Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding

Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

Natural variation and genetic loci underlying resistance to grain shattering in standing crop of modern wheat

Modern wheat (Triticum aestivum L.) cultivars have a free-threshing habit, which allows for easy manual or mechanical threshing. However, when harvesting is delayed or extreme weather events occur at harvest time, grain shattering can cause severe loss of harvestable yield. In the past, grain size was considered a predisposing factor as large, plump kernels can lead to buckling and breaking of the outer glume, but the correlation between glume strength and shattering is not strong in modern wheat, and it is hypothesised that there may be other genetic mechanisms. Data from two bi-parent populations and a wheat diversity panel were analyzed to explore the underlying genetic basis for grain shattering observed in multiple field experiments through quantitative trait loci (QTL) analysis. Grain shattering had a significant and negative association with grain yield, irrespective of populations and environments. The correlation with plant height was positive in all populations, but correlations with phenology were population specific, being negative in the diversity panel and the Drysdale × Waagan population, and positive in the Crusader × RT812 population. In the wheat diversity panel, allelic variations at well-known major genes (Rht-B1, Rht-D1 and Ppd-D1) showed minimal association with grain shattering. Instead, the genome-wide analysis identified a single locus on chromosome 2DS, which explained 50% of the phenotypic variation, and mapping to ~ 10 Mb from Tenacious glume (Tg) gene. In the Drysdale × Waagan cross, however, the reduced height (Rht) genes showed major effects on grain shattering. At the Rht-B1 locus, the Rht-B1b allele was associated with 10.4 cm shorter plant height, and 18% decreased grain shattering, whereas Rht-D1b reduced plant height by 11.4 cm and reduced grain shattering by 20%. Ten QTL were detected in the Crusader × RT812, including a major locus detected on the long arm of chromosome 5A. All the QTL identified in this population were non-pleiotropic, as they were still significant even after removing the influence of plant height. In conclusion, these results indicated a complex genetic system for grain shattering in modern wheat, which varied with genetic background, involved pleiotropic as well as independent gene actions, and which might be different from shattering in wild wheat species caused by major domestication genes. The influence of Rht genes was confirmed, and this provides valuable information in breeding crops of the future. Further, the SNP marker close to Tg on chromosome 2DS should be considered for utility in marker-assisted selection.

The impact of growth at elevated [CO2] on stomatal anatomy and behavior differs between wheat species and cultivars

The ability of plants to respond to changes in the environment is crucial to their survival and reproductive success. The impact of increasing the atmospheric CO2 concentration (a[CO2]), mediated by behavioral and developmental responses of stomata, on crop performance remains a concern under all climate change scenarios, with potential impacts on future food security. To identify possible beneficial traits that could be exploited for future breeding, phenotypic variation in morphological traits including stomatal size and density, as well as physiological responses and, critically, the effect of growth [CO2] on these traits, was assessed in six wheat relative accessions (including Aegilops tauschii, Triticum turgidum ssp. Dicoccoides, and T. turgidum ssp. dicoccon) and five elite bread wheat T. aestivum cultivars. Exploiting a range of different species and ploidy, we identified key differences in photosynthetic capacity between elite hexaploid wheat and wheat relatives. We also report differences in the speed of stomatal responses which were found to be faster in wheat relatives than in elite cultivars, a trait that could be useful for enhanced photosynthetic carbon gain and water use efficiency. Furthermore, these traits do not all appear to be influenced by elevated [CO2], and determining the underlying genetics will be critical for future breeding programmes.

Evolution and origin of bread wheat

Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.

Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement

Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.

Improvement and Re-Evolution of Tetraploid Wheat for Global Environmental Challenge and Diversity Consumption Demand

Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.

Spanish Spelt Wheat: From an Endangered Genetic Resource to a Trendy Crop

Spelt wheat (Triticum aestivum L. ssp. spelta Thell.) is an ancient wheat that was widely cultivated in the past. This species derived from a cross between emmer wheat (T. turgidum spp. dicoccum Schrank em. Thell.) and Aegilops tauschii Coss. Its main origin was in the Fertile Crescent (Near East), with a secondary center of origin in Europe due to a second hybridization event between emmer and hexaploid wheat. This species has been neglected in most of Europe; however, the desire for more natural foods has driven a revival in interest. Iberian spelt is classified as a geographical group differing to the rest of European spelt. In this review, the particularities, genetic diversity and current situation of Spanish spelt, mainly for quality traits, are discussed.

QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice

Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small-grain crops. Marker-aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F₁ progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping-both within-family and combined across families-with a robust phenotypic dataset collected from four unique year-by-location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large-effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.

