A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes

Molecular cytological analysis of alien introgressions in common wheat lines created by crossing of Triticum aestivum with T. dicoccoides and T. dicoccum

Wild and domesticated emmer (ВВАА, 2n = 28) are of significant interest for expanding the genetic diversity of common wheat as sources of a high protein and microelement grain content, resistance to many biotic and abiotic factors. Particular interest in these species is also determined by their close relationship with Triticum aestivum L., which facilitates interspecific hybridization. The objective of this work was to analyze the nature of alien introgressions in hybrid lines from crossing common wheat varieties with T. dicoccoides and T. dicoccum, and to assess the effect of their genome fragments on the cytological stability of introgression lines. A C-banding technique and genotyping with SNP and SSR markers were used to determine localization and length of introgression fragments. Assessment of cytological stability was carried out on the basis of chromosome behavior in microsporogenesis. A molecular cytogenetic analysis of introgression wheat lines indicated that the inclusion of the genetic material of wild and domesticated emmer was carried out mainly in the form of whole arms or large fragments in the chromosomes of the B genome and less extended inserts in the A genome. At the same time, the highest frequency of introgressions of the emmer genome was observed in chromosomes 1A, 1B, 2B, and 3B. The analysis of the final stage of meiosis showed a high level of cytological stability in the vast majority of introgression wheat lines (meiotic index was 83.0-99.0 %), which ensures the formation of functional gametes in an amount sufficient for successful reproduction. These lines are of interest for the selection of promising material with agronomically valuable traits and their subsequent inclusion in the breeding process.

Dissection of Structural Reorganization of Wheat 5B Chromosome Associated With Interspecies Recombination Suppression

Chromosomal rearrangements that lead to recombination suppression can have a significant impact on speciation, and they are also important for breeding. The regions of recombination suppression in wheat chromosome 5B were identified based on comparisons of the 5B map of a cross between the Chinese Spring (CS) variety of hexaploid wheat and CS-5Bdic (genotype CS with 5B substituted with its homologue from tetraploid Triticum dicoccoides) with several 5B maps of tetraploid and hexaploid wheat. In total, two regions were selected in which recombination suppression occurred in cross CS × CS-5Bdic when compared with other maps: one on the short arm, 5BS_RS, limited by markers BS00009810/BS00022336, and the second on the long arm, 5BL_RS, between markers Ra_c10633_2155 and BS00087043. The regions marked as 5BS_RS and 5BL_RS, with lengths of 5 Mb and 3.6 Mb, respectively, were mined from the 5B pseudomolecule of CS and compared to the homoeologous regions (7.6 and 3.8 Mb, respectively) of the 5B pseudomolecule of Zavitan (T. dicoccoides). It was shown that, in the case of 5BS_RS, the local heterochromatin islands determined by the satellite DNA (119.2) and transposable element arrays, as well as the dissimilarity caused by large insertions/deletions (chromosome rearrangements) between 5BSs aestivum/dicoccoides, are likely the key determinants of recombination suppression in the region. Two major and two minor segments with significant loss of similarity were recognized within the 5BL_RS region. It was shown that the loss of similarity, which can lead to suppression of recombination in the 5BL_RS region, is caused by chromosomal rearrangements, driven by the activity of mobile genetic elements (both DNA transposons and long terminal repeat retrotransposons) and their divergence during evolution. It was noted that the regions marked as 5BS_RS and 5BL_RS are associated with chromosomal rearrangements identified earlier by С-banding analysis of intraspecific polymorphism of tetraploid emmer wheat. The revealed divergence in 5BS_RS and 5BL_RS may be a consequence of interspecific hybridization, plant genetic adaptation, or both.

