCLUSIONS

This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.

Vector Quantized Spectral Clustering Applied to Whole Genome Sequences of Plants

We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of spectral clustering (SC) and vector quantization (VQ) sampling for grouping genome sequences of plants. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in terms of the input size). Although the combination of SC and VQ is not new, the novelty of our work is in developing the crucial similarity matrix in SC as well as use of k-medoids in VQ, both adapted for the plant genome data. For Soybean, we compare our approach with commonly used techniques like Un-weighted Pair Graph Method with Arithmetic mean (UPGMA) and Neighbor Joining (NJ). Experimental results show that our VQSC outperforms both these techniques significantly in terms of cluster quality (average improvement of 21% over UPGMA and 24% over NJ) as well as time complexity (order of magnitude faster than both UPGMA and NJ).

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

BACKGROUND

Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences.

RESULTS

We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture.

CONCLUSIONS

We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

Establishment of an In Vitro Fertilization System in Wheat (Triticum aestivum L.)

In vitro fertilization (IVF) systems using isolated gametes have been utilized to dissect post-fertilization events in angiosperms, since the female gametophytes of plants are deeply embedded within ovaries. In addition, IVF systems have been used to produce hybrid and polyploid zygotes. Complete IVF systems have been established in maize and rice, two of three major crop species providing the majority of human energy intake. Among those crop species, gametes of wheat have not been used to establish a complete IVF system successfully. In this study, a wheat IVF system was developed to introduce the advantages of this technology to wheat research. Fusion of gametes was performed via a modified electrofusion method, and the fusion product, a zygote, formed a cell wall and two nucleoli. The first division of zygotes was observed 19-27 h after fusion, and the resulting two-celled embryo developed into 10-20-celled globular-like embryos and multicellular club-shaped embryos by 3 and 7-10 d after fusion, respectively. Such zygotic division profiles were mostly consistent with those in the embryo sac, suggesting that the division profile of IVF-produced early embryos reflects that of early embryos in planta. Although the IVF-produced club-shaped embryos did not develop into differentiated embryos but into compact embryonic calli, fertile plants could be regenerated from the embryonic calli, and the seeds harvested from those plants grew normally into seedlings. The IVF system described here might become an important technique for generating new genotypes of wheat and/or new hybrids as well as for investigating fertilization-induced events in wheat.

Changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters

Cis-regulatory elements in promoters are major determinants of binding specificity of transcription factors (TFs) for transcriptional regulation. To improve our understanding of how these short DNA sequences regulate gene expression, synthetic promoters consisting of both classical (CACGTG) and variant G-box core sequences along with different flanking sequences derived from the promoters of three different highly expressing soybean genes, were constructed and used to regulate a green fluorescent protein (gfp) gene. Use of the classical 6-bp G-box provided information on the base level of GFP expression while modifications to the 2-4 flanking bases on either side of the G-box influenced the intensity of gene expression in both transiently transformed lima bean cotyledons and stably transformed soybean hairy roots. The proximal 2-bp sequences on either flank of the G-box significantly affected G-box activity, while the distal 2-bp flanking nucleotides also influenced gene expression albeit with a decreasing effect. Manipulation of the upstream 2- to 4-bp flanking sequence of a G-box variant (GACGTG), found in the proximal region of a relatively weak soybean glycinin promoter, significantly enhanced promoter activity using both transient and stable expression assays, if the G-box variant was first converted into a classical G-box (CACGTG). In addition to increasing our understanding of regulatory element composition and structure, this study shows that minimal targeted changes in native promoter sequences can lead to enhanced gene expression, and suggests that genome editing of the promoter region can result in useful and predictable changes in native gene expression.

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

BACKGROUND

Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences.

RESULTS

We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture.

CONCLUSIONS

We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

Plant genome sequences: past, present, future

The green plants (Viridiplantae) are an essential kingdom of life, responsible via photosynthesis for the majority of global primary production, and directly utilized by humankind for nutrition, animal feed, fuel, clothing, medicine and other purposes. There are an estimated 391 000 species of land plants, in addition to 8000 species of green algae. Their genomes are unusually diverse compared to those of other kingdoms, ranging in size from ∼10 Mb to over 100 Gb. Knowledge of plant genomes initially lagged behind those of other kingdoms but has greatly increased with the development of new technologies for DNA sequencing; bioinformatic analysis, rather than data production, is increasingly the bottleneck to further knowledge. Recent proposals are now contemplating the sequencing, assembly and annotation of the genomes of all of the world's plant species; meanwhile, low coverage sequencing to measure diversity across collections and wild populations has already become commonplace for many species, especially those utilized as crops.