Molecular Cytogenetic Identification of Wheat-Aegilops Biuncialis 5Mb Disomic Addition Line with Tenacious and Black Glumes

Production of wheat-alien disomic addition lines is of great value to the exploitation and utilization of elite genes originated from related species to wheat. In this study, a novel wheat-Aegilops biuncialis 5Mb disomic addition line WA317 was characterized by in situ hybridization (ISH) and specific-locus amplified fragment sequencing (SLAF-seq) markers. Compared to its parent Chinese Spring (CS), the glumes of WA317 had black color and were difficult to remove after harvesting, suggesting chromosome 5Mb carried gene(s) related to glume development and Triticeae domestication process. A total of 242 Ae. biuncialis SLAF-based markers (298 amplified patterns) were developed and further divided into four categories by Ae. biuncialis Y17, Ae. umbellulata Y139 and Ae. comosa Y258, including 172 markers amplifying the same bands of U and M genome, six and 102 markers amplifying U-specific and M-specific bands, respectively and eighteen markers amplifying specific bands in Y17. Among them, 45 markers had the specific amplifications in WA317 and were 5Mb specific markers. Taken together, line WA317 with tenacious and black glumes should serve as the foundation for understanding of the Triticeae domestication process and further exploitation of primitive alleles for wheat improvement. Ae. biuncialis SLAF-based markers can be used for studying syntenic relationships between U and M genomes as well as rapid tracking of U and M chromosomal segments in wheat background.

Dissecting genetic loci affecting grain morphological traits to improve grain weight via nested association mapping

The quantitative trait loci (QTLs) for grain morphological traits were identified via nested association mapping and validated in a natural wheat population via haplotype analysis. Grain weight, one of the three most important components of crop yield, is largely determined by grain morphological traits. Dissecting the genetic bases of grain morphology could facilitate the improvement of grain weight and yield production. In this study, four wheat recombinant inbred line populations constructed by crossing the modern variety Yanzhan 1 with three semi-wild wheat varieties (i.e., Chayazheda, Yutiandaomai, and Yunnanxiaomai from Xinjiang, Tibet, and Yunnan, respectively) and one exotic accession Hussar from Great Britain were investigated for grain weight and eight morphological traits in seven environments. Eighty-eight QTLs for all measured traits were totally identified through nested association mapping utilizing 14,643 high-quality polymorphic single nucleotide polymorphism (SNP) markers generated by 90 K SNP array. Among them, 64 (72.7%) QTLs have the most favorable alleles donated by semi-wild wheat varieties. For 14 QTL clusters affecting at least two grain morphological traits, nine QTL clusters were located in similar position with known genes/QTL, and the other five were novel. Three important novel QTLs (i.e., qTGW-1B.1, qTGW-1B.2, and qTGW-1A.1) were further validated in a natural wheat population via haplotype analysis. The favorable haplotypes for these three QTLs might be used in marker-assisted selection for the improvement of wheat yield by modifying morphological traits.

Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat

Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg^2A and Tg^2B as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.

Pleiotropic effects of the wheat domestication gene Q on yield and grain morphology

Transformation from q to Q during wheat domestication functioned outside the boundary of threshability to increase yield, grains m^-2, grain weight and roundness, but to reduce grains per spike/spikelet. Mutation of the Q gene, well-known affecting wheat spike structure, represents a key domestication step in the formation of today's free-threshing, economically important wheats. In a previous study, multiple yield components and spike characteristics were associated with the Q gene interval in the bread wheat 'Forno' × European spelt 'Oberkulmer' recombinant inbred line population. Here, we reported that this interval was also associated with grain yield, grains m^-2, grain morphology, and spike dry weight at anthesis. To clarify the roles of Q in agronomic trait performance, a functional marker for the Q gene was developed. Analysis of allelic effects showed that the bread wheat Q allele conferred free-threshing habit, soft glumes, and short and compact spikes compared with q. In addition, the Q allele contributed to higher grain yield, more grains m^-2, and higher thousand grain weight, whereas q contributed to more grains per spike/spikelet likely resulting from increased preanthesis spike growth. For grain morphology, the Q allele was associated with reduced ratio of grain length to height, indicating a rounder grain. These results are supported by analysis of four Q mutant lines in the Chinese Spring background. Therefore, the transition from q to Q during wheat domestication had profound effects on grain yield and grain shape evolution as well, being a consequence of pleiotropy.

Interspecific and intergeneric hybridization as a source of variation for wheat grain quality improvement

The hybridization events with wild relatives and old varieties are an alternative source for enlarging the wheat quality variability. This review describes these process and their effects on the technological and nutritional quality. Wheat quality and its end-uses are mainly based on variation in three traits: grain hardness, gluten quality and starch. In recent times, the importance of nutritional quality and health-related aspects has increased the range of these traits with the inclusion of other grain components such as vitamins, fibre and micronutrients. One option to enlarge the genetic variability in wheat for all these components has been the use of wild relatives, together with underutilised or neglected wheat varieties or species. In the current review, we summarise the role of each grain component in relation to grain quality, their variation in modern wheat and the alternative sources in which wheat breeders have found novel variation.