Harnessing the diversity of wild emmer wheat for genetic improvement of durum wheat

The multiple derivative lines (MDLs) characterized in this study offer a promising strategy for harnessing the diversity of wild emmer wheat for durum and bread wheat improvement. Crop domestication has diminished genetic diversity and reduced phenotypic plasticity and adaptation. Exploring the adaptive capacity of wild progenitors offer promising opportunities to improve crops. We developed a population of 178 BC₁F₆ durum wheat (Triticum turgidum ssp. durum) lines by crossing and backcrossing nine wild emmer wheat (T. turgidum ssp. dicoccoides) accessions with the common durum wheat cultivar 'Miki 3'. Here, we describe the development of this population, which we named as multiple derivative lines (MDLs), and demonstrated its suitability for durum wheat breeding. We genotyped the MDL population, the parents, and 43 Sudanese durum wheat cultivars on a Diversity Array Technology sequencing platform. We evaluated days to heading and plant height in Dongola (Sudan) and in Tottori (Japan). The physical map length of the MDL population was 9 939 Mb with an average of 1.4 SNP/Mb. The MDL population had greater diversity than the Sudanese cultivars. We found high gene exchange between the nine wild emmer accessions and the MDL population, indicating that the MDL captured most of the diversity in the wild emmer accessions. Genome-wide association analysis identified three loci for days to heading on chromosomes 1A and 5A in Dongola and one on chromosome 3B in Tottori. For plant height, common genomic loci were found on chromosomes 4A and 4B in both locations, and one genomic locus on chromosome 7B was found only in Dongola. The results revealed that the MDLs are an effective strategy towards harnessing wild emmer wheat diversity for wheat genetic improvement.

Detecting major introgressions in wheat and their putative origins using coverage analysis

Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Detecting major introgressions in wheat and their putative origins using coverage analysis

Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Genetic Analysis of Hexaploid Wheat (Triticum aestivum L.) Using the Complete Sequencing of Chloroplast DNA and Haplotype Analysis of the Wknox1 Gene

The aim of the presented study is a genetic characterization of the hexaploid wheat Triticum aestivum L. Two approaches were used for the genealogical study of hexaploid wheats—the complete sequencing of chloroplast DNA and PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth-exon region of Wknox1b. The complete chloroplast DNA sequences of 13 hexaploid wheat samples were determined: Free-threshing—T. aestivum subsp. aestivum, one sample; T. aestivum subsp. compactum, two samples; T. aestivum subsp. sphaerococcum, one sample; T. aestivum subsp. carthlicoides, four samples. Hulled—T. aestivum subsp. spelta, three samples; T. aestivum subsp. vavilovii jakubz., two samples. The comparative analysis of complete cpDNA sequences of 20 hexaploid wheat samples (13 samples in this article plus 7 samples sequenced in this laboratory in 2018) was carried out. PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth exon region of Wknox1b of all 20 hexaploid wheat samples was carried out. The 20 hexaploid wheat samples (13 samples in this article plus 7 samples in 2018) can be divided into two groups—T. aestivum subsp. spelta, three samples and T. aestivum subsp. vavilovii collected in Armenia, and the remaining 16 samples, including T. aestivum subsp. vavilovii collected in Europe (Sweden). If we take the cpDNA of Chinese Spring as a reference, 25 SNPs can be identified. Furthermore, 13–14 SNPs can be identified in T. aestivum subsp. spelta and subsp. vavilovii (Vav1). In the other samples up to 11 SNPs were detected. 22 SNPs are found in the intergenic regions, 2 found in introns, and 10 SNPs were found in the genes, of which seven are synonymous. PCR-based haplotype analysis of the fourth intron of Wknox1d and the fifth-to-sixth-exon region of Wknox1b provides an opportunity to make an assumption that hexaploid wheats T. aestivum subsp. macha var. palaeocolchicum and var. letshckumicum differ from other macha samples by the absence of a 42 bp insertion in the fourth intron of Wknox1d. One possible explanation for this observation would be that two Aegilops tauschii Coss. (A) and (B) participated in the formation of hexaploids through the D genome: Ae. tauschii (A)—macha (1–5, 7, 8, 10–12), and Ae. tauschii (B)—macha M6, M9, T. aestivum subsp. aestivum cv. ‘Chinese Spring’ and cv. ‘Red Doly’.

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

BACKGROUND

Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species.

METHODS

Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a-e, II a and II b).

RESULTS

The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.

Identification and characterization of large-scale genomic rearrangements during wheat evolution

Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they might have occurred via unequal intra-strand recombination or double-strand break (DSB) events. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.