Organization and evolution of the chalcone synthase gene family in bread wheat and relative species

Background

Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species.

Results

The nucleotide sequences of the eight Chs copies in T. aestivum were identified. Among them, two homoeologous sets of the Chs genes were located on the short (Chs-A1, −B1, −D1) and the long (Chs-A4, −B4, −D4) arms of homoeologous group 2 chromosomes. Two paralogous gene copies in the B-genome (Chs-B2, −B3) were located in the distal regions of 2BS chromosome. To clarify the origin of Chs duplications in the B-genome the phylogenetic analysis with the Chs sequences of Triticum and Aegilops species carrying ancestral genomes was conducted. It was estimated that the first duplication event occurred in the genome of the common ancestor of Triticum and Aegilops genera about 10–12 million years ago (MYA), then another copy was formed in the ancestor of the B-genome about 6–7 MYA. A homology modeling revealed high sequence similarity of bread wheat CHS enzymes. A number of short deletions in coding regions of some Chs sequences are not expected to have any significant functional effects. Estimation of transcriptional activity of the Chs copies along with a comparative analysis of their promoters structure suggested their functional specialization, which likely contributed to the maintaining of the duplicated Chs genes in wheat genome.

Conclusions

From possible ten Chs copies in bread wheat genome, eight members of this family retained their intact structure and activity, while two copies appear to be lost at the level of diploid and tetraploid ancestors. Transcriptional assay along with a comparative analysis of the cis-regulatory elements revealed their functional diversification. The multiple functions supported by the Chs family are assumed to be a driving force for duplications of the Chs gene and their retention in plant genome.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0727-y) contains supplementary material, which is available to authorized users.

Machine Learning Models for Error Detection in Metagenomics and Polyploid Sequencing Data

Metagenomics studies, as well as genomics studies of polyploid species such as wheat, deal with the analysis of high variation data. Such data contain sequences from similar, but distinct genetic chains. This fact presents an obstacle to analysis and research. In particular, the detection of instrumentation errors during the digitalization of the sequences may be hindered, as they can be indistinguishable from the real biological variation inside the digital data. This can prevent the determination of the correct sequences, while at the same time make variant studies significantly more difficult. This paper details a collection of ML-based models used to distinguish a real variant from an erroneous one. The focus is on using this model directly, but experiments are also done in combination with other predictors that isolate a pool of error candidates.

Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium

BACKGROUND

After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers among them. A telomere-centric reduction model was proposed previously to explain chromosome number reduction. With Brachpodium as an intermediate linking different major lineages of grasses and a model plant of the Pooideae plants, we wonder whether it mediated the evolution from ancestral grass karyotype to Triticeae karyotype.

RESULTS

By inferring the homology among Triticeae, rice, and Brachpodium chromosomes, we reconstructed the evolutionary trajectories of the Triticeae chromosomes. By performing comparative genomics analysis with rice as a reference, we reconstructed the evolutionary trajectories of Pooideae plants, including Ae. Tauschii (2n = 14, DD), barley (2n = 14), Triticum turgidum (2n = 4x = 28, AABB), and Brachypodium (2n = 10). Their extant Pooidea and Brachypodium chromosomes were independently produced after sequential nested chromosome fusions in the last tens of millions of years, respectively, after their split from rice. More frequently than would be expected by chance, in Brachypodium, the 'invading' and 'invaded' chromosomes are homoeologs, originating from duplication of a common ancestral chromosome, that is, with more extensive DNA-level correspondence to one another than random chromosomes, nested chromosome fusion events between homoeologs account for three of seven cases in Brachypodium (P-value≈0.00078). However, this phenomenon was not observed during the formation of other Pooideae chromosomes.

CONCLUSIONS

Notably, we found that the Brachypodium chromosomes formed through exclusively distinctive trajectories from those of Pooideae plants, and were well explained by the telomere-centric model. Our work will contribute to understanding the structural and functional innovation of chromosomes in different Pooideae lineages and beyond.

Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps

Wild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of all modern cultivated tetraploid wheat. Its genome is large (> 10 Gb) and contains over 80% repeated sequences. The successful whole-genome-shotgun assembly of the wild emmer (accession Zavitan) genome sequence (WEW_v1.0) was an important milestone for wheat genomics. In an effort to improve this assembly, an optical map of accession Zavitan was constructed using Bionano Direct Label and Stain (DLS) technology. The map spanned 10.4 Gb. This map and another map produced earlier by us with the Bionano’s Nick Label Repair and Stain (NLRS) technology were used to improve the current wild emmer assembly. The WEW_v1.0 assembly consisted of 151,912 scaffolds. Of them, 3,102 could be confidently aligned on the optical maps. Forty-seven were chimeric. They were disjoined and new scaffolds were assembled with the aid of the optical maps. The total number of scaffolds was reduced from 151,912 to 149,252 and N50 increased from 6.96 Mb to 72.63 Mb. Of the 149,252 scaffolds, 485 scaffolds, which accounted for 97% of the total genome length, were aligned and oriented on genetic maps, and new WEW_v2.0 pseudomolecules were constructed. The new pseudomolecules included 333 scaffolds (68.51 Mb) which were originally unassigned, 226 scaffolds (554.84 Mb) were placed into new locations, and 332 scaffolds (394.83 Mb) were re-oriented. The improved wild emmer genome assembly is an important resource for understanding genomic modification that occurred by domestication.

Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity

In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.

Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting

Pre-harvest sprouting (PHS) is one of the most important factors having adverse effects on yield and grain quality all over the world, particularly in wet harvest conditions. PHS is controlled by both genetic and environmental factors and the interaction of these factors. Breeding varieties with high PHS resistance have important implications for reducing yield loss and improving grain quality. The rapid advancements in the wheat genomic database along with transcriptomic and proteomic technologies have broadened our knowledge for understanding the regulatory mechanism of PHS resistance at transcriptomic and post-transcriptomic levels. In this review, we have described in detail the recent advancements on factors influencing PHS resistance, including grain color, seed dormancy, α-amylase activity, plant hormones (especially abscisic acid and gibberellin), and QTL/genes, which are useful for mining new PHS-resistant genes and developing new molecular markers for multi-gene pyramiding breeding of wheat PHS resistance, and understanding the complicated regulatory mechanism of PHS resistance.

Physical location of tandem repeats in the wheat genome and application for chromosome identification

A general distribution of tandem repeats (TRs) in the wheat genome was predicted and a new web page combined with fluorescence in situ hybridization experiments, and the newly developed Oligo probes will improve the resolution for wheat chromosome identification. Comprehensive sequence analysis of tandem repeats (TR) in the wheat reference genome permits discovery and application of TRs for chromosome identification. Genome-wide localization of TRs was identified in the reference sequences of Chinese Spring using Tandem Repeat Finder (TRF). A database of repeats unit size, array number, and physical coverage length of TRs in the wheat genome was built. The distribution of TRs occupied 3-5% of the wheat chromosomes, with non-random dispersal across the A, B, and D genomes. Three classes of TRs surrounding the predicted genes were compared. An optimized computer-assisted website page B2DSC was constructed for the general distribution and chromosomally enriched zones of TR sequences to be displayed graphically. The physical distribution of predicted TRs in the wheat genome by B2DSC matched well with the corresponding hybridization signals obtained with fluorescence in situ hybridization (FISH). We developed 20 oligonucleotide probes representing 20-60 bp lengths of high copy number of TRs and verified by FISH. An integrated physical map of TR-Oligo probes for wheat chromosome identification was constructed. Our results suggest that the combination of both molecular cytogenetics and genomic research will significantly benefit wheat breeding through chromosome manipulation and engineering.

From markers to genome-based breeding in wheat

Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050. There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality.

Progress in plant genome sequencing: research directions

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

Global status of 47 major wheat loci controlling yield, quality, adaptation and stress resistance selected over the last century

BACKGROUND

Wheat breeding over the last 100 years has increased productivity by adapting genotypes to local conditions, but the genomic changes and selection signals that caused phenotypic change during breeding are essentially unknown. Studying and understanding human selection of multiple important genes controlling key phenotypic traits will promote wheat molecular breeding.