Identification of QTL for Grain Size and Shape on the D Genome of Natural and Synthetic Allohexaploid Wheats with Near-Identical AABB Genomes

Grain size and shape associated with yield and milling quality are important traits in wheat domestication and breeding. To reveal the genetic factors on the D genome that control grain size and shape variation, we conducted analysis of quantitative trait loci (QTL) using the F₂ and F_2:3 populations derived from a common allohexaploid wheat line TAA10 and a synthetic allohexaploid wheat XX329, which have near-identical AABB genomes and different DD genomes. Based on genotyping using wheat 660K single nucleotide polymorphism (SNP) array, TAA10 and XX329 exhibited 96.55, 98.10, and 66.26% genetic similarities of A, B, and D genomes, respectively. Phenotypic evaluation revealed that XX329 had higher thousand grain weight (TGW), grain length, width, area and perimeter than TAA10 across all environments, and the grain yield per plot of XX329 increased by 17.43-30.36% compared with that of TAA10 in two environments. A total of nine environmentally stable QTL associated with grain size and shape were mapped on chromosomes 2D and 7D and verified using near isogenic lines (NILs), with the synthetic allohexaploid wheat XX329 contributing favorable alleles. Notably, a novel QTL QTgw.cau-2D controlling grain weight was first identified from the synthetic allohexaploid wheat, which may be a more desirable target for genetic improvement in wheat breeding. Collectively, these results provide further insights into the genetic factors that shaped the grain morphology during wheat evolution and domestication.

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today's fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat

Wheat vernalization requirement is mainly controlled by the VRN1, VRN2, VRN3, and VRN4 genes. The first three have been cloned and have homoeologs in all three genomes. VRN4 has been found only in the D genome (VRN-D4) and has not been cloned. We constructed a high-density genetic map of the VRN-D4 region and mapped VRN-D4 within a 0.09 cM interval in the centromeric region of chromosome 5D. Using telocentric 5D chromosomes generated from the VRN-D4 donor Triple Dirk F, we determined that VRN-D4 is located on the short arm. The VRN-D4 candidate region is colinear with a 2.24 Mb region on Brachypodium distachyon chromosome 4, which includes 127 predicted genes. Ten of these genes have predicted roles in development but we detected no functional polymorphisms associated to VRN-D4. Two recombination events separated VRN-D4 from TaVIL-D1, the wheat homolog of Arabidopsis vernalization gene VIL1, confirming that this gene is not a candidate for VRN-D4. We detected significant interactions between VRN-D4 and other four genes controlling vernalization requirement (Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3), which confirmed that VRN-D4 is part of the vernalization pathway and that it is either upstream or is part of the regulatory feedback loop involving VRN1, VRN2 and VRN3 genes. The precise mapping of VRN-D4 and the characterization of its interactions with other vernalization genes provide valuable information for the utilization of VRN-D4 in wheat improvement and for our current efforts to clone this vernalization gene.

Copy number variation of chromosome 5A and its association with Q gene expression, morphological aberrations, and agronomic performance of winter wheat cultivars

KEY MESSAGE

Our investigations combine chromosome 5A copy number variation associated with relative 5A Q gene expression and morphological and agronomic data to characterize the occurrence of speltoid plants in winter wheat cultivars. The occurrence of speltoid aberrants in wheat breeding is a serious problem that may result in rejection of a candidate cultivar during licensing. The spear-shaped, hard threshing spike is caused by copy number reduction of the domestication gene Q, located on the long arm of wheat chromosome 5A. As a member of the APETALA2-like transcription factor family, the 5AQ gene is involved in flower development and pleiotropically controls other agronomic traits. In this report, a characterization of instability of chromosome 5A is given and effects due to the loss of the Q gene and other genes are discussed. Based on pyrosequencing, we correctly predicted the 5AQ copy number for 392 of 402 tested offspring plants (97.5 %) originating from single speltoid plants of eleven wheat cultivars. The findings indicate that the resulting speltoid plants were either reduced in chromosome 5A copy number or possessed a partial deletion of the distal end of chromosome arm 5AL. 5AQ specific real-time PCR analysis revealed varying transcription levels among cultivars. During early spike development, the relative transcription of the 5AQ gene was always lower in speltoids than in normal square headed wheat plants, most likely leading to the occurrence of the characteristic speltoid spike phenotype. The parallel analysis of 18 agronomic traits revealed pleiotropic effects governed by genes located on 5A. Our results demonstrate that through pyrosequencing one can identify aneuploidy or deletions within chromosome 5A to select against the occurrence of speltoid plants in wheat seedlings.

