From genome to gene: a new epoch for wheat research?

Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits

Na+ exclusion from above-ground tissues via the Na+-selective transporter HKT1;5 is a major salt-tolerance mechanism in crops. Using the expression genome-wide association study and yeast-one-hybrid screening, we identified TaSPL6-D, a transcriptional suppressor of TaHKT1;5-D in bread wheat. SPL6 also targeted HKT1;5 in rice and Brachypodium. A 47-bp insertion in the first exon of TaSPL6-D resulted in a truncated peptide, TaSPL6-DIn, disrupting TaHKT1;5-D repression exhibited by TaSPL6-DDel. Overexpressing TaSPL6-DDel, but not TaSPL6-DIn, led to inhibited TaHKT1;5-D expression and increased salt sensitivity. Knockout of TaSPL6-DDel in two wheat genotypes enhanced salinity tolerance, which was attenuated by a further TaHKT1;5-D knockdown. Spike development was preserved in Taspl6-dd mutants but not in Taspl6-aabbdd mutants. TaSPL6-DIn was mainly present in landraces, and molecular-assisted introduction of TaSPL6-DIn from a landrace into a leading wheat cultivar successfully improved yield on saline soils. The SPL6-HKT1;5 module offers a target for the molecular breeding of salt-tolerant crops.

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.

TaSRO1 plays a dual role in suppressing TaSIP1 to fine tune mitochondrial retrograde signalling and enhance salinity stress tolerance

Initially discovered in yeast, mitochondrial retrograde signalling has long been recognised as an essential in the perception of stress by eukaryotes. However, how to maintain the optimal amplitude and duration of its activation under natural stress conditions remains elusive in plants. Here, we show that TaSRO1, a major contributor to the agronomic performance of bread wheat plants exposed to salinity stress, interacted with a transmembrane domain-containing NAC transcription factor TaSIP1, which could translocate from the endoplasmic reticulum (ER) into the nucleus and activate some mitochondrial dysfunction stimulon (MDS) genes. Overexpression of TaSIP1 and TaSIP1-∆C (a form lacking the transmembrane domain) in wheat both compromised the plants' tolerance of salinity stress, highlighting the importance of precise regulation of this signal cascade during salinity stress. The interaction of TaSRO1/TaSIP1, in the cytoplasm, arrested more TaSIP1 on the membrane of ER, and in the nucleus, attenuated the trans-activation activity of TaSIP1, therefore reducing the TaSIP1-mediated activation of MDS genes. Moreover, the overexpression of TaSRO1 rescued the inferior phenotype induced by TaSIP1 overexpression. Our study provides an orchestrating mechanism executed by the TaSRO1-TaSIP1 module that balances the growth and stress response via fine tuning the level of mitochondria retrograde signalling.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Identification and Mapping of QTL for Stripe Rust Resistance in the Chinese Wheat Cultivar Shumai126

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a damaging disease of wheat globally, and breeding resistant cultivars is the best control strategy. The Chinese winter wheat cultivar Shumai126 (SM126) exhibited strong resistance to P. striiformis f. sp. tritici in the field for more than 10 years. The objective of this study was to identify and map quantitative trait loci (QTL) for resistance to stripe rust in a population of 154 recombinant inbred lines (RILs) derived from a cross between cultivars Taichang29 (TC29) and SM126. The RILs were tested in six field environments with a mixture of the Chinese prevalent races (CYR32, CYR33, CYR34, Zhong4, and HY46) of P. striiformis f. sp. tritici and in growth chamber with race CYR34 and genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Six QTL were mapped on chromosomes 1BL, 2AS, 2AL, 6AS, 6BS, and 7BL, respectively. All QTL were contributed by SM126 except QYr.sicau-2AL. The QYr.sicau-1BL and QYr.sicau-2AS had major effects, explaining 27.00 to 39.91% and 11.89 to 17.11% of phenotypic variances, which may correspond to known resistance genes Yr29 and Yr69, respectively. The QYr.sicau-2AL, QYr.sicau-6AS, and QYr.sicau-6BS with minor effects are likely novel. QYr.sicau-7BL was only detected based on growth chamber seedling data. Additive effects were detected for the combination of QYr.sicau-1BL, QYr.sicau-2AS, and QYr.sicau-2AL. SNP markers linked to QYr.sicau-1BL (AX-111056129 and AX-108839316) and QYr.sicau-2AS (AX-111557864 and AX-110433540) were converted to breeder-friendly Kompetitive allele-specific PCR (KASP) markers that would facilitate the deployment of stripe rust resistance genes in wheat breeding.

Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta-QTL analysis

Leaf rust, caused by the fungus Puccinia triticina Erikss (Pt), is a destructive disease affecting wheat (Triticum aestivum L.) and a threat to food security. Developing resistant cultivars represents a useful method of disease control, and thus, understanding the genetic basis for leaf rust resistance is required. To this end, a comprehensive bibliographic search for leaf rust resistance quantitative trait loci (QTL) was performed, and 393 QTL were collected from 50 QTL mapping studies. Afterward, a consensus map with a total length of 4,567 cM consisting of different types of markers (simple sequence repeat [SSR], diversity arrays technology [DArT], chip-based single-nucleotide polymorphism [SNP] markers, and SNP markers from genotyping-by-sequencing) was used for QTL projection, and meta-QTL (MQTL) analysis was performed on 320 QTL. A total of 75 MQTL were discovered and refined to 15 high-confidence MQTL (hcmQTL). The candidate genes discovered within the hcmQTL interval were then checked for differential expression using data from three transcriptome studies, resulting in 92 differentially expressed genes (DEGs). The expression of these genes in various leaf tissues during wheat development was explored. This study provides insight into leaf rust resistance in wheat and thereby provides an avenue for developing resistant cultivars by incorporating the most important hcmQTL.

Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools

Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.

Identification and development of novel salt-responsive candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (mir-SSRs) in bread wheat (Triticum aestivum)

Salt stress adversely affects the global wheat production and productivity. To improve salinity tolerance of crops, identification of robust molecular markers is highly imperative for development of salt-tolerant cultivars to mimic yield losses under saline conditions. In this study, we mined 171 salt-responsive genes (including 10 miRNAs) from bread wheat genome using the sequence information of functionally validated salt-responsive rice genes. Salt-stress, tissue and developmental stage-specific expression analysis of RNA-seq datasets revealed the constitutive as well as the inductive response of salt-responsive genes in different tissues of wheat. Fifty-four genotypes were phenotyped for salt stress tolerance. The stress tolerance index of the genotypes ranged from 0.30 to 3.18. In order to understand the genetic diversity, candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (miR-SSRs) were mined from 171 members of salt-responsive genes of wheat and validated among the contrasting panels of 54 tolerant as well as susceptible wheat genotypes. Among 53 SSR markers screened, 10 cg-SSRs and 8 miR-SSRs were found to be polymorphic. Polymorphic information content between the wheat genotypes ranged from 0.07 to 0.67, indicating the extant of wide genetic variation among the salt tolerant and susceptible genotypes at the DNA level. The genetic diversity analysis based on the allelic data grouped the wheat genotypes into three separate clusters of which single group encompassing most of the salt susceptible genotypes and two of them containing salt tolerance and moderately salt tolerance wheat genotypes were in congruence with penotypic data. Our study showed that both salt-responsive genes and miRNAs based SSRs were more diverse and can be effectively used for diversity analysis. This study reports the first extensive survey on genome-wide analysis, identification, development and validation of salt-responsive cg-SSRs and miR-SSRs in wheat. The information generated in the present study on genetic divergence among genotypes having a differential response to salt will help in the selection of suitable lines as parents for developing salt tolerant cultivars in wheat.

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

BACKGROUND

Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield.

RESULT

In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R²) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding.

CONCLUSION

Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

Association Analysis Identifies New Loci for Resistance to Chinese Yr26-Virulent Races of the Stripe Rust Pathogen in a Diverse Panel of Wheat Germplasm

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive fungal diseases of wheat worldwide. The expanding Yr26-virulent Pst race (V26) group overcomes almost all currently deployed resistance genes in China and has continued to accumulate new virulence. Investigating the genetic architecture of stripe rust resistance in common wheat is an important basis for a successful utilization of resistance in breeding programs. A panel of 410 exotic wheat germplasms was used for characterizing new stripe rust resistance loci. This panel was genotyped using high-density wheat 660K single-nucleotide polymorphism (SNP) array, and phenotypic evaluation of seedlings for stripe rust resistance was performed using multiple Pst races. Thirty-five loci conferring resistance were identified through genome-wide association mapping, and explained phenotypic variances ranged from 53 to 75%. Of these, 14 were colocated in the proximity of the known loci, including cataloged Yr genes Yr9, Yr10, Yr26, Yr33, Yr47, Yr56, Yr57, Yr64, Yr67, Yr72, and Yr81 and three temporarily designated as YrCen, YrNP63, and YrRC detected in our quantitative trait locus (QTL) mapping studies. Seven of them (Yr9, Yr10, Yr24/26, Yr81, YrCEN, YrNP63, and YrRC) were confirmed by molecular detection or genetic analysis. New loci that were identified to be different from reported Yr genes need further confirmation. Nine QTL with significantly large phenotypic effect on resistance to all tested races were considered as major loci for effective resistance. The identified loci enrich our stripe rust resistance gene pool, and the linked SNPs should be useful for marker-assisted selection in breeding programs.