RESULTS

A total of 1152 diverse global wheat materials were genotyped based on KASP markers from 47 genes controlling grain yield, grain quality, adaptation, and stress resistance. Significant phenotypic variations between landraces and modern cultivars were found in 11 adaptive and yield-related traits. Thirty-six improvement-selective favorable alleles, including 22 positive prolonged and 14 negative selection alleles, were identified through comparing frequency spectra. Sus1-7A-Hap-H, Sus1-7B-Hap-T, Sus2-2A-Hap-A, TGW6-A1a, Cwi-4A-Hap-C, vrn-A1, PHS1-PHS+ and Lr34+ were subjected to strong selection, and overwhelmingly strong selection had occurred before improvement selection at Psy-A1b, Psy-B1a or b, Psy-D1a and Cwi-5D-Hap-C. However, Rht-B1b, Rht-D1b and 1BL.1RS were rare or absent in Chinese landraces but present in modern Chinese cultivars and introduced accessions. Importantly, Lr68+, Fhb1+, Wx-B1b and Yr15+, currently existing at a low frequency, should be regarded as further major improvement targets in global wheat breeding. Gene flow analysis showed that introduced cultivars especially from the former USSR and Italy contributed to enriched genetic variation in modern Chinese cultivars.

CONCLUSIONS

This work objectively reports human selection on favorable alleles of multiple crucial genes in Asia, Europe, North America and CIMMYT, and traces the distribution of important genes in global wheat for molecular breeding.

An Exploration of Deep-Learning Based Phenotypic Analysis to Detect Spike Regions in Field Conditions for UK Bread Wheat

Wheat is one of the major crops in the world, with a global demand expected to reach 850 million tons by 2050 that is clearly outpacing current supply. The continual pressure to sustain wheat yield due to the world's growing population under fluctuating climate conditions requires breeders to increase yield and yield stability across environments. We are working to integrate deep learning into field-based phenotypic analysis to assist breeders in this endeavour. We have utilised wheat images collected by distributed CropQuant phenotyping workstations deployed for multiyear field experiments of UK bread wheat varieties. Based on these image series, we have developed a deep-learning based analysis pipeline to segment spike regions from complicated backgrounds. As a first step towards robust measurement of key yield traits in the field, we present a promising approach that employ Fully Convolutional Network (FCN) to perform semantic segmentation of images to segment wheat spike regions. We also demonstrate the benefits of transfer learning through the use of parameters obtained from other image datasets. We found that the FCN architecture had achieved a Mean classification Accuracy (MA) >82% on validation data and >76% on test data and Mean Intersection over Union value (MIoU) >73% on validation data and and >64% on test datasets. Through this phenomics research, we trust our attempt is likely to form a sound foundation for extracting key yield-related traits such as spikes per unit area and spikelet number per spike, which can be used to assist yield-focused wheat breeding objectives in near future.

Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication

Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.

Identification and Characterization of the EXO70 Gene Family in Polyploid Wheat and Related Species

The EXO70 gene family is involved in different biological processes in plants, ranging from plant polar growth to plant immunity. To date, analysis of the EXO70 gene family has been limited in Triticeae species, e.g., hexaploidy Triticum aestivum and its ancestral/related species. By in silico analysis of multiple Triticeae sequence databases, a total of 200 EXO70 members were identified. By homologue cloning approaches, 15 full-length cDNA of EXO70s were cloned from diploid Haynaldia villosa. Phylogenetic relationship analysis of 215 EXO70 members classified them into three groups (EXO70.1, EXO70.2, and EXO70.3) and nine subgroups (EXO70A to EXO70I). The distribution of most EXO70 genes among different species/sub-genomes were collinear, implying their orthologous relationship. The EXO70A subgroup has the most introns (at least five introns), while the remaining seven subgroups have only one intron on average. The expression profiling of EXO70 genes from wheat revealed that 40 wheat EXO70 genes were expressed in at least one tissue (leaf, stem, or root), of which 25 wheat EXO70 genes were in response to at least one biotic stress (stripe rust or powdery mildew) or abiotic stress (drought or heat). Subcellular localization analysis showed that ten EXO70-V proteins had distinct plasma membrane localization, EXO70I1-V showed a distinctive spotted pattern on the membrane. The 15 EXO70-V genes were differentially expressed in three tissue. Apart from EXO70D2-V, the remaining EXO70-V genes were in response to at least one stress (flg22, chitin, powdery mildew, drought, NaCl, heat, or cold) or phytohormones (salicylic acid, methyl jasmonate, ethephon, or abscisic acid) and hydrogen peroxide treatments. This research provides a genome-wide glimpse of the Triticeae EXO70 gene family and those up- or downregulated genes require further validation of their biological roles in response to biotic/abiotic stresses.

Global Methylome and gene expression analysis during early Peanut pod development

BACKGROUND

Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis.

RESULTS

To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods.

CONCLUSION

A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.