The origin of spelt and free-threshing hexaploid wheat

It is widely believed that hexaploid wheat originated via hybridization of hulled tetraploid emmer with Aegilops tauschii (genomes DD) and that the nascent hexaploid was spelt, from which free-threshing wheat evolved by mutations. To reassess the role of spelt in the evolution of Triticum aestivum, 4 disomic substitution lines of Ae. tauschii chromosome 2D in Chinese Spring wheat were developed and one of them was used to map the Tg locus, which controls glume tenacity in Ae. tauschii, relative to simple sequence repeat (SSR) and expressed sequence tag loci on wheat chromosome 2D. The segregation of SSR markers was used to assess the presence of Tg alleles in 11 accessions of spelt, both from Europe and from Asia. Ten of them had an inactive tg allele in the D genome and most had an active Tg allele in the B genome. This is consistent with spelt being derived from free-threshing hexaploid wheat by hybridization of free-threshing wheat with hulled emmer. It is proposed that the tetraploid parent of hexaploid wheat was not hulled emmer but a free-threshing form of tetraploid wheat.

Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification

The evolution of the polyploid Triticum wheats is distinctive in that domestication, natural hybridization and allopolyploid speciation have all had significant impacts on their diversification. In this review, I outline the phylogenetic relationships of cultivated wheats and their wild relatives and provide an overview of the recent progress and remaining issues in understanding the genetic and ecological factors that favored their evolution. An attempt is made to view the evolution of the polyploid Triticum wheats as a continuous process of diversification that was initiated by domestication of tetraploid emmer wheat and driven by various natural events ranging from interploidy introgression via hybridization to allopolyploid speciation of hexaploid common wheat, instead of viewing it as a group of discrete evolutionary processes that separately proceeded at the tetraploid and hexaploid levels. This standpoint underscores the important role of natural hybridization in the reticulate diversification of the tetraploid-hexaploid Triticum wheat complex and highlights critical, but underappreciated, issues that concern the allopolyploid speciation of common wheat.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

BACKGROUND

A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.

RESULTS

Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.

CONCLUSIONS

In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

Genotyping of the Q locus in wheat by a simple PCR-RFLP method

The Q locus located on the long arm of chromosome 5A is a key factor in evolution and widespread cultivation of domesticated wheat. The Q locus pleiotropically affects many agronomically important traits including threshability, glume shape and tenacity, rachis fragility and others. Genotyping of the Q locus based on the complex traits is ambiguous due to their multi-genetic control through interactions with the Q locus. To determine the Q locus genotype of wheat accessions possessing A genome, we developed a method based on polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) analysis. The Q and q alleles were clearly distinguished by PCR-RFLP analysis at six conserved single nucleotide polymorphisms in common wheat and wild and cultivated einkorn, emmer and timopheevi wheat. The Q locus genotype of Triticum sinskajae, which is one of the einkorn wheat species and exhibits free-threshing trait, was determined to be qq as expected. This simple PCR-RLFP-based genotyping method should serve as a useful tool in studying the origin of Q and thus wheat evolution after domestication and the following widespread cultivation.

The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci

Threshability is an important crop domestication trait. The wild wheat progenitors have tough glumes enveloping the floret that make spikes difficult to thresh, whereas cultivated wheats have soft glumes and are free-threshing. In hexaploid wheat, the glume tenacity gene Tg along with the major domestication locus Q control threshability. The Q gene was isolated recently and found to be a member of the AP2 class of transcription factors. However, only a few studies have reported on the tough glume trait. Here, we report comparative mapping of the soft glume (sog) gene of diploid Triticum monococcum L. and tenacious glume (Tg) gene of hexaploid T. aestivum L. using chromosome-specific SSR and RFLP markers. The sog gene was flanked by Xgwm71 and Xbcd120 in a 6.8 cM interval on chromosome 2A(m)S of T. monococcum whereas Tg was targeted to a 8.1 cM interval flanked by Xwmc503 and Xfba88 on chromosome 2DS of T. aestivum. Deletion bin mapping of the flanking markers assigned sog close to the centromere on 2AS, whereas Tg was mapped to the most distal region on 2DS. Both 2AS and 2DS maps were colinear ruling out the role of chromosome rearrangements for their non-syntenic positions. Therefore, sog and Tg are not true orthologues suggesting the possibility of a diverse origin.

