Aegilops Species Research Articles

Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping.

Fluorescence in situ hybridization karyotypes have been widely used for evolutionary analysis on chromosome organization and genetic/genomic diversity in the wheat alliance (tribe Triticeae of Poaceae). The karyotpic diversity of Aegilops umbellulata, Ae. markgrafii, Ae. comosa subsp. comosa and subsp. subventricosa, and Ae. uniaristata was evaluated by the fluorescence in situ hybridization (FISH) probes oligo-pSc119.2 and pTa71 in combination with (AAC)5, (ACT)7, and (CTT)12, respectively. Abundant intra- and interspecific genetic variation was discovered in Ae. umbellulata, Ae. markgrafii, and Ae. comosa, but not Ae. uniaristata. Chromosome 7 of Ae. umbellulata had more variants (six variants) than the other six U chromosomes (2–3 variants) as revealed by probes oligo-pSc119.2 and (AAC)5. Intraspecific variation in Ae. markgrafii and Ae. comosa was revealed by oligo-pSc119.2 in combination with (ACT)7 and (CTT)12, respectively. At least five variants were found in every chromosome of Ae. markgrafii and Ae. comosa, and up to 18, 10, and 15 variants were identified for chromosomes 2 of Ae. markgrafii, 4 of Ae. comosa subsp. comosa, and 6 of Ae. comosa subsp. subventricosa. The six Ae. uniaristata accessions showed identical FISH signal patterns. A large number of intra-specific polymorphic FISH signals were observed between the homologous chromosomes of Ae. markgrafii and Ae. comosa, especially chromosomes 1, 2, 4, and 7 of Ae. markgrafii, chromosome 4 of Ae. comosa subsp. comosa, and chromosome 6 of Ae. comosa subsp. subventricosa. Twelve Ae. comosa and 24 Ae. markgrafii accessions showed heteromorphism between homologous chromosomes. Additionally, a translocation between the short arms of chromosomes 1 and 7 of Ae. comosa PI 551038 was identified. The FISH karyotypes can be used to clearly identify the chromosome variations of each chromosome in these Aegilops species and also provide valuable information for understanding the evolutionary relationships and structural genomic variation among Aegilops species.

Development of Wheat-Aegilops caudata Introgression Lines and Their Characterization Using Genome-Specific KASP Markers.

Aegilops caudata L. [syn. Ae. markgrafii (Greuter) Hammer], is a diploid wild relative of wheat (2n = 2x = 14, CC) and a valuable source for new genetic diversity for wheat improvement. It has a variety of disease resistance factors along with tolerance for various abiotic stresses and can be used for wheat improvement through the generation of genome-wide introgressions resulting in different wheat–Ae. caudata recombinant lines. Here, we report the generation of nine such wheat–Ae. caudata recombinant lines which were characterized using wheat genome-specific KASP (Kompetitive Allele Specific PCR) markers and multi-color genomic in situ hybridization (mcGISH). Of these, six lines have stable homozygous introgressions from Ae. caudata and will be used for future trait analysis. Using cytological techniques and molecular marker analysis of the recombinant lines, 182 KASP markers were physically mapped onto the seven Ae. caudata chromosomes, of which 155 were polymorphic specifically with only one wheat subgenome. Comparative analysis of the physical positions of these markers in the Ae. caudata and wheat genomes confirmed that the former had chromosomal rearrangements with respect to wheat, as previously reported. These wheat–Ae. caudata recombinant lines and KASP markers are useful resources that can be used in breeding programs worldwide for wheat improvement. Additionally, the genome-specific KASP markers could prove to be a valuable tool for the rapid detection and marker-assisted selection of other Aegilops species in a wheat background.

Production and phenotypic characterization of nascent synthetic decaploids derived from interspecific crosses between a durum wheat cultivar and hexaploid Aegilops species

Wheat and its relatives include some allopolyploid species such as Aegilops juvenalis (Thell.) Eig (DDMMUU) and Aegilops vavilovii (Zhuk.) Chenn. (DDMMSS). Here, we successfully produced for the first time three allodecaploid lines with the AABBDDMMUU and AABBDDMMSS genomes through interspecific crosses between a tetraploid wheat cultivar and the two Aegilops species. Spike architecture of the synthetic lines showing a brittle rachis phenotype strongly resembled that of the parental hexaploid Aegilops species, but not that of the parental tetraploid wheat. Phenotypic differences of the spike and spikelet morphology were caused by one of the parental Aegilops species. Glumes of the synthetic decaploids were extremely hard, and all three synthetic lines had a soft texture with a smooth starch surface in endosperm cells. The soft-textured grains of the synthetic decaploids were due to accumulation of the puroindoline proteins derived from the genomes of parental allohexaploid Aegilops species. Therefore, the nascent synthetic decaploid lines highly reflect the phenotypic characteristics of the pollen parents. With further wheat breeding, the synthetic decaploids could have great potential to improve various traits.

