Wheat D-genome Research Articles

Triticum monococcum subsp. monococcum and aegilopoides: new sources of resistance to the dipteran pest, Hessian fly (Diptera: Cecidomyiidae).

The Hessian fly, Mayetiola destructor (Say) belonging to the order Diptera (family: Cecidomyiidae), is a destructive pest of host wheat (Triticum aestivum L.) causing significant economic losses. Although planting resistant wheat cultivars harboring an effective Hessian fly resistance gene (H) is the most economical and environmentally friendly pest management strategy, it imposes selection pressure on the insect populations and can lead to the evolution of Hessian fly virulence. This results in the eventual failure of the deployed H gene. New sources and novel types of resistance are urgently needed to expand the repertoire of H genes and enable strategies that are more effective and durable over the long-term. New sources of Hessian fly resistance have been identified from tetraploid (T. turgidum L., AABB) and hexaploid (T. aestivum, AABBDD) wheat species, as well as from wheat's D-genome donor (Aegilops tauschii Coss., DD). In contrast, diploid einkorn wheat (T. monococcum L., AA) has not been extensively explored for Hessian fly resistance. In this study, we phenotyped 506 T. monococcum accessions belonging to 2 subspecies, T. monococcum L. subsp. monococcum (205 accessions) and T. monococcum subsp. aegilopoides (Link) Thell. (301 accessions), for resistance against 2 predominant Hessian fly biotypes, L and GP (Great Plains). Three and 6 accessions belonging to subsp. monococcum and aegilopoides, respectively, showed > 70% resistance. These accessions provide additional resources for improving wheat cultivars as mitigating strategies for Hessian fly management.

Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii.

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii. Then, 54 TaJAZs were identified in common wheat. A systematic examination of the gene structures, conserved protein domains, and phylogenetic relationships of this gene family was performed. Five new JAZ genes were identified as being derived from tandem duplication after wheat divergence from other species. We integrated RNA-seq data and yield QTL information and found that tandemly duplicated TaJAZ genes were prone to association with spike-related traits. Moreover, 12 TaJAZ genes were located within breeding selection sweeps, including 9 tandemly duplicated ones. Haplotype variation analysis of selected JAZ genes showed significant association of TaJAZ7A and TaJAZ13A with thousand-grain weight. Our work provides a clearer picture of wheat JAZ gene evolution and puts forward the possibility of using these genes for wheat yield improvement.

Genome-wide association mapping of Fusarium crown rot resistance in Aegilops tauschii.

Fusarium crown rot (FCR), caused by various Fusarium species, is a primary fungal disease in most wheat-growing regions worldwide. A. tauschii, the diploid wild progenitor of the D-genome of common wheat, is a reservoir of genetic diversity for improving bread wheat biotic and abiotic resistance/tolerance. A worldwide collection of 286 A. tauschii accessions was used to evaluate FCR resistance. Population structure analysis revealed that 115 belonged to the A. tauschii ssp. strangulata subspecies, and 171 belonged to the A. tauschii ssp. tauschii subspecies. Five accessions with disease index values lower than 20 showed moderate resistance to FCR. These five originated from Afghanistan, China, Iran, Uzbekistan, and Turkey, all belonging to the tauschii subspecies. Genome-wide association mapping using 6,739 single nucleotide polymorphisms (SNPs) revealed that two SNPs on chromosome 2D and four SNPs on chromosome 7D were significantly associated with FCR resistance. Almost all FCR resistance alleles were presented in accessions from the tauschii subspecies, and only 4, 11, and 19 resistance alleles were presented in accessions from the strangulata subspecies. Combining phenotypic correlation analysis and genome-wide association mapping confirmed that FCR resistance loci were independent of flowering time, heading date, and plant height in this association panel. Six genes encoding disease resistance-related proteins were selected as candidates for further validation. The identified resistant A. tauschii accessions will provide robust resistance gene sources for breeding FCR-resistant cultivars. The associated loci/genes will accelerate and improve FCR in breeding programs by deploying marker-assisted selection.

Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat.

