Microsatellite analysis of Aegilops tauschii germplasm

The highly polymorphic diploid grass Aegilops tauschii isthe D-genome donor to hexaploid wheat and represents a potential source for bread wheat improvement. In the present study microsatellite markers were used for germplasm analysis and estimation of the genetic relationship between 113 accessions of Ae. tauschii from the gene bank collection at IPK, Gatersleben. Eighteen microsatellite markers, developed from Triticum aestivum and Ae. tauschii sequences, were selected for the analysis. All microsatellite markers showed a high level of polymorphism. The number of alleles per microsatellite marker varied from 11 to 25 and a total of 338 alleles were detected. The number of alleles per locus in cultivated bread wheat germplasm had previously been found to be significantly lower. The highest levels of genetic diversity for microsatellite markers were found in accessions from the Caucasian countries (Georgia, Armenia and the Daghestan region of Russia) and the lowest in accessions from the Central Asian countries (Uzbekistan and Turkmenistan). Genetic dissimilarity values between accessions were used to produce a dendrogram of the relationships among the accessions. The result showed that all of the accessions could be distinguished and clustered into two large groups in accordance with their subspecies taxonomic classification. The pattern of clustering of the Ae. tauschii accessions is according to their geographic distribution. The data suggest that a relatively small number of microsatellites can be used to estimate genetic diversity in the germplasm of Ae. tauschii and confirm the good suitability of microsatellite markers for the analysis of germplasm collections. Received: 8 September 1999 / Accepted: 7 October 1999     

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

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

Genetic mapping of a novel recessive allele for non-glaucousness in wild diploid wheat <Emphasis Type="Italic">Aegilops tauschii</Emphasis>: implications for the evolution of common wheat

Cuticular wax on the aerial surface of plants has a protective function against many environmental stresses. The bluish–whitish appearance of wheat leaves and stems is called glaucousness. Most modern cultivars of polyploid wheat species exhibit the glaucous phenotype, while in a wild wheat progenitor, Ae. tauschii, both glaucous and non-glaucous accessions exist. Iw2, a wax inhibitor locus on the short arm of chromosome 2D, is the main contributor to this phenotypic variation in Ae. tauschii, and the glaucous/non-glaucous phenotype of Ae. tauschii is usually inherited by synthetic hexaploid wheat. However, a few synthetic lines show the glaucous phenotype although the parental Ae. tauschii accessions are non-glaucous. Molecular marker genotypes indicate that the exceptional non-glaucous Ae. tauschii accessions share the same genotype in the Iw2 chromosomal region as glaucous accessions, suggesting that these accessions have a different causal locus for their phenotype. This locus was assigned to the long arm of chromosome 3D using an F₂ mapping population and designated W4, a novel glaucous locus in Ae. tauschii. The dominant W4 allele confers glaucousness, consistent with phenotypic observation of Ae. tauschii accessions and the derived synthetic lines. These results implied that glaucous accessions of Ae. tauschii with the W2W2iw2iw2W4W4 genotype could have been the D-genome donor of common wheat.     

Population structure of wild wheat D‐genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat

Aegilops tauschii Coss. is the D‐genome progenitor of hexaploid wheat. Aegilops tauschii, a wild diploid species, has a wide natural species range in central Eurasia, spreading from Turkey to western China. Amplified fragment length polymorphism (AFLP) analysis using a total of 122 accessions of Ae. tauschii was conducted to clarify the population structure of this widespread wild wheat species. Phylogenetic and principal component analyses revealed two major lineages in Ae. tauschii. Bayesian population structure analyses based on the AFLP data showed that lineages one (L1) and two (L2) were respectively significantly divided into six and three sublineages. Only four out of the six L1 sublineages were diverged from those of western habitats in the Transcaucasia and northern Iran region to eastern habitats such as Pakistan and Afghanistan. Other sublineages including L2 were distributed to a limited extent in the western region. Subspecies strangulata seemed to be differentiated in one sublineage of L2. Among three major haplogroups (HG7, HG9 and HG16) previously identified in the Ae. tauschii population based on chloroplast variation, HG7 accessions were widely distributed to both L1 and L2, HG9 accessions were restricted to L2, and HG16 accessions belonged to L1, suggesting that HG9 and HG16 were formed from HG7 after divergence of the first two lineages of the nuclear genome. These results on the population structure of Ae. tauschii and the genealogical relationship among Ae. tauschii accessions should provide important agricultural and evolutionary knowledge on genetic resources and conservation of natural genetic diversity.     

Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species,as genome progenitors of bread wheat,using SCoT markers

We assessed the molecular genetic diversity and relationships among some Aegilops and Triticum species using 15 start codon-targeted (SCoT) polymorphism markers. A total of 166 bands amplified, of which 164 (98.79%) were polymorphic. Analysis of molecular variance and inter-population differentiation (Gst) indicated high genetic variation within the studied populations. Our analyses revealed high genetic diversity in T. boeoticum, Ae. cylindrica, T. durum and Ae. umbellulata, low diversity in Ae. crassa, Ae. caudata and Ae. speltoides, and a close relationship among Ae. tauschii, T. aestivum, T. durum, T. urartu, and T. boeoticum. Cluster analysis indicated 180 individuals divided into 8 genome homogeneous clades and 11 sub-groups. T. aestivum and T. durum accessions were grouped together, and accessions with the C and U genomes were grouped into the same clade. Our results support the hypothesis that T. urartu and Ae. tauschii are two diploid ancestors of T. aestivum, and also that Ae. caudata and Ae. umbellulata are putative donors of C and U genomes for other Aegilops species that possess these genomes. Our results also revealed that the SCoT technique is informative and can be used to assess genetic relationships among wheat germplasm.     

Genealogical use of chloroplast DNA variation for intraspecific studies of Aegilops tauschii Coss.

Intraspecific patterns of chloroplast DNA variation was studied in Aegilops tauschii Coss., the D-genome progenitor of bread wheat. Nucleotide sequences of ten chloroplast microsatellite loci were analyzed for 63 accessions that cover the central part of the species distribution. As is often the case with nuclear microsatellites, those of chloroplasts of Ae. tauschii bear complex mutations. Several types of mutations other than change in the microsatellite repeat number were found, including base substitutions and length mutations in flanking regions. In total, eight mutations were present in the flanking regions of four loci. Most mutations in the flanking regions of microsatellite repeats are associated with biallelic polymorphisms. Phylogeographic analyses showed that such biallelic polymorphisms are useful to investigate intraspecific patterns of monophyletic lineage divergence. In contrast, most microsatellite repeat sites are multiallelic, variable within intraspecific lineages, and useful to compare degrees of genetic diversity between lineages. These findings show that the chloroplast genome harbors evolutionary variations informative for intraspecific studies of Ae. tauschii and can be analyzed by genealogical approaches.Electronic Supplementary Material Supplementary material is available for this article at     

Identification and genetic characterization of an <Emphasis Type="Italic">Aegilops tauschii</Emphasis> ortholog of the wheat leaf rust disease resistance gene <Emphasis Type="Italic">Lr1</Emphasis>

Aegilops tauschii (goat grass) is the progenitor of the D genome in hexaploid bread wheat. We have screened more than 200 Ae. tauschii accessions for resistance against leaf rust (Puccinia triticina) isolates, which are avirulent on the leaf rust resistance gene Lr1. Approximately 3.5% of the Ae. tauschii accessions displayed the same low infection type as the tester line Thatcher Lr1. The accession Tr.t. 213, which showed resistance after artificial infection with Lr1 isolates both in Mexico and in Switzerland, was chosen for further analysis. Genetic analysis showed that the resistance in this accession is controlled by a single dominant gene, which mapped at the same chromosomal position as Lr1 in wheat. It was delimited in a 1.3-cM region between the restriction fragment length polymorphism (RFLP) markers ABC718 and PSR567 on chromosome 5DL of Ae. tauschii. The gene was more tightly linked to PSR567 (0.47 cM) than to ABC718 (0.79 cM). These results indicate that the resistance gene in Ae. tauschii accession Tr.t. 213 is an ortholog of the leaf rust resistance gene Lr1 of bread wheat, suggesting that Lr1 originally evolved in diploid goat grass and was introgressed into the wheat D genome during or after domestication of hexaploid wheat. Compared to hexaploid wheat, higher marker polymorphism and recombination frequencies were observed in the region of the Lr1 ortholog in Ae. tauschii. The identification of Lr1^Ae, the orthologous gene of wheat Lr1, in Ae. tauschii will allow map-based cloning of Lr1 from this genetically simpler, diploid genome.Hong-Qing Ling and Jiwen Qiu have contributed equally to this work     

Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat

Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as ‘Ug99’) race group. The diploid D genome donor species Aegilops tauschii (2n = 2x = 14, DD) is a readily accessible source of resistance to TTKSK and its derivatives that can be transferred to hexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD). To expedite transfer of TTKSK resistance from Ae. tauschii, a direct hybridization approach was undertaken that integrates gene transfer, mapping, and introgression into one process. Direct crossing of Ae. tauschii accessions with an elite wheat breeding line combines the steps of gene transfer and introgression while development of mapping populations during gene transfer enables the identification of closely linked markers. Direct crosses were made using TTKSK-resistant Ae. tauschii accessions TA1662 and PI 603225 as males and a stem rust-susceptible T. aestivum breeding line, KS05HW14, as a female. Embryo rescue enabled recovery of F₁ (ABDD) plants that were backcrossed as females to the hexaploid recurrent parent. Stem rust-resistant BC₁F₁ plants from each Ae. tauschii donor source were used as males to generate BC₂F₁ mapping populations. Bulked segregant analysis of BC₂F₁ genotypes was performed using 70 SSR loci distributed across the D genome. Using this approach, stem rust resistance genes from both accessions were located on chromosome arm 1DS and mapped using SSR and EST-STS markers. An allelism test indicated the stem rust resistance gene transferred from PI 603225 is Sr33. Race specificity suggests the stem rust resistance gene transferred from TA1662 is unique and this gene has been temporarily designated SrTA1662. Stem rust resistance genes derived from TA1662 and PI 603225 have been made available with selectable molecular markers in genetic backgrounds suitable for stem rust resistance breeding.     

Development and study of spring bread wheat variety Pamyati Maystrenko with introgression of genetic material from synthetic hexaploid Triticum timopheevii Zhuk. × Aegilops tauschii Coss.

Synthetic hexaploids are bridges for transferring new genes that determine resistance to stress factors from wild-type species to bread wheat. In the present work, the method of developing the spring bread wheat variety Pamyati Maystrenko and the results of its study are described. This variety was obtained using one of the immune lines produced earlier via the hybridization of the spring bread wheat variety Saratovskaya 29 with the synthetic hexaploid T. timopheevii Zhuk. × Ae. tauschii Coss. The C-staining of chromosomes in the Pamyati Maystrenko variety revealed substitutions of 2B and 6B chromosomes by the homeologous chromosomes of the G genome of T. timopheevii and the substitution of chromosome 1D by an orthologous chromosome of Ae. tauschii. It was found that this variety is characterized by resistance to leaf and stem rust, powdery mildew, and loose smut as well as by high grain and bread-making qualities. The role of the alien genetic material introgressed into the bread-wheat genome in the expression of adaptive and economically valuable traits in the Pamyati Maystrenko variety is discussed.     

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheats genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.     

A population of wheat multiple synthetic derivatives: an effective platform to explore,harness and utilize genetic diversity of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> for wheat improvement

Key message

The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding.

Abstract

Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding.

     

Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat

Aegilops tauschii, the diploid progenitor of the wheat D genome, is a readily accessible germplasm pool for wheat breeding as genes can be transferred to elite wheat cultivars through direct hybridization followed by backcrossing. Gene transfer and genetic mapping can be integrated by developing mapping populations during backcrossing. Using direct crossing, two genes for resistance to the African stem rust fungus race TTKSK (Ug99), were transferred from the Ae. tauschii accessions TA10187 and TA10171 to an elite hard winter wheat line, KS05HW14. BC₂ mapping populations were created concurrently with developing advanced backcross lines carrying rust resistance. Bulked segregant analysis on the BC₂ populations identified marker loci on 6DS and 7DS linked to stem rust resistance genes transferred from TA10187 and TA10171, respectively. Linkage maps were developed for both genes and closely linked markers reported in this study will be useful for selection and pyramiding with other Ug99-effective stem rust resistance genes. The Ae. tauschii-derived resistance genes were temporarily designated SrTA10187 and SrTA10171 and will serve as valuable resources for stem rust resistance breeding.     

Characterisation of high- and low-molecular weight glutenin subunits associated to the D genome of Aegilops tauschii in a collection of synthetic hexaploid wheats

Synthetic hexaploid wheats (2n=6x=42, AABBDD) involving genomes from Triticum turgidum (2n= 4x=28, AABB) and Aegilops tauschii (2n=2x=14, DD) have been produced as a means for introducing desirable characteristics into bread wheat. In the present work we describe the genetic variability present at the Glu-D ^t 1 and Glu-D ^t 3 loci, encoding high- (HMW) and low-molecular-weight (LMW) glutenin subunits respectively, derived from Ae. tauschii, using electrophoretic and chromatographic methods, in a collection of synthetic hexaploid wheats. A wide variation both in mobility and surface hydrophobicity of HMW glutenin subunits was observed between different accessions of Ae. tauschii used in the production of the synthetic hexaploids. A combination of electrophoretic and chromatographic methods improves the identification of HMW glutenin subunits; in fact subunits with identical apparent mobility were revealed to have a different surface hydrophobicity by reversed-phase high performance liquid chromatography. None of the Dx5^t subunits present in Ae. tauschii showed the presence of the extra cysteine residue found in the HMW glutenin subunit Dx5 of Triticum aestivum, as revealed by selective amplification with polymerase chain reaction (PCR). The wide variability and the high number of subunits encoded by the Glu-D ^t 3 locus suggests that Ae. tauschii may be a rich source for enhancing the genetic variability of glutenin subunits in bread wheat and improving bread-making properties. Received: 3 March 2001 / Accepted: 23 March 2001     