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm

This study was initiated to identify genomic regions conferring resistance to Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). A GWAS of 6,382 high-quality DArTseq SNPs revealed 15 significant SNPs (P-value <10−3) on chromosomes 2D, 3B, 4D and 7B that were associated with KB resistance in individual years. In particular, two SNPs (chromosome 4D) had the maximum R2 values: SNP 1114200 | F | 0–63:T > C at 1.571 cM and R2 of 12.49% and SNP 1103052 | F | 0–61:C > A at 1.574 cM and R2 of 9.02%. These two SNPs displayed strong linkage disequilibrium (LD). An in silico analysis of SNPs on chromosome 4D identified two candidate gene hits, TraesCS4D02G352200 (TaNox8; an NADPH oxidase) and TraesCS4D02G350300 (a rhomboid-like protein belonging to family S54), with SNPs 1103052 | F | 0–61:C > A and 1101835 | F | 0–5:C > A, respectively, both of which function in biotic stress tolerance. The epistatic interaction analysis revealed significant interactions among 4D and 7B loci. A pedigree analysis of confirmed resistant PBLs revealed that Aegilops species is one of the parents and contributed the D genome in these resistant PBLs. These identified lines can be crossed with any elite cultivar across the globe to incorporate novel KB resistance identified on 4B.

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

BackgroundTriticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.ResultsGenetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.ConclusionsRNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

Development and characterization of Triticum turgidum - Aegilops comosa and T. turgidum - Ae. markgrafii amphidiploids.

Aegilops comosa and Ae. markgrafii are diploid progenitors of polyploidy species of Aegilops sharing M and C genomes, respectively. Transferring valuable genes/traits from Aegilops into wheat is an alternative strategy for wheat genetic improvement. The amphidiploids between diploid species of Aegilops and tetraploid wheat can act as bridges to overcome obstacles from direct hybridization and can be developed by the union of unreduced gametes. In this study, we developed seven Triticum turgidum - Ae. comosa and two T. turgidum - Ae. markgrafii amphidiploids. The unreduced gametes mechanisms, including first-division restitution (FDR) and single-division meiosis (SDM), were observed in triploid F1 hybrids of T. turgidum - Ae. comosa (STM) and T. turgidum - Ae. markgrafii (STC). Only FDR was observed in STC hybrids, whereas FDR or both FDR and SDM were detected in the STM hybrids. All seven pairs of M chromosomes of Ae. comosa and C chromosomes of Ae. markgrafii were distinguished by fluorescent in situ hybridization (FISH) probes pSc119.2 and pTa71 combinations with pTa-535 and (CTT)12/(ACT)7, respectively. Meanwhile, the chromosomes of tetraploid wheat and diploid Aegilops parents were distinguished by the same FISH probes. The amphidiploids possessed specific valuable traits such as multiple tillers, large seed size related traits, and stripe rust resistance that could be utilized in the genetic improvement of wheat.

Genetic diversity analysis using DArTseq and SNP markers in populations of Aegilops species from Azerbaijan

Despite a large number of Aegilops L. species and their diversity in Azerbaijan, a majority of this genetic material has not been characterized at molecular levels. The current study has implemented DArTseq technology to evaluate genetic diversity among 150 accessions of different Aegilops species from Azerbaijan. A total of 61,574 SilicoDArTseq and 30,433 SNP markers were used to assess genetic diversity in Aegilops species. Genetic diversity was measured using Shannon’s genetic diversity index, which was equal to 0.852. Dendrograms were built to establish the relationship among Aegilops species. Both the DArTseq and SNP markers could completely segregate the U genome species from those with D genome with high confidence and allowed assigning most species to separate subclusters. The pattern of clustering within the Aegilops tauschii Coss. to certain extent was related to their geographical regions. Genetic structure among the 150 Aegilops accessions was similar with the cluster analysis. Two groups were identified in the studied population, which were exactly corresponded to two clusters in the dendrogram. Principal coordinate analysis confirmed sub-grouping obtained by cluster analysis. The first two principal coordinates explained 82.34% of the total variation. The study reported a sufficient level of genetic diversity of Aegilops from different eco-geographical regions of Azerbaijan, which can be very useful for their conservation and management, as well as for profitable diversifying the gene pool of hexaploid wheat.