Comparative genomic analysis and expression of the APETALA2-like genes from barley, wheat, and barley-wheat amphiploids

BACKGROUND

The APETALA2-like genes form a large multi-gene family of transcription factors which play an important role during the plant life cycle, being key regulators of many developmental processes. Many studies in Arabidopsis have revealed that the APETALA2 (AP2) gene is implicated in the establishment of floral meristem and floral organ identity as well as temporal and spatial regulation of flower homeotic gene expression.

RESULTS

In this work, we have cloned and characterised the AP2-like gene from accessions of Hordeum chilense and Hordeum vulgare, wild and domesticated barley, respectively, and compared with other AP2 homoeologous genes, including the Q gene in wheat. The Hordeum AP2-like genes contain two plant-specific DNA binding motifs called AP2 domains, as does the Q gene of wheat. We confirm that the H. chilense AP2-like gene is located on chromosome 5Hch. Patterns of expression of the AP2-like genes were examined in floral organs and other tissues in barley, wheat and in tritordeum amphiploids (barley x wheat hybrids). In tritordeum amphiploids, the level of transcription of the barley AP2-like gene was lower than in its barley parental and the chromosome substitutions 1D/1Hch and 2D/2Hch were seen to modify AP2 gene expression levels.

CONCLUSION

The results are of interest in order to understand the role of the AP2-like gene in the spike morphology of barley and wheat, and to understand the regulation of this gene in the amphiploids obtained from barley-wheat crossing. This information may have application in cereal breeding programs to up- or down-regulate the expression of AP2-like genes in order to modify spike characteristics and to obtain free-threshing plants.

Introgression of wheat chromosome 2D or 5D into tritordeum leads to free-threshing habit

Hexaploid tritordeum is the amphiploid derived from the cross between the diploid wild barley Hordeum chilense and durum wheat. The non-free-threshing habit is a constraint to this species becoming a new crop. Three tritordeum lines (HT374, HT376, and HT382) showing the free-threshing habit were selected from crosses between tritordeum and bread wheat. All three lines were euploids, as revealed by mitotic chromosome counting. Genomic in situ hybridization analysis made it possible to distinguish differences among these lines. While the line HT382 carries only 10 chromosomes from H. chilense, the lines HT374 and HT376 have 12. These results suggest that HT382 is a double chromosome substitution line between H. chilense and the wheat D genome, while HT374 and HT376 each have one pair of H. chilense (Hch) chromosomes substituted by wheat D chromosomes. Molecular characterization revealed that HT382 is a 1D/(1Hch), 2D/(2Hch) chromosome substitution line, whereas HT374 and HT376 have 5D/(5Hch) substitutions. On the basis of previous knowledge, it seems that the absence of chromosome 2Hch or 5Hch is more important for producing the free-threshing habit than the presence of chromosome 2D or 5D, while chromosome 1Hch seems to be unrelated to the trait. These free-threshing tritordeum lines constitute an important advance in the tritordeum breeding program.

Map-based analysis of genetic loci on chromosome 2D that affect glume tenacity and threshability, components of the free-threshing habit in common wheat (Triticum aestivum L.)

During the domestication of bread wheat (Triticum aestivum L.), evolutionary modifications that took place in seed dispersal mechanisms enhanced its suitability for agricultural production. One of these modifications involved the evolution of the free-threshing or hulless characteristic. In this study, we studied quantitative trait loci (QTL) affecting components of the free-threshing habit (threshability and glume tenacity) on chromosome 2D in a recombinant inbred line (RIL) population developed by the International Triticeae Mapping Initiative (ITMI) as well as the tenacious glumes 1 (Tg1) gene in F(2) progeny (CS/CS2D F(2)) of a cross between Chinese Spring and the 2D2 substitution line [Chinese Spring (Ae. tauschii 2D)]. In the ITMI population, two QTL affected threshability (QFt.orst-2D.1 and QFt.orst-2D.2) and their location coincided with QTL affecting glume tenacity (QGt.orst-2D.1 and QGt.orst-2D.2). In the CS/CS2D F(2) population, the location of QTL that affected glume tenacity (QGt.orst-2D.1), the size of a glume base scar after detachment (QGba.orst-2D), and Tg1 (12-cM interval between Xwmc112 and Xbarc168) also coincided. Map comparisons suggest that QFt-orst-2D.1, QGt.orst-2D.1, and QGba.orst-2D correspond to Tg1 whereas QFt.orst-2D.2 and QGt.orst-2D.2 appear to represent separate loci. The observation of coincident QTL for threshability and glume tenacity suggests that threshability is a function of glume adherence. In addition, the observation of the coincident locations of Tg1 and QTL for the force required to detach a glume and the size of a glume base scar after detachment suggests that Tg1's effect on both glume tenacity and threshability resides on its ability to alter the level of physical attachment of glumes to the rachilla of a spikelet.

Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.)

The mature spike rachis of wild emmer [Triticum turgidum L. ssp. dicoccoides (Körn. ex Asch. and Graebner) Thell.] disarticulates spontaneously between each spikelet leading to the dispersion of wedge-type diaspores. By contrast, the spike rachis of domesticated emmer (Triticum turgidum L. ssp. turgidum) fails to disarticulate and remains intact until it is harvested. This major distinguishing feature between wild and domesticated emmer is controlled by two major genes, brittle rachis 2 (Br-A2) and brittle rachis 3 (Br-A3) on the short arms of chromosomes 3A and 3B, respectively. Because of their biological and agricultural importance, a map-based analysis of these genes was undertaken. Using two recombinant inbred chromosome line (RICL) populations, Br-A2, on chromosome 3A, was localized to a approximately 11-cM region between Xgwm2 and a cluster of linked loci (Xgwm666.1, Xbarc19, Xcfa2164, Xbarc356, and Xgwm674), whereas Br-A3, on chromosome 3B, was localized to a approximately 24-cM interval between Xbarc218 and Xwmc777. Comparative mapping analyses suggested that both Br-A2 and Br-A3 were present in homologous regions on chromosomes 3A and 3B, respectively. Furthermore, Br-A2 and Br-A3 from wheat and Btr1/Btr2 on chromosome 3H of barley (Hordeum vulgare L.) also were homologous suggesting that the location of major determinants of the brittle rachis trait in these species has been conserved. On the other hand, brittle rachis loci of wheat and barley, and a shattering locus on rice chromosome 1 did not appear to be orthologous. Linkage and deletion-based bin mapping comparisons suggested that Br-A2 and Br-A3 may reside in chromosomal areas where the estimated frequency of recombination was approximately 4.3 Mb/cM. These estimates indicated that the cloning of Br-A2 and Br-A3 using map-based methods would be extremely challenging.

Genetic variability of the low-molecular-weight glutenin subunits in spelt wheat (Triticum aestivum ssp. spelta L. em Thell.)

The low-molecular-weight glutenin subunit composition of a collection of 403 accessions of spelt wheat ( Triticum aestivum ssp. spelta L. em. Thell) was analyzed by SDS-PAGE. Extensive variation was found, including 46 different patterns for zone B and 16 for zone C. Patterns within zone B exhibited from two to six bands and patterns in zone C had between four and six bands in SDS-PAGE gels. A higher number of bands was observed when urea was added to the gels. Zone B exhibited between six and 11 bands, and we identified 14 new patterns in this zone. For zone C, up to ten new patterns that comprised between five and nine bands were detected. For both zones, 86 patterns were found. The variability detected in this material is greater than that detected in other hulled wheats.

Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat

To understand the origin and evolution of common wheat, chloroplast (ct) and nuclear DNA variations were studied in five hexaploid and three tetraploid wheat subspecies. Based on chloroplast simple sequence repeats at 24 loci, they were classified into two major plastogroups. Plastogroup I consisted of 11 plastotypes, including the major plastotype H10 that occurred at the highest frequency (59%) in common wheat. Plastogroup II consisted of five plastotypes and occurred in eight out of 27 accessions of T. aestivum ssp. spelta and one accession of ssp. aestivum. As for nuclear DNA variations, AFLP data using 10 primer sets revealed two major clades of a phylogenetic tree constructed by UPGMA (unweighted pair-group method with arithmetic mean), one consisting of common wheat and the other of emmer wheat. The clade of common wheat was further divided into two major and six minor subclades. One of the major subclades consisted only of non-free-threshing ssp. spelta accessions, which were grouped into two clusters, one consisting only of accessions with plastogroup I ctDNA and the other with both plastogroups I and II. T. aestivum ssp. macha, another non-free-threshing common wheat, formed the other cluster. Taken together, our data indicate the existence of at least two maternal lineages in common wheat and support the hypothesis that European spela wheat originated in Europe separately from other groups of common wheat.

About the origin of European spelt ( Triticum spelta L.): allelic differentiation of the HMW Glutenin B1-1 and A1-2 subunit genes

To investigate the origin of European spelt ( Triticum spelta L., genome AABBDD) and its relation to bread wheat ( Triticum aestivum L., AABBDD), we analysed an approximately 1-kb sequence, including a part of the promoter and the coding region, of the high-molecular-weight (HMW) glutenin B1-1 and A1-2 subunit genes in 58 accessions of hexa- and tetraploid wheat from different geographical regions. Six Glu-B1-1 and five Glu-A1-2 alleles were identified based on 21 and 19 informative sites, respectively, which suggests a polyphyletic origin of the A- and B-genomes of hexaploid wheat. In both genes, a group of alleles clustered in a distinct, so-called beta subclade. High frequencies of alleles from the Glu-B1-1 and Glu-A1-2 beta subclades differentiated European spelt from Asian spelt and bread wheat. This indicates different origins of European and Asian spelt, and that European spelt does not derive from the hulled progenitors of bread wheat. The conjoint differentiation of alleles of the A- and B-genome in European spelt suggests the introgression of a tetraploid wheat into free-threshing hexaploid wheat as the origin of European spelt.

Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness in wheat ( Triticum aestivum L.)

Recombinant inbred lines of the International Triticeae Mapping Initiative (ITMI) mapping population were used to localize genetic loci that affect traits related to the free-threshing habit (percent threshability, glume tenacity, and spike fragility) and to spike morphology (spike length, spikelet number, and spike compactness) of wheat ( Triticum aestivum L.). The ITMI population was planted in three environments during 1999 and 2000, and phenotypic and genotypic data were used for composite interval mapping. Two quantitative trait loci (QTL) that consistently affected threshability-associated traits were localized on chromosomes 2D and 5A. Coincident QTL on the short arm of 2D explained 44% of the variation in threshability, 17% of the variation in glume tenacity, and 42% of the variation in rachis fragility. QTL on chromosomes 2D probably represent the effect of Tg, a gene for tenacious glumes. Coincident QTL on the long arm of 5A explained 21% and 10% of the variation in glume tenacity and rachis fragility, respectively. QTL on 5A are believed to represent the effect of Q. Overall, free-threshing-related characteristics were predominantly affected by Tg and to a lesser extent by Q. Other QTL that were significantly associated with threshability-related traits in at least one environment were localized on chromosomes 2A, 2B, 6A, 6D, and 7B. Four QTL on chromosomes 1B, 4A, 6A, and 7A consistently affected spike characteristics. Coincident QTL on the short arm of chromosome 1B explained 18% and 7% of the variation in spike length and spike compactness, respectively. QTL on the long arm of 4A explained 11%, 14%, and 12% of the variation in spike length, spike compactness, and spikelet number, respectively. A QTL on the short arm of 6A explained 27% of the phenotypic variance for spike compactness, while a QTL on the long arm of 7A explained 18% of the variation in spikelet number. QTL on chromosomes 1B and 6A appear to affect spike dimensions by modulating rachis internode length, while QTL on chromosomes 4A and 7A do so by affecting the formation of spikelets. Other QTL that were significantly associated with spike morphology-related traits, in at least one environment, were localized on chromosomes 2B, 3A, 3D, 4D, and 5A.

Genetics and geography of wild cereal domestication in the near east

About 12,000 years ago, humans began the transition from hunter-gathering to a sedentary, agriculture-based society. From its origins in the Near East, farming expanded throughout Europe, Asia and Africa, together with various domesticated plants and animals. Where, how and why agriculture originated is still debated. But newer findings, on the basis of genome-wide measures of genetic similarity, have traced the origins of some domesticated cereals to wild populations of naturally occurring grasses that persist in the Near East. A better understanding of the genetic differences between wild grasses and domesticated crops adds important facets to the continuing debate on the origin of Western agriculture and the societies to which it gave rise.

Loss of chromosomes 2R and 5RS in octoploid triticale selected for agronomic traits

The advanced lines of octoploid triticale which have been bred for nearly a half century in China show significant improvements in agronomic traits such as plant height, fertility, threshability, maturity and seed plumpness, although no intentional cytological selection had been performed. In this study, eight primary and six advanced lines were analyzed by fluorescence and genomic in situ hybridization to elucidate their chromosome constitutions. In the advanced lines, about 70% of the plants examined had 2n = 56 chromosomes (range: 50 to 58). Almost all advanced lines, however, had lost rye chromosome 2R and the short arm of 5R (5RS). The exceptions were lines Y1005 and Y4683: The former had lost only the 2R chromosome and the latter only 5RS. The reduction of rye chromosomes was compensated by an extra pair of 2D or A-genome (possibly 2A) chromosomes in plants with 2n = 56. This suggests that the loss of 2R and 5RS chromosomes contributes to the improvement of octoploid triticale. Since the plants with chromosome 2R are non-free threshing and chromosome 2D of synthetic wheat is known to carry the Tg (tenacious glumes) gene, it is possible that chromosome 2R carries a gene affecting the threshability, and we carried out selection to remove it. We also discuss the possible relationshipbetween 5RS and the genetic stability of octoploid triticale.