Molecular mapping of major QTL conferring resistance to orange wheat blossom midge (Sitodiplosis mosellana) in Chinese wheat varieties with selective populations

Two novel midge resistance QTL were mapped to a 4.9-Mb interval on chromosome arm 4AL based on the genetic maps constructed with SNP markers. Orange wheat blossom midge (OWBM) is a devastating insect pest affecting wheat production. In order to detect OWBM resistance genes and quantitative trait loci (QTL) for wheat breeding, two recombinant inbred line (RIL) populations were established and used for molecular mapping. A total of seven QTL were detected on chromosomes 2D, 4A, 4D and 7D, respectively, of which positive alleles were all from the resistant parents except for the QTL on 7D. Two stable QTL (QSm.hbau-4A.2-1 and QSm.hbau-4A.2-2) were detected in both populations with the LOD scores ranging from 5.58 to 29.22 under all three environments, and they explained a combined phenotypic variation of 24.4-44.8%. These two novel QTL were mapped to a 4.9-Mb physical interval. The single-nucleotide polymorphism (SNP) markers AX-109543456, AX-108942696 and AX-110928325 were closely linked to the QTL and could be used for marker-assisted selection (MAS) for OWBM resistance in wheat breeding programs.

Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments

Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F₆ RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.

Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments

Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F₆ RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.

Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor

Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat. We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5S^se, which targeted them for recombination. We genotyped 28 BC₁F₁ and 84 F₂ progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC₁F₁ and F₂ genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5S^se chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5S^se was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.

Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.)

This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent through marker-assisted selection. Based on five independent BC₃F_3:4 segregating populations derived from BC₃F₃ plants with different heterozygous segments for the target QTL site and the results of genotyping analysis performed using the Wheat660 K SNP array, it was possible to delimit the QTL region to a physical interval of approximately 6.5 Mb (677.11-683.61 Mb, IWGSC Ref Seq v1.0). Field trials across multiple environments showed that NILs^JD6 had a consistent effect on increasing the TGW by 5.16-27.48% and decreasing the grain number per spike (GNS) by 3.98-32.91% compared to the corresponding NILs^ND3338, which exhibited locus-specific TGW-GNS trade-offs. Moreover, by using RNA sequencing (RNA-Seq) of whole grains at 10 days after pollination stage of multiple NILs, we found that differentially expressed genes between the NIL pairs were significantly enriched for cell cycle and the replication of chromosome-related genes, hence affecting cell division and cell proliferation. Overall, our results provide a basis for map-based cloning of the major QTL and determining the mechanisms underlying TGW-GNS trade-offs in wheat, which would help to fine-tune these two components and maximize the grain yield for breeders.

Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs

Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for [Formula: see text] were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.

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

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

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

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

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B

Comparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B. Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.

Introgression of the Aegilops speltoides Su1-Ph1 Suppressor into Wheat

Meiotic pairing between homoeologous chromosomes in polyploid wheat is inhibited by the Ph1 locus on the long arm of chromosome 5 in the B genome. Aegilops speltoides (genomes SS), the closest relative of the progenitor of the wheat B genome, is polymorphic for genetic suppression of Ph1. Using this polymorphism, two major suppressor loci, Su1-Ph1 and Su2-Ph1, have been mapped in Ae. speltoides. Su1-Ph1 is located in the distal, high-recombination region of the long arm of the Ae. speltoides chromosome 3S. Its location and tight linkage to marker Xpsr1205-3S makes Su1-Ph1 a suitable target for introgression into wheat. Here, Xpsr1205-3S was introgressed into hexaploid bread wheat cv. Chinese Spring (CS) and from there into tetraploid durum wheat cv. Langdon (LDN). Sequential fluorescence in situ hybridization and genomic in situ hybridization showed that an Ae. speltoides segment with Xpsr1205-3S replaced the distal end of the long arm of chromosome 3A. In the CS genetic background, the chromosome induced homoeologous chromosome pairing in interspecific hybrids with Ae. peregrina but not in progenies from crosses involving alien disomic substitution lines. In the LDN genetic background, the chromosome induced homoeologous chromosome pairing in both interspecific hybrids and progenies from crosses involving alien disomic substitution lines. We conclude that the recombined chromosome harbors Su1-Ph1 but its expression requires expression of complementary gene that is present in LDN but absent in CS. We suggest that it is unlikely that Su1-Ph1 and ZIP4-1, a paralog of Ph1 located on wheat chromosomes 3A and 3B and Ae. tauschii chromosome 3D, are equivalent. The utility of Su1-Ph1 for induction of recombination between homoeologous chromosomes in wheat is illustrated.