Heteromorphic seeds of wheat wild relatives show germination niche differentiation.

Crop wild relatives are fundamental genetic resources for crop improvement. Wheat wild relatives often produce heteromorphic seeds that differ in morphological and physiological traits. Several Aegilops and Triticum species possess, within the same spikelet, a dimorphic seed pair, with one seed being larger than the other. A comprehensive analysis is needed to understand which traits are involved in seed dimorphism and if these aspects of variation in dimorphic pairs are functionally related. To this end, dispersal units of Triticum urartu and five Aegilops species were X-rayed and the different seed morphs weighed. Germination tests were carried out on seeds, both dehulled and left in their dispersal units. Controlled ageing tests were performed to detect differences in seed longevity among seed morphs, and the antioxidant profile was assessed in terms of antioxidant compounds equipment and expression of selected antioxidant genes. We used PCA to group seed morphs sharing similar patterns of germination traits, longevity estimates and antioxidant profile. Different seed morphs differed significantly in terms of mass, final germination, germination timing, longevity estimates and antioxidant profile in most of the tested species. Small seeds germinated slower, had lower germination when left in their dispersal units, a higher antioxidant potential and were longer-lived than large seeds. The antioxidant gene expression varied between morphs, with different patterns across species but not clearly reflecting the phenotypic observations. The results highlight different trait trade-offs in dimorphic seeds of Aegilops and T.urartu, affecting their germination phenology and longevity, thereby resulting in recruitment niche differentiation.

A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat

BackgroundTransposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the wheat genome remains largely unclear.ResultsIn this study, we discovered a miniature (307 bp in length) TE-like sequence in exon 6 of a gene that encodes for 5-formyltetrahydrofolate, in two accessions of wild emmer wheat (T. turgidum ssp. dicoccoides) and has interfered with the gene translation by creating a shorter reading frame as a result of a stop codon. The sequence that was termed Mariam, does not show any structural similarity to known TEs. It does not possess terminal inverted repeats (TIRs) that would allow us to assign this element to one of the TIR DNA super-families, and it does not possess characteristic features of SINE, such as a Pol-III promotor or a poly-A tail. In-silico analysis of five publicly available genome drafts of Triticum and Aegilops species revealed that Mariam element appears in a very low copy number (1–3 insertions) in diploid wheat species and ~ 12 insertions in tetraploid and hexaploidy wheat species. In addition, Mariam element was found to be unique to wheat, as it was not found in other plant genomes. The dynamic nature of Mariam in the wheat genome was assessed by site-specific PCR analysis and revealed that it retained activity in wild emmer populations in a population-specific manner.ConclusionsThis study provides additional insight into the evolutionary impact of TEs in wheat.

In silico determination of transposon-derived miRNAs and targets in Aegilops species

Transposable elements (TEs) are found almost in all living organism, shaping organisms’ genomes. miRNAs are noncoding RNA types which are especially important in gene expression regulations. Many previously determined plant miRNAs are identical/homologous to transposons (TE-MIR). The aim of this study was computational characterization of novel TE-related miRNAs and their targets in Aegilops genome by using stringent criteria. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed by BLAST2GO. Seventeen novel TE-related miRNAs in Aegilops genome were identified for the first time. GO analyses indicated that 40 targets played different roles in biological processes, cellular components and molecular functions. Moreover, these genes were involved in 10 metabolic pathways such as purine metabolism, nitrogen metabolism, oxidative phosphorylation, etc. as a result of KEGG analyses. Identification of miRNAs and their targets are significant to understand miRNA-TEs relationships and even how TEs affect plant growth and development. Obtaining results of this study are expected to provide possible new insight into Aegilops and its related species, wheat, with respect to miRNAs evolution and domestication.Communicated by Ramaswamy H. Sarma

Chromosome specific microsatellite analysis of common wheat lines resistant to powdery mildew