High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F₂ population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.

TaCYP81D5, one member in a wheat cytochrome P450 gene cluster, confers salinity tolerance via reactive oxygen species scavenging

As one of the largest gene families in plants, the cytochrome P450 monooxygenase genes (CYPs) are involved in diverse biological processes including biotic and abiotic stress response. Moreover, P450 genes are prone to expanding due to gene tandem duplication during evolution, resulting in generations of novel alleles with the neo-function or enhanced function. Here, the bread wheat (Triticum aestivum) gene TaCYP81D5 was found to lie within a cluster of five tandemly arranged CYP81D genes, although only a single such gene (BdCYP81D1) was present in the equivalent genomic region of the wheat relative Brachypodium distachyon. The imposition of salinity stress could up-regulate TaCYP81D5, but the effect was abolished in plants treated with an inhibitor of reactive oxygen species synthesis. In SR3, a wheat cultivar with an elevated ROS content, the higher expression and the rapider response to salinity of TaCYP81D5 were related to the chromatin modification. Constitutively expressing TaCYP81D5 enhanced the salinity tolerance both at seedling and reproductive stages of wheat via accelerating ROS scavenging. Moreover, an important component of ROS signal transduction, Zat12, was proven crucial in this process. Though knockout of solely TaCYP81D5 showed no effect on salinity tolerance, knockdown of BdCYP81D1 or all TaCYP81D members in the cluster caused the sensitivity to salt stress. Our results provide the direct evidence that TaCYP81D5 confers salinity tolerance in bread wheat and this gene is prospective for crop improvement.

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.

Utilization of the Genomewide Wheat 55K SNP Array for Genetic Analysis of Stripe Rust Resistance in Common Wheat Line P9936

Breeding for resistance to stripe rust (caused by Puccinia striiformis f. tritici) is essential for reducing losses in yield and quality in wheat. To identify genes for use in breeding, a biparental population of 186 recombinant inbred lines (RILs) from a cross of the Chinese landrace Mingxian 169 and CIMMYT-derived line P9936 was evaluated in field nurseries either artificially or naturally inoculated in two crop seasons. Each of the RILs and parents was genotyped with the wheat 55K single-nucleotide polymorphism (SNP) 'Breeders' array and a genetic linkage map with 8,225 polymorphic SNP markers spanning 3,593.37 centimorgans was constructed. Two major quantitative trait loci (QTL) and two minor QTL were identified. The major QTL QYr.nwafu-3BS.2 and QYr.nwafu-7BL on chromosomes arms 3BS and 7BL were detected in all field locations and explained an average 20.4 and 38.9% of phenotypic variation stripe rust severity, respectively. QYr.nwafu-3BS.2 likely corresponds to the locus Yr30/Sr2 and QYr.nwafu-7BL may be a resistance allele identified previously in CIMMYT germplasm. The other minor QTL had limited individual effects but increased resistance when in combinations with other QTL. Markers linked to QYr.nwafu-7BL were converted to kompetitive allele-specific polymerase chain reaction markers and validated in a panel of wheat accessions. Wheat accessions carrying the same haplotype as P9936 at the identified SNP loci had lower average stripe rust severity than the average severity of all other haplotypes.

A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance

Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.

Genetic transformation of einkorn (Triticum monococcum L. ssp. monococcum L.), a diploid cultivated wheat species

BACKGROUND

Domesticated einkorn (Triticum monococcum L.) is one of the oldest cultivated cereal crops in the world. Its small genome size (~ 5.7 GB), low ploidy (2n = 2x = 14, AmAm) and high genetic polymorphism make this species very attractive for use as a diploid model for understanding the genomics and proteomics of Triticeae. Einkorn, however, is still a recalcitrant monocotyledonous species for the application of modern biotechnologies, including transgenesis. This paper reports the factors that may influence transgene delivery, integration, expression and inheritance in einkorn.