Stem rust resistance genes, SrRL5271 and Sr672.1 as well as SrCPI110651, from Aegilops tauschii, the diploid D genome progenitor of wheat, are sequence variants of Sr46 differing by 1-2 nucleotides leading to non-synonymous amino acid substitutions. The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the stem rust resistance (Sr) gene(s) in both accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas resistance segregated at two loci (SR672.1 and SR672.2) for a cross of CPI110672. Bulked segregant analysis placed SrRL5271 and Sr672.1 in a region on chromosome arm 2DS that encodes Sr46. Molecular marker screening, mapping and genomic sequence analysis demonstrated SrRL5271 and Sr672.1 are alleles of Sr46. The amino acid sequence of SrRL5271 and Sr672.1 is identical but differs from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and is thus designated Sr46_h2. Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the protein encoded by the susceptible allele of Ae. tauschii accession AL8/78 differed from these resistance proteins by 54 amino acid substitutions (94% nucleotide sequence gene identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a valuable source for improving stem resistance in wheat.

Introgression of gluten protein genes associated with the D-genome of bread wheat into durum wheat

In the past thirty years many attempts have been addressed to the possibility to improve the breadmaking characteristics of durum wheat. Since the low breadmaking quality of durum wheat was mainly attributed to the absence of suitable high (HMW-GS) – and low (LMW-GS) molecular weight glutenin subunits, different approaches have been used to introgress D-genome associated LMW-GS HMW-GS, present at the linked Gli-D1/Glu-D3 and Glu-D1 loci. In this paper two sets of durum wheat lines with different introgressions of the D-related glutenin proteins transferred on the short and long arm of chromosome 1A of the recipient variety Svevo, have been characterised. The first set included two lines possessing either the Chinese Spring- (CS) or the Cheyenne- (CNN) type of major alleles at the Gli-D1/Glu-D3 loci, transferred on the short arm of Svevo chromosome 1A. The second group included four lines obtained from crosses between the two lines with the CNN- or CS-type of 1DS alleles with previously obtained durum wheat lines carrying translocations involving the HMW-GS loci Glu-D1a (2 + 12) or Glu-D1d (5 + 10). Quality traits and rheological data were determined for the six translocation lines grown in two different years and compared with the durum variety Svevo. The two translocation lines carrying the two different variants (CS- or CNN-type) at the Gli-D1/Glu-D3 loci behaved differently, the former showing increase of quality characteristics and rheological parameter compared to Svevo, the latter being substantially similar to Svevo. On the contrary, all four double recombinant lines showed maximum values of gluten index and major effects on alveographic parameters due to the presence of the Glu-D1 HMW-GS.

Introgressive hybridization and wheat heterosis

<p indent="0mm">To continue feeding the increasing global population, the amount of wheat produced in the next <sc>50 years</sc> will need to exceed the total amount of wheat produced over the past <sc>10000 years.</sc> This challenge is coupled with a shrinking resource base and the likely onset of climate change. Moreover, a wheat yield plateau seems to have been reached in many regions, leading to concerns that the increasing global demand will not be met without breeding innovations. Heterosis may be exploited to enhance and stabilize wheat yields, but the commercial application of hybrid wheat has been limited by the low level of heterosis. Although the genetic mechanism underlying wheat heterosis is still uncharacterized, strong heterosis is often related to the high genetic diversity of the parents. Introgressive hybridization is a powerful method for expanding the germplasm base by transferring alien genes into wheat populations, with considerable implications for advancing wheat heterosis. In addition to increasing genetic diversity, introgressed alien genes may exhibit distinct spatiotemporal expression patterns or regulatory characteristics in the receptor genetic background, which may affect heterosis. Wheat has rich wild relatives and an allohexaploid genome structure, which is conducive to gene introgression. Generally, there are two ways to introgress alien genes. First, individual chromosomal segments may be introgressed through homoeologous recombination to generate translocations that are mediated by chromosome engineering. The resulting translocations have limited use in classical wheat breeding because the introgression is accompanied by the loss of the corresponding wheat chromosomal region. However, the introgression may be beneficial for the application of heterosis because it and the corresponding wheat chromosome are maintained. Second, homologous-directed recombination enables the simultaneous introgression of multiple chromosomal regions to substantially reshape the wheat genome structure. The triplication of many genes in wheat (i.e., three homeologs) provides a buffering effect, such that the allelic variation of one of the copies may have only a minor phenotypic effect. In contrast, combining a number of novel introgressed segments in a single genotype produces a significant positive effect in classical wheat breeding. The utility of homologous-directed introgression for the commercial application of hybrid wheat remains unclear. However, the genetic needs vary between classical breeding and the application of heterosis. A high rate of alien introgression may be harmful for classical breeding, but may be beneficial for generating strong heterosis. The genetic base of the three wheat subgenomes can be simultaneously restructured by using re-synthetic hexaploid wheat, which is derived from a cross between tetraploid wheat and <italic>Aegilops tauschii</italic>, as the introgression bridge. Alternatively, the three wheat subgenomes can be independently improved by using the three diploid progenitors and the closely related diploids. The resulting hybrid genomes are named A′, B′ and D′, which may serve as foundational materials for promoting the application of wheat heterosis. Increasing the use of the untapped genetic diversity of<italic> A</italic>.<italic> tauschii</italic> should be prioritized to diversify the wheat D-genome, which is the least diverse wheat subgenome.