Identification of a UDP-glucosyltransferase conferring deoxynivalenol resistance in Aegilops tauschii and wheat

Aegilops tauschii is the diploid progenitor of the wheat D subgenome and a valuable resource for wheat breeding, yet, genetic analysis of resistance against Fusarium head blight (FHB) and the major Fusarium mycotoxin deoxynivalenol (DON) is lacking. We treated a panel of 147 Ae. tauschii accessions with either Fusarium graminearum spores or DON solution and recorded the associated disease spread or toxin-induced bleaching. A k-mer-based association mapping pipeline dissected the genetic basis of resistance and identified candidate genes. After DON infiltration nine accessions revealed severe bleaching symptoms concomitant with lower conversion rates of DON into the non-toxic DON-3-O-glucoside. We identified the gene AET5Gv20385300 on chromosome 5D encoding a uridine diphosphate (UDP)-glucosyltransferase (UGT) as the causal variant and the mutant allele resulting in a truncated protein was only found in the nine susceptible accessions. This UGT is also polymorphic in hexaploid wheat and when expressed in Saccharomyces cerevisiae only the full-length gene conferred resistance against DON. Analysing the D subgenome helped to elucidate the genetic control of FHB resistance and identified a UGT involved in DON detoxification in Ae. tauschii and hexaploid wheat. This resistance mechanism is highly conserved since the UGT is orthologous to the barley UGT HvUGT13248 indicating descent from a common ancestor of wheat and barley.     

Genealogical analysis of subspecies divergence and spikelet-shape diversification in central Eurasian wild wheat Aegilops tauschii Coss.

The genealogical and geographic structure of variation in spikelet morphology was analyzed for central Eurasian wild wheat Aegilops tauschii Coss. using a diverse array of 203 sample accessions that represented the entire species range. In this sample set, two subspecies were identified on the basis of sensu-stricto criteria: only the accessions having markedly moniliform spikes were assigned to Ae. tauschii Coss. subspecies strangulata (Eig) Tzvel., whereas those having mildly moniliform and cylindrical spikes to Ae. tauschii Coss. subspecies tauschii. In a graph of the first two axes from a principal component analysis based on nine spikelet traits, the plots of the two subspecies formed separate clusters, indicating that subspecies strangulata sens. str. is a practically usable taxon. Chloroplast-DNA-based genealogical analyses suggested that subspecies strangulata diverged from an ancestor that carried a specific chloroplast DNA type, whereas, after divergence, this subspecies became polyphyletic, likely through hybridization. Geographically, significant longitudinal and latitudinal clines were detected for spikelet size, with spikelets tending to be small in the eastern and southern regions. These results shed some light on the patterns of subspecies divergence and spikelet-shape diversification in the course of Ae. tauschii’s long-distance dispersal from the Transcaucasus to China.     

A high-density genetic linkage map of Aegilops tauschii, the D-genome progenitor of bread wheat

 Aegilops tauschii is the diploid D-genome progenitor of bread wheat (Triticum aestivum L. em Thell, 2n=6x=42, AABBDD). A genetic linkage map of the Ae. tauschii genome was constructed, composed of 546 loci. One hundred and thirty two loci (24%) gave distorted segregation ratios. Sixty nine probes (13%) detected multiple copies in the genome. One hundred and twenty three of the 157 markers shared between the Ae. tauschii genetic and T. aestivum physical maps were colinear. The discrepancy in the order of five markers on the Ae. tauschii 3DS genetic map versus the T. aestivum 3D physical map indicated a possible inversion. Further work is needed to verify the discrepancies in the order of markers on the 4D, 5D and 7D Ae. tauschii genetic maps versus the physical and genetic maps of T. aestivum. Using common markers, 164 agronomically important genes were assigned to specific regions on Ae. tauschii linkage, and T. aestivum physical, maps. This information may be useful for map-based cloning and marker-assisted plant breeding. Received: 23 March 1998 / Accepted: 27 October 1998