Aim. Determine the chromosome localization of introgressions containing alien genes for resistance to powdery mildew transferred to the wheat genome from three Aegilops species: Ae. sharonensis, Ae. speltoides, and Ae. umbellulata. Methods. Comparative microsatellite analysis of amplicons’ spectra, derived from PCR with primers to SSR loci localized on seven chromosomes of wheat D subgenome. Results. Spectra of amplification of products with DNA of Aurora cultivar, genome substitution amphidiploids Aurosis, Aurodes and Aurolata, using primers to 44 microsatellite loci localized on seven chromosomes of common wheat D subgenome have been obtained. Absence of genome specificity has been determined for most of the analyzed loci. All the studied introgressive lines have been characterized by allele polymorphism for different number of microsatellite loci from all seven chromosomes of D subgenome. This polymorphism included new components in amplicons spectra, which have been different from components of Aurora and genome substituted amphidiploids. Heterozygous genotypes have been also observed. A part of polymorphic loci has been uninformative because the chromosome of genome substituted amphidiploid had null-allele for such loci. For specification of the information about homeological identity of alien chromatin in resistant lines, genes of morphological traits with known chromosome localization have been used. Conclusions. Screening of resistant to powdery mildew wheat introgressive lines for microsatellite loci does not allow an unambiguous identification of chromosome localization of resistance gene because of high polymorphism of microsatellite loci in the genomes of introgressive lines, and because many loci are non-informative. Assumptions have been made about possible connections of resistance genes with chromosomes of homeological groups 3 and 6 in lines derived from Aurodes; 1, 2, 3, and 6 – in lines derived from Aurolata; and homeological group 2 in lines derived from Aurosis.

Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat.

A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.

Molecular cytogenetic analysis reveals evolutionary relationships between polyploid Aegilops species

We applied fluorescent in situ hybridization (FISH) using (GAA)10 microsatellite repeat alone or in combination with oligo pSc119.2-1, pTa535-1, pAs1-1, 5S and 45S rDNA probes to identify individual chromosomes and produce banded karyotypes for five allopolyploid Aegilops species that were thought to possess M subgenome. Labelling patterns of GAA repeats allow identification of individual chromosomes in the studied species including diploid Ae. comosa subsp. heldreichii (2n = MhMh) and Ae. umbellulata (2n = UU); and allopolyploid Ae. biuncialis (2n = UbUbMbMb), Ae. geniculata (2n = UgUgMgMg), Ae. columnaris (2n = UcUcXcXc), Ae. neglecta (2n = UnUnXnXn) and Ae. crassa (2n = 4x = D1D1XcrXcr and 2n = 6x = D1D1XcrXcrDcrDcr). Intraspecific polymorphisms of GAA labelling patterns were observed between different genotypes in each species. FISH results showed that the X* subgenomes of Ae. columnaris and Ae. neglecta are highly similar, implying that both species originated from a common ancestor. However, these X* subgenomes were also distinct from and more heterochromatic when compared to the M* subgenomes of Ae. biuncialis and Ae. geniculata. This suggests that the X* subgenomes may not have originated from the Ae. comosa, as previously thought. Although (GAA)n bands are relatively few and weak in Ae. tauschii (DD genome), all 4x Ae. crassa (D1D1XcrXcr genome) chromosomes showed distinct GAA patterns. (GAA)10 probe alone was not sufficient for the discrimination of all the chromosomes of 6x Ae. crassa (D1D1XcrXcrDcrDcr), which needs a combination of (GAA)10 with the pTa535-1 or pAs1-1 probes.

An Update of Recent Use of Aegilops Species in Wheat Breeding.

Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.

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

BackgroundFlavonoid 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.ResultsThe 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.ConclusionsFrom 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.