New insights into the dispersion history and adaptive evolution of taxon Aegilops tauschii in China

Aegilops tauschii, the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement, has a wide natural distribution from eastern Turkey to China. However, the phylogenetic relationship and dispersion history of Ae. tauschii in China has not been scientifically clarified. In this study, we genotyped 208 accessions (with 104 in China) using ddRAD sequencing and 55K SNP array, and classified the population into six sublineages. Three possible spreading routes or events were identified, resulting in specific distribution patterns, with four sublineages found in Xinjiang, one in Qinghai, two in Shaanxi and one in Henan. We also established the correlation of SNP-based, karyotype-based and spike-morphology-based techniques to demonstrate the internal classification of Ae. tauschii, and developed consensus dataset with 1245 putative accessions by merging data previously published. Our analysis suggested that eight inter-lineage accessions could be assigned to the putative Lineage 3 and these accessions would help to conserve the genetic diversity of the species. By developing the consensus phylogenetic relationships of Ae. tauschii, our work validated the hypothesis on the dispersal history of Ae. tauschii in China, and contributed to the efficient and comprehensive germplasm-mining of the species.

Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

AbstractAegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2.

Plant nucleotide-binding leucine-rich repeat receptors (NLRs) act as intracellular sensors for pathogen-derived effector proteins and trigger an immune response, frequently resulting in the hypersensitive cell death response (HR) of the infected host cell. The wheat (Triticum aestivum) NLR Pm2 confers resistance against the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) if the isolate contains the specific RNase-like effector AvrPm2. We identified and isolated seven new Pm2 alleles (Pm2e-i) in the wheat D-genome ancestor Aegilops tauschii and two new natural AvrPm2 haplotypes from Bgt. Upon transient co-expression in Nicotiana benthamiana, we observed a variant-specific HR of the Pm2 variants Pm2a and Pm2i towards AvrPm2 or its homolog from the AvrPm2 effector family, BgtE-5843, respectively. Through the introduction of naturally occurring non-synonymous single nucleotide polymorphisms and structure-guided mutations, we identified single amino acids in both the wheat NLR Pm2 and the fungal effector proteins AvrPm2 and BgtE-5843 responsible for the variant-specific HR of the Pm2 variants. Exchanging these amino acids led to a modified HR of the Pm2-AvrPm2 interaction and allowed the identification of the effector head epitope, a 20-amino-acid long unit of AvrPm2 involved in the HR. Swapping of the AvrPm2 head epitope to the non-HR-triggering AvrPm2 family member BgtE-5846 led to gain of a HR by Pm2a. Our study presents a molecular approach to identify crucial effector surface structures involved in the HR and demonstrates that natural and induced diversity in an immune receptor and its corresponding effectors can provide the basis for understanding and modifying NLR-effector specificity.

The Use of Pentaploid Crosses for the Introgression of Amblyopyrum muticum and D-Genome Chromosome Segments Into Durum Wheat.