Analysis of the resistance of Aegilops squarrosa to the wheatgrass mildew fungus by using the gene-for-gene reationship

Pm10 and Pm15, resistance genes to Erysiphe graminis f. sp. agropyri, are located on the D genome of common wheat. It was determined whether or not they were carried by existing lines of the D genome donor, Aegilops squarrosa, using the gene-for-gene relationship. Two lines of Ae. squarrosa tested (one was var. meyeri and the other was var. anathera) were susceptible to culture Tk-1 of E. graminis f. sp. tritici and were highly resistant to culture Ak-1 of E. graminis f. sp. agropyri. The two lines were inoculated with an F1 population derived from the cross Ak-1 × Tk-1. Comparative analyses of the segregation patterns revealed that Ppm10 and Ppm15, avirulence genes corresponding to Pm10 and Pm15, respectively, are involved in the avirulence of Ak-1 on var. meyeri and var. anathera, respectively. According to the gene-for-gene relationship, var. meyeri and var. anathera were inferred to carry Pm10 and Pm15, respectively. Analysis with a synthetic hexaploid confirmed the inference.

Hybrid seed development and viability in crosses of T. aestivum (cv. Chinese Spring) monosomic lines with S. cereale

The diploid and tetraploid wheats have a crossing barrier that inhibits development and viability of the F1 hybrid seeds which result from their pollination with rye. This barrier is ineffective in synthetic or natural hexaploid wheat × rye crosses. From the results obtained by crossing the Chinese Spring monosomic series to a diploid rye composite, it was concluded that the breakdown of this barrier in hexaploid wheats is determined by polygenes, but may also involve genedosage effects. While more than half of the hexaploidwheat chromosomes may contribute to the breakdown of the barrier, chromosome 1D had the strongest effect. Its absence resulted in shrivelled and inviable hybrid kernels similar to those obtained when the T. durum cultivar Langdon was crossed with rye.

HOMOEOLOGY BETWEEN AGROPYRON ELONGATUM CHROMOSOMES AND TRITICUM AESTIVUM CHROMOSOMES

Genetic compensation of Agropyron chromosomes for wheat chromosomes in the male gametophyte and compensation of Agropyron chromosomes for wheat chromosomes in disomic substitutions were used to investigate relationships between the chromosomes of Agropyron elongatum (Host.) P.B. (2n = 2x = 14) and Triticum aestivum L. emend. Thell. (2n = 6x = 42). Gametophytic compensation indicated that A. elongatum chromosomes I, II, III, IV, and VII were related to wheat chromosomes of homoeologous groups 1, 7, 4, 3, and 6, respectively, and were designated 1E, 7E, 4E, 3E, and 6E. Chromosomes V and VI appeared to be related to homoeologous group 2. Other analyses showed that chromosomes V and VI originated from arm exchanges between chromosome 2E and other Agropyron chromosomes. An unaltered disome of Agropyron chromosome 2E was added to the wheat chromosome complement. In the disomic substitutions Agropyron chromosomes 1E, 6E, and 7E compensated for all three wheat homoeologues of the respective homoeologous groups. Chromosome 4E fully compensated for chromosome 4D but only partially for chromosomes 4A and 4B. Chromosomes V and VI compensated poorly or not at all for wheat chromosomes of group 2.

DISOMIC AND DITELOSOMIC ADDITIONS OF DIPLOID AGROPYRON ELONGATUM CHROMOSOMES TO TRITICUM AESTIVUM

A set of disomic addition lines was produced in which each chromosome of Agropyron elongatum (2n = 14) was added to the chromosome complement of Triticum aestivum cv. Chinese Spring. In addition a complete set of ditelosomic addition lines involving Agropyron chromosome arms IS, IIα, IIIα, IVS, IVL, VS, VL, VIS and VIIα, was developed. Except for disomic addition line VII which is similar to Chinese Spring, each added alien chromosome pair was found to have a specific effect on plant morphology. Five disomic addition lines had reduced fertility. Agropyron chromosome arms carrying genes for anthocyanin production, waxless foliage, tenacious glumes, and several other traits were identified. The single Agropyron chromosomes in the monosomic addition lines usually have either minor effects or no effect on plant morphology and fertility.The disomic addition lines are similar in many characters to tetrasomics of the corresponding homoeologous wheat chromosomes and show characters that are not present in either Ag. elongatum or the amphiploid, T. aestivum × Ag. elongatum. Thus many of the effects are due to gene dosage. If individual disomic addition lines are compared with the amphiploid a significant role of interchromosomal gene interactions is apparent.In combination with knowledge of the homoeologous relationships among wheat and alien chromosomes, sets of disomic addition lines can provide valuable information on the evolutionary past of genomes in Triticinae. In monosomic addition lines only Agropyron chromosome IV paired with a wheat chromosome and it is concluded that it is improbable that Agropyron genomes played any role in the evolution of the polyploid series of Aegilops and Triticum.