RESULTS

In this study, we report the successful genetic transformation of einkorn using biolistic-mediated DNA delivery. Immature embryo-derived tissues of spring einkorn were bombarded with a plasmid containing the reporter gene GFP (green fluorescent protein) driven by the rice actin promoter (act1) and the selectable bar gene (bialaphos resistance gene) driven by the maize ubiquitin promoter (ubi1). Adjustments to various parameters such as gas pressure, microcarrier size and developmental stage of target tissue were essential for successful transient and stable transformation. Bombarded einkorn tissues are recalcitrant to regenerating plants, but certain modifications of the culture medium have been shown to increase the production of transgenic events. In various experiments, independent transgenic plants were produced at frequencies ranging from 0.0 to 0.6%. Molecular analysis, marker gene expression and herbicide treatment demonstrated that gfp/bar genes were stably integrated into the einkorn genome and successfully inherited over several generations. The transgenes, as dominant loci, segregated in both Mendelian and non-Mendelian fashion due to multiple insertions. Fertile homozygous T1-T2 populations of transgenic einkorn that are resistant to herbicides were selected.

CONCLUSION

To the best of our knowledge, this is the first report of the production of genetically modified einkorn plants. We believe that the results of our research could be a starting point for the application of the current biotechnological-based technologies, such as transgenesis and genome editing, to accelerate comparative functional genomics in einkorn and other cereals.

Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat (Triticum aestivum L.)

Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat (Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named m68. Genetic analysis showed that the leaf senescence phenotype of m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of m68, but also facilitate the study of leaf senescence in wheat.

An early-flowering einkorn wheat mutant with deletions of PHYTOCLOCK 1/LUX ARRHYTHMO and VERNALIZATION 2 exhibits a high level of VERNALIZATION 1 expression induced by vernalization

Using heavy-ion beam mutagenesis of Triticum monococcum strain KU104-1, we identified a mutant that shows extra early-flowering; it was named extra early-flowering 3 (exe3). Here, we carried out expression analyses of clock-related genes, clock downstream genes and photoperiod pathway genes, and found that the clock component gene PHYTOCLOCK 1/LUX ARRHYTHMO (PCL1/LUX) was not expressed in exe3 mutant plants. A PCR analysis of DNA markers indicated that the exe3 mutant had a deletion of wheat PCL1/LUX (WPCL1), and that the WPCL1 deletion was correlated with the mutant phenotype in the segregation line. We confirmed that the original strain KU104-1 carried a mutation that produced a null allele of a flowering repressor gene VERNALIZATION 2 (VRN2). As a result, the exe3 mutant has both WPCL1 and VRN2 loss-of-function mutations. Analysis of plant development in a growth chamber showed that vernalization treatment accelerated flowering time in the exe3 mutant under short day (SD) as well as long day (LD) conditions, and the early-flowering phenotype was correlated with the earlier up-regulation of VRN1. The deletion of WPCL1 affects the SD-specific expression patterns of some clock-related genes, clock downstream genes and photoperiod pathway genes, suggesting that the exe3 mutant causes a disordered SD response. The present study indicates that VRN1 expression is associated with the biological clock and the VRN1 up-regulation is not influenced by the presence or absence of VRN2.

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat. German wheat cultivar "Friedrichswerther" has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F_2:3 lines and F₆ recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F_2:3 lines and F₆ RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

Development and Validation of KASP-SNP Markers for QTL Underlying Resistance to Stripe Rust in Common Wheat Cultivar P10057

Stripe rust (Puccinia striiformis f. sp. tritici) is among the most important diseases of wheat (Triticum aestivum L.) globally. Utilization of adult plant resistance (APR) constitutes a key tool for maintaining protection against this disease. The CIMMYT wheat cultivar P10057 displayed a high level of APR to stripe rust in germplasm evaluation in field environments. To clarify the genetic basis and identify quantitative trait loci (QTLs) involved in stripe rust resistance in P10057, three wheat populations were used: 150 F_5:6 recombinant inbred lines (RILs) derived from the cross Mingxian 169 × P10057, and 161 and 140 F_2:3 lines from Avocet S × P10057 and Zhengmai 9023 × P10057, respectively. These three populations were evaluated for infection type (IT) and disease severity (DS) in Shaanxi, Gansu, and Sichuan during the 2014-15 and 2015-16 cropping seasons. Genotyping was performed with Kompetitive Allelic Specific PCR (KASP) and simple sequence repeat (SSR) markers linked to the resistance loci. Using QTL analysis, two genomic regions associated with resistance were found on chromosome arms 2BS and 3BS, respectively. These two stable QTLs, designated Qyrlov.nwafu-2BS and Qyrlov.nwafu-3BS, were detected across all environments and explained average 22.6 to 31.6% and 21.3 to 32.3% of stripe rust severity phenotypic variation, respectively. Qyrlov.nwafu-2BS may be the resistance allele derived from CIMMYT germplasm and Qyrlov.nwafu-3BS likely corresponds to the locus Sr2/Lr27/Yr30/Pbc. The KASP markers IWA5377, IWA2674, and IWA5830 linked to QYrlov.nwafu-2BS and IWB57990 and IWB6491 linked to Qyrlov.nwafu-3BS were reliable for marker-assisted selection (MAS) in the Zhengmai 9023 × P10057 population. These QTLs with KASP markers are expected to contribute in developing wheat cultivars with improved stripe rust resistance.