The wild relatives of wheat provide an important source of genetic variation for wheat improvement. Much of the work in the past aimed at transferring genetic variation from wild relatives into wheat has relied on the exploitation of the ph1b mutant, located on the long arm of chromosome 5B. This mutation allows homologous recombination to occur between chromosomes from related but different genomes, e.g. between the chromosomes of wheat and related chromosomes from a wild relative resulting in the generation of interspecific recombinant chromosomes. However, the ph1b mutant also enables recombination to occur between the homologous genomes of wheat, e.g. A/B, A/D, B/D, resulting in the generation of wheat intergenomic recombinant chromosomes. In this work we report on the presence of wheat intergenomic recombinants in the genomic background of hexaploid wheat/Amblyopyrum muticum introgression lines. The transfer of genomic rearrangements involving the D-genome through pentaploid crosses provides a strategy by which the D-genome of wheat can be introgressed into durum wheat. Hence, a pentaploid crossing strategy was used to transfer D-genome segments, introgressed with either the A- and/or the B-genome, into the tetraploid background of two durum wheat genotypes Karim and Om Rabi 5 in either the presence or absence of different Am. muticum (2n = 2x = 14, TT) introgressions. Introgressions were monitored in backcross generations to the durum wheat parents via multi-color genomic in situ hybridization (mc-GISH). Tetraploid lines carrying homozygous D-genome introgressions, as well as simultaneous homozygous D- and T-genome introgressions, were developed. Introgression lines were characterized via Kompetitive Allele-Specific PCR (KASP) markers and multi-color fluorescence in situ hybridization (FISH). Results showed that new wheat sub-genomic translocations were generated at each generation in progeny that carried any Am. muticum chromosome introgression irrespective of the linkage group that the segment was derived from. The highest frequencies of homologous recombination were observed between the A- and the D-genomes. Results indicated that the genotype Karim had a higher tolerance to genomic rearrangements and T-genome introgressions compared to Om Rabi 5. This indicates the importance of the selection of the parental genotype when attempting to transfer/develop introgressions into durum wheat from pentaploid crosses.

Hybridization preceded radiation in diploid wheats

Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). This scenario of reticulation has been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.6 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~3.0–4.0 Ma ago, and did not indicate additional hybridization events. Conflicting ABBA-BABA tests suggestive of further reticulation were shown here to result from ancestral population structure rather than hybridization. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into the majority of extant diploid as well as allopolyploid wild wheats.

Effective introgression of wheat D-genome chromosomes into hexaploid triticale (× Triticosecale Wittm.) using trigeneric hybrids

Given the narrow genetic variability of hexaploid triticale, introgressive hybridization is an efficient means to enrich the available genetic pool. The wheat D-genome chromosomes harbor valuable genes for triticale improvement, such as enhancement of biotic and abiotic stress resistance, bread baking quality, and agronomically useful characters. Introducing the wheat D-genome chromosome into triticale may thus improve its agronomic performance and quality. In the present study, we successfully developed the six hexaploid triticale D-genome chromosome introgression lines derived from wheat–rye–Psathyrostachys huashanica trigeneric hybrids. Genomic and fluorescence in situ hybridization (GISH and FISH) karyotyping revealed that K16-4173-3, K16-1565-6, K16-1565-7, and K16-601-1 were 2D(2R), 3D(3B), 3D, 5D(3B, 5R), and 5D(5B) chromosome substitution lines, respectively. K16-4121-3 was found to be a disomic chromosome addition line having a pair of 6D chromosomes. In addition, line K16-1566-4 carried 28 A- and B-genome, 12 R-genome (lacking two 4Rs), two 4D, and two 7D chromosomes. Analysis of these lines using wheat simple sequence repeats (SSRs) and rye specific molecular markers confirmed that corresponding triticale B or R chromosomes had been replaced by D chromosomes of wheat, an observation perfectly consistent with the FISH and GISH results. Furthermore, these lines except for K16-601-1 were highly resistant to the stripe rust pathogen prevalent in China, than Zhongsi828 plants at the adult stages. Our data suggest that the use of trigeneric hybrids as a bridge between triticale and amphiploid wild-wheat forms is an effect strategy for transferring D-genome chromatin into triticale from other breeding programs. The triticale D-genome introgression lines created in this study may serve as new bridging germplasm for hexaploid triticale breeding and should likewise be useful for enhancing triticale genetic diversity.