β-glucan content in a panel of Triticum and Aegilops genotypes

Non-starch polysaccharides are the main components of dietary fibre, not digested in the small intestine, and with beneficial effects on human health. Among cereals, barley, oats and rye have the highest β-glucan content in the grain (from 3 to 10%), while wheat, rice and corn contain percentages lower than 1%. In this paper, we report the screening of a collection of cultivated and wild wheats for β-glucan content to identify useful genotypes for wheat breeding programs. β-glucan content was determined in a panel of 43 wild and cultivated accessions of diploid, tetraploid and hexaploid wheat (Triticum and Aegilops species), grown in replicated field trials for two years. The average content of β-glucans in durum wheat was 0.51% and 0.55% in 2016 and 2017, respectively, with a range of variation between 0.39 and 0.70%; the bread wheat showed always a β-glucan content lower than 1%. The Triticum wild species showed concentrations ranging between 0.41 and 1.33%. High β-glucan contents were found in some Aegilops species (Ae. markrafii, Ae. umbellulata, Ae. biuncialis and Ae. negletta) with values up to 7.1%. On the overall, the results obtained indicated a wide genetic diversity for β-glucans in some Aegilops species, which can be considered in interspecific gene transfer programs to constitute wheat varieties with β-glucan content higher than 2%, concentration adequate for a 10–15% reduction of cholesterol in the blood.

Broadening the bread wheat D genome.

Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. In this review, we discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. The D genome of allohexaploid bread wheat (Triticum aestivum, 2n = AABBDD) is the least diverse of the three wheat genomes and is unarguably less diverse than that of diploid progenitor Aegilops tauschii (2n = DD). Useful genetic variation and phenotypic traits also exist within each of the wheat group species containing a copy of the D genome: allopolyploid Aegilops species Ae. cylindrica (2n = DcDcCcCc), Ae. crassa 4x (2n = D1D1XcrXcr), Ae. crassa 6x (2n = D1D1XcrXcrDcrDcr), Ae. ventricosa (2n = DvDvNvNv), Ae. vavilovii (2n = D1D1XcrXcrSvSv) and Ae. juvenalis (2n = D1D1XcrXcrUjUj). Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. Some of these D genomes appear to be modified relative to the bread wheat and Ae. tauschii D genomes, and others present in the allopolyploids may also contain useful variation as a result of adaptation to an allopolyploid, multi-genome environment. We summarise the genetic relationships, karyotypic variation and phenotypic traits known to be present in each of the D genome species that could be of relevance for bread wheat improvement and discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. Better understanding of factors controlling chromosome inheritance and recombination in wheat group interspecific hybrids, as well as effective utilisation of new and developing genetics and genomics technologies, have great potential to improve the agronomic potential of the bread wheat D genome.

Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops.

Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).

The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.

Assessing Genetic Diversity to Breed Competitive Biofortified Wheat With Enhanced Grain Zn and Fe Concentrations.

Breeding wheat with enhanced levels of grain zinc (Zn) and iron (Fe) is a cost-effective, sustainable solution to malnutrition problems. Modern wheat varieties have limited variation in grain Zn and Fe, but large-scale screening has identified high levels of Zn and Fe in wild relatives and progenitors of cultivated wheat. The most promising sources of high Zn and Fe are einkorn (Triticum monococcum), wild emmer (T. dicoccoides), diploid progenitors of hexaploid wheat (such as Aegilops tauschii), T. spelta, T. polonicum, and landraces of T. aestivum. This study evaluate the effects of translocations from rye and different Aegilops species in a “Pavon-76” wheat genetic background and utilized in the wheat biofortification breeding program at CIMMYT that uses diverse genetic resources, including landraces, recreated synthetic hexaploids, T. spelta and pre-breeding lines. Four translocations were identified that resulted significantly higher Zn content in “Pavon 76” genetic background than the check varieties, and they had increased levels of grain Fe as well-compared to “Pavon 76.” These lines were also included in the breeding program aimed to develop advanced high Zn breeding lines. Advanced lines derived from diverse crosses were screened under Zn-enriched soil conditions in Mexico during the 2017 and 2018 seasons. The Zn content of the grain was ranging from 35 to 69 mg/kg during 2017 and 38 to 72 mg/kg during 2018. Meanwhile grain Fe ranged from 30 to 43 mg/kg during 2017 and 32 to 52 mg/kg during 2018. A highly significant positive correlation was found between Zn and Fe (r = 0.54; P < 0.001) content of the breeding lines, therefore it was possible to breed for both properties in parallel. Yield testing of the advanced lines showed that 15% (2017) and 24% (2018) of the lines achieved 95–110% yield potential of the commercial checks and also had 12 mg/kg advantage in the Zn content suggesting that greater genetic gains and farmer-preferred wheat varieties were developed and deployed. A decade of research and breeding efforts led to the selection of “best-bet” breeding lines and the release of eight biofortified wheat varieties in target regions of South Asia and in Mexico.