From Genetic Stock to Genome Editing: Gene Exploitation in Wheat

Bread wheat (Triticum aestivum) ranks as one of our most important staple crops. However, its hexaploid nature has complicated our understanding of the genetic bases underlying many of its traits. Historically, functional genetic studies in wheat have focused on identifying natural variations and have contributed to assembling and enriching its genetic stock. Recently, mold-breaking advances in whole genome sequencing, exome-capture based mutant libraries, and genome editing have revolutionized strategies for genetic research in wheat. We review new trends in wheat functional genetic studies along with germplasm conservation and innovation, including the relevance of genetic stocks, and the application of sequencing-based mutagenesis and genome editing. We also highlight the potential of multiplex genome editing toolkits in addressing species-specific challenges in wheat.

Revisiting Pivotal-Differential Genome Evolution in Wheat

An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as 'pivotal-differential' genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved. We suggest that, in light of recent advances in genome sequencing and related technologies in the wheat group, the time has come to reopen the investigation into pivotal-differential genome evolution.

Emerging Avenues for Utilization of Exotic Germplasm

Breeders have been successful in increasing crop performance by exploiting genetic diversity over time. However, the reported annual yield increases are not sufficient in view of rapid human population growth and global environmental changes. Exotic germplasm possesses high levels of genetic diversity for valuable traits. However, only a small fraction of naturally occurring genetic diversity is utilized. Moreover, the yield gap between elite and exotic germplasm widens, which increases the effort needed to use exotic germplasm and to identify beneficial alleles and for their introgression. The advent of high-throughput genotyping and phenotyping technologies together with emerging biotechnologies provide new opportunities to explore exotic genetic variation. This review will summarize potential challenges for utilization of exotic germplasm and provide solutions.

Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays

Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014-2015 and 2015-2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS.

Quantitative Disease Resistance: Dissection and Adoption in Maize

Maize is the world's most produced crop, providing food, feed, and biofuel. Maize production is constantly threatened by the presence of devastating pathogens worldwide. Characterization of the genetic components underlying disease resistance is a major research area in maize which is highly relevant for resistance breeding programs. Quantitative disease resistance (QDR) is the type of resistance most widely used by maize breeders. The past decade has witnessed significant progress in fine-mapping and cloning of genes controlling QDR. The molecular mechanisms underlying QDR remain poorly understood and exploited. In this review we discuss recent advances in maize QDR research and strategy for resistance breeding.

A novel allele of L-galactono-1,4-lactone dehydrogenase is associated with enhanced drought tolerance through affecting stomatal aperture in common wheat

In higher plants, L-galactono-1,4-lactone dehydrogenase (GLDH) plays important roles in ascorbic acid (AsA) biosynthesis and assembly of respiration complex I. Here we report three homoeologous genes (TaGLDH-A1, -B1 and -D1) encoding common wheat GLDH isozymes and a unique allelic variant (TaGLDH-A1b) associated with enhanced drought tolerance. TaGLDH-A1, -B1 and -D1 were located on chromosomes 5A, 5B and 5D, respectively, and their transcripts were found in multiple organs. The three homoeologs each conferred increased GLDH activity when ectopically expressed in tobacco. Decreasing TaGLDH expression in wheat significantly reduced GLDH activity and AsA content. TaGLDH-A1b differed from wild type allele TaGLDH-A1a by an in-frame deletion of three nucleotides. TaGLDH-A1b was biochemically less active than TaGLDH-A1a, and the total GLDH activity levels were generally lower in the cultivars carrying TaGLDH-A1b relative to those with TaGLDH-A1a. Interestingly, TaGLDH-A1b cultivars showed stronger water deficiency tolerance than TaGLDH-A1a cultivars, and TaGLDH-A1b co-segregated with decreased leaf water loss in a F₂ population. Finally, TaGLDH-A1b cultivars generally exhibited smaller leaf stomatal aperture than TaGLDH-A1a varieties in control or water deficiency environments. Our work provides new information on GLDH genes and function in higher plants. TaGLDH-A1b is likely useful for further studying and improving wheat tolerance to drought stress.

Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research

Background

The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research.

Results

We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat.

Conclusions

Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2257-y) contains supplementary material, which is available to authorized users.