Genome-Wide Association Mapping of Grain Micronutrients Concentration in Aegilops tauschii.

Bread wheat is an important and the most consumed cereal worldwide. However, people with predominantly cereal-based diets are increasingly affected by micronutrient deficiencies, suggesting the need for biofortified wheat varieties. The limited genetic diversity in hexaploid wheat warrants exploring the wider variation present in wheat wild relatives, among these Aegilops tauschii, the wild progenitor of the bread wheat D genome. In this study, a panel of 167 Ae. tauschii accessions was phenotyped for grain Fe, Zn, Cu, and Mn concentrations for 3 years and was found to have wide variation for these micronutrients. Comparisons between the two genetic subpopulations of Ae. tauschii revealed that lineage 2 had higher mean values for Fe and Cu concentration than lineage 1. To identify potentially new genetic sources for improving grain micronutrient concentration, we performed a genome-wide association study (GWAS) on 114 non-redundant Ae. tauschii accessions using 5,249 genotyping-by-sequencing (GBS) markers. Best linear unbiased predictor (BLUP) values were calculated for all traits across the three growing seasons. A total of 19 SNP marker trait associations (MTAs) were detected for all traits after applying Bonferroni corrected threshold of -log10(P-value) ≥ 4.68. These MTAs were found on all seven chromosomes. For grain Fe, Zn, Cu, and Mn concentrations, five, four, three, and seven significant associations were detected, respectively. The associations were linked to the genes encoding transcription factor regulators, transporters, and phytosiderophore synthesis. The results demonstrate the utility of GWAS for understanding the genetic architecture of micronutrient accumulation in Ae. tauschii, and further efforts to validate these loci will aid in using them to diversify the D-genome of hexaploid wheat.

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii.

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1–L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

Transcriptomic analysis of Aegilops tauschii during long-term salinity stress.

Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398bp and an N50 of 2269bp. Functional annotation of the unigenes showed that 93,742 (36.69%) had at least a significant BLAST hit in the SwissProt database, while 174,079 (68.14%) showed significant similarity to proteins in the NCBI nr database. Differential expression analysis identified 4506 salt stress-responsive unigenes. Bioinformatic analysis of the differentially expressed unigenes (DEUs) revealed a number of biological processes and pathways involved in the establishment of ion homeostasis, signaling processes, carbohydrate metabolism, and post-translational modifications. Fine regulation of starch and sucrose content may be important features involved in salt tolerance in Ae. tauschii. Moreover, 82% of DEUs mapped to the D-subgenome, including known QTL for salt tolerance, and these DEUs showed similar salt stress responses in other accessions of Ae. tauschii. These results could provide fundamental insight into the regulatory process underlying salt tolerance in Ae. tauschii and wheat and facilitate identification of genes involved in their salt tolerance mechanisms.

Hybrid incompatibilities in interspecific crosses between tetraploid wheat and its wild diploid relative Aegilops umbellulata.

Hybrid abnormalities, severe growth abortion and grass-clump dwarfism, were found in the tetraploid wheat/Aegilops umbellulata hybrids, and the gene expression changes were conserved in the hybrids with those in other wheat synthetic hexaploids. Aegilops umbellulata Zhuk., a diploid goatgrass species with a UU genome, has been utilized as a genetic resource for wheat breeding. Here, we examine the reproductive barriers between tetraploid wheat cultivar Langdon (Ldn) and various Ae. umbellulata accessions by conducting interspecific crossings. Through systematic cross experiments, three types of hybrid incompatibilities were found: seed production failure in crosses, hybrid growth abnormalities and sterility in the ABU hybrids. Hybrid incompatibilities were widely distributed over the entire range of the natural species, and in about 50% of the cross combinations between tetraploid Ldn and Ae. umbellulata accessions, ABU F1 hybrids showed one of two abnormal growth phenotypes: severe growth abortion (SGA) or grass-clump dwarfism. Expression of the shoot meristem maintenance-related and cell cycle-related genes was markedly repressed in crown tissues of hybrids showing SGA, suggesting dysfunction of mitotic cell division in the shoot apices. The grass-clump dwarf phenotype may be explained by down-regulation of wheat APETALA1-like MADS box genes, which act as flowering promoters, and altered expression in crown tissues of the miR156/SPLs module, which controls tiller number and branching. These gene expression changes in growth abnormalities were well conserved between the Ldn/Ae. umbellulata plants and interspecific hybrids from crosses of Ldn and wheat D-genome progenitor Ae. tauschii.

Aegilops tauschii Accessions with Geographically Diverse Origin Show Differences in Chromosome Organization and Polymorphism of Molecular Markers Linked to Leaf Rust and Powdery Mildew Resistance Genes.

Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae. tauschii using various repetitive sequences mainly from the BAC library of wheat cultivar Chinese Spring. Results obtained for Ae. tauschii chromosomes revealed many similarities between analyzed accessions, however, some hybridization patterns were specific for accessions, which become from cognate regions of the World. The most noticeable differences were observed for accessions from China which were characterized by presence of distinct signals of pTa-535 in the interstitial region of chromosome 3D, less intensity of pTa-86 signals in chromosome 2D, as well as lack of additional signals of pTa-86 in chromosomes 1D, 5D, or 6D. Ae. tauschii of Chinese origin appeared homogeneous and separate from landraces that originated in western Asia. Ae. tauschii chromosomes showed similar hybridization patterns to wheat D-genome chromosomes, but some differences were also observed among both species. What is more, we identified reciprocal translocation between short arm of chromosome 1D and long arm of chromosome 7D in accession with Iranian origin. High polymorphism between analyzed accessions and extensive allelic variation were revealed using molecular markers associated with resistance genes. Majority of the markers localized in chromosomes 1D and 2D showed the diversity of banding patterns between accessions. Obtained results imply, that there is a moderate or high level of polymorphism in the genome of Ae. tauschii determined by a geographical origin, which we proved by cytogenetic and molecular markers analysis. Therefore, selected accessions might constitute an accessible source of variation for improvement of Triticeae species like wheat and triticale.

Fine mapping and genetic association analysis of Net2, the causative D-genome locus of low temperature-induced hybrid necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii.

Hybrid necrosis has been observed in many interspecific hybrids from crosses between tetraploid wheat and the wheat D-genome donor Aegilops tauschii. Type II necrosis is a kind of hybrid incompatibility that is specifically characterized by low-temperature induction and growth suppression. Two complementary genes, Net1 on the AB genome and Net2 on the D genome, putatively control type II necrosis in ABD triploids and synthetic hexaploid wheat. Toward map-based cloning of Net2, a fine map around the Net2 region on 2DS was constructed in this study. Using the draft genome sequence of Ae. tauschii and the physical map of the barley genome, the Net2 locus was mapped within a 0.6cM interval between two closely linked markers. Although local chromosomal rearrangements were observed in the Net2-corresponding region between the barley/Brachypodium and Ae. tauschii genomes, the two closely linked markers were significantly associated with type II necrosis in Ae. tauschii. These results suggest that these markers will aid efficient selection of Net2 non-carrier individuals from the Ae. tauschii population and intraspecific progeny, and could help with introgression of agriculturally important genes from Ae. tauschii to common wheat.

Identification and characterization of a high kernel weight mutant induced by gamma radiation in wheat (Triticum aestivum L.).

BackgroundInducing mutations are considered to be an effective way to create novel genetic variations and hence novel agronomical traits in wheat. This study was conducted to assess the genetic differences between Shi4185 and its mutant line Fu4185, produced by gamma radiation with larger grain, and to identify quantitative trait loci (QTLs) for thousand kernel weight (TKW).ResultsPhenotypic analysis revealed that the TKW of Fu4185 was much higher than that of Shi4185 under five different environments. At the genomic level, 110 of 2019 (5.4 %) simple sequence repeats (SSR) markers showed polymorphism between Shi4185 and Fu4185. Notably, 30 % (33 out of 110) polymorphic SSR markers were located on the D-genome, which was higher than the percentage of polymorphisms among natural allohexaploid wheat genotypes, indicating that mutations induced by gamma radiation could be a potential resource to enrich the genetic diversity of wheat D-genome. Moreover, one QTL, QTkw.cau-5D, located on chromosome 5DL, with Fu4185 contributing favorable alleles, was detected under different environments, especially under high temperature conditions.ConclusionsQTkw.cau-5D is an environmental stable QTL, which may be a desired target for genetic improvement of wheat kernel weight.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0285-x) contains supplementary material, which is available to authorized users.

Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D‐genome

In a recent Letter to New Phytologist Li et al. (2015) presented a re-evaluation of our recent finding from a phylogenomics study that the bread wheat D-genome lineage is probably of homoploid hybrid origin (Marcussen et al., 2014). The authors claim to present evidence from chloroplast phylogeny and gene tree topologies that necessitate additional hybridization events compared to the phylogeny proposed by us. Unfortunately Li et al.'s (2015) conclusions appear to be confounded by differences in nomenclatures used to describe the major Triticum/Aegilops clades (Fig. 1) and a misunderstanding concerning the temporal dimension of our phylogenetic model (i.e. when hybridization happened) (Fig. 1). In our original paper we presented phylogenomic data suggesting that one or more basal hybridization(s) between the ancestor of the A-genome and the ancestor of the B-genome in modern bread wheat gave rise to an ancestor of the bread wheat D-genome lineage 5–6 million years ago (Fig. 1). We used the terms ‘A-genome lineage’, ‘B-genome lineage’, and ‘D-genome lineage’ to refer to the three deep lineages encompassing all extant species in the Triticum/Aegilops clade (Fig. 1 in this Letter; Figs 2, 3, and S6 and their captions in Marcussen et al., 2014). This informal nomenclature was chosen because Marcussen et al. (2014) was part of a series of papers on the hexaploid bread wheat genome constituents (i.e. A, B and D) (International Wheat Genome Sequencing Consortium (IWGSC), 2014; Pfeifer et al., 2014) in addition to the lack of a phylogenetic infrageneric classification of Triticum/Aegilops. Thus, our use of ‘D-genome lineage’ in Marcussen et al. (2014) refers to the entire lineage containing T. aestivum-D, Ae. tauschii, and Ae. sharonensis (Fig. 1). This is not synonymous with how Li et al. (2015) define the ‘D-genome’ according to the haplome nomenclature of wheats (Fig. 1 and summarized in Table 1 of Li et al., 2015). Hence, in their re-evaluation of our hypothesis Li et al. (2015) consider the D-lineage as encompassing Aegilops tauschii only, while Ae. sharonensis is considered to belong to an S*+M clade (Fig. 1). One sentence from the Li et al. (2015) Letter that highlights this misunderstanding is: ‘Marcussen et al. (2014) proposed that A. tauschii originated from homoploid hybridization between A. speltoides and the ancestor of modern T. urartu/T. monococcum.’ This is a factual error. Marcussen et al. (2014) never claimed that Ae. tauschii evolved through a homoploid hybridization. What we proposed was that a homoploid hybridization gave rise to an ancestor of all D+S*+M clade species (including Ae. tauschii and Ae. sharonensis) (Fig. 1). In addition, Li et al. (2015) seem to have overlooked the timescale of our phylogenetic analyses. We report on an ancient hybridization (illustrated clearly in Fig. 2b in Marcussen et al., 2014) several million years before Aegilops tauschii and Ae. sharonensis existed as species. The hybrid history of the D-genome lineage (as Marcussen et al., 2014 refers to) is therefore not restricted to Ae. tauschii but encompasses the entire D+S*+M clade. The very same chloroplast phylogeny that Li et al. (2015) use to re-evaluate our conclusions is therefore completely congruent with our proposed phylogenetic network for wheats. Finally, we fully agree with Li et al. (2015) that the evolutionary history of Tritium/Aegilops is likely to be even more complex than we currently understand it to be. Judging from the young age of the Triticeae and the numerous reports of suspected reticulations, sequencing and analysis of additional diploid and polyploid Triticum/Aegilops genomes will most likely provide evidence for additional hybridization events not yet detected.