Increasing crop production is necessary to feed the world’s expanding population, and crop breeders often utilize genetic variations to improve crop yield and quality. However, the narrow diversity of the wheat D genome seriously restricts its selective breeding. A practical solution is to exploit the genomic variations of Aegilops tauschii via introgression. Here, we established a rapid introgression platform for transferring the overall genetic variations of A. tauschii to elite wheats, thereby enriching the wheat germplasm pool. To accelerate the process, we assembled four new reference genomes, resequenced 278 accessions of A. tauschii and constructed the variation landscape of this wheat progenitor species. Genome comparisons highlighted diverse functional genes or novel haplotypes with potential applications in wheat improvement. We constructed the core germplasm of A. tauschii, including 85 accessions covering more than 99% of the species’ overall genetic variations. This was crossed with elite wheat cultivars to generate an A. tauschii-wheat synthetic octoploid wheat (A-WSOW) pool. Laboratory and field analysis with two examples of the introgression lines confirmed its great potential for wheat breeding. Our high-quality reference genomes, genomic variation landscape of A. tauschii and the A-WSOW pool provide valuable resources to facilitate gene discovery and breeding in wheat.
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All raw data of the genome, RNA sequencing and resequencing of A. tauschii were deposited in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA663737. All raw data of the wild population resequencing of A. tauschii were deposited in NCBI under BioProject number PRJNA705859. The assembly and annotation of these four genomes are available at China National GeneBank (CNGB) under accession number CNP0001325. All germplasm materials generated from this research have been stored in the State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University. These materials can be shared with researchers for academic purposes upon request to C.-P.S., Y.Z., H. Li or C.Z. Source data are provided with this paper.
The custom pipelines and scripts used in the project have been deposited in GitHub (https://github.com/slbai01/Introgression-region-detect).
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We are grateful to J. Dvorak (University of California, Davis), J. Wang (Sichuan Agricultural University), W. Ji (Northwest A&F University) and Z. Ru (Henan Institute of Science and Technology) for sharing germplasm. We thank M.-C. Luo (University of California, Davis), Y. Jiao (Institute of Botany, Chinese Academy of Sciences (CAS)), Z. Ni (China Agricultural University), Z. Tian (Institute of Genetics and Developmental Biology, CAS), W. Song (Northwest A&F University), L. Mao (Institute of Crop Sciences, CAAS), D. Wang (Henan Agricultural University) and J. Sun (Institute of Crop Sciences, CAAS) for helpful discussion on the project. We also thank E. Wang (Institute of Plant Physiology and Ecology, CAS), S. Song (University of Pennsylvania) and J. Adams (Nanjing University) for critical reading of the manuscript. This project was supported by grants from the Ministry of Agriculture of China (2016ZX08009), National Natural Science Foundation of China (31430061, 32001492 and 31871615) and Natural Science Foundation of Henan Province (202300410053).
The authors declare no competing interests.
Peer review information Nature Plants thanks Alexandra Przewieslik-Allen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
a, The workflow represents the process from the production of inter-hybrids to the stable introgression population of elite wheat. The upper picture indicates the cross between Ae. tauschii and wheat, which produces the tetra-haploid (ABDD). The orange capital A, B, and D letter represent the wheat A, B, and D genome, respectively. The purple D indicates the genome of Ae. tauschii, and the pink D indicates the genome formed by the chromosomal exchange between Ae. tauschii and wheat. b, Distribution of the introgression alleles across the D genome of wheat in Ae. tauschii T015-wheat cultivar Z18 A-WI population. Purple lines represent the introgression alleles from Ae. tauschii. The nicks on the pseudochromosome represent the position of the centromere region. c, Genome-FISH indicated that a genome fragment of Ae. tauschii (i) recombined to the end of 5DS of the wheat (ii), which formed a novel introgression line (iii). White: probe oligo-pSc119.2 and oligo-pTa71, green: oligo-(GAA)10, red: oligo-pTa535.
Extended Data Fig. 2 The A-WSOW pool formed by crossing between wheat and 85 core germplasm of Ae. tauschii.
a, Components of the core germplasm of Ae. tauschii. The core germplasm pool consists of 85 accessions from all sublineages, including 24 L1EX accessions, 38 L1EY accessions, three L1E accessions, two L1W accessions, five L2W accessions, and 13 L2E accessions. The name of each sublineage is the same as described in Fig. 2. L1E represents inter-sublineage accessions between L1EX and L1EY. The numbers in parentheses indicate the accession number of each sublineage. b, Spike and grain phenotype of partial A-WSOWs. AK58 and T093 represent wheat cultivar and Ae. tauschii, respectively. c, Karyotypic pattern of partial A-WSOWs. Most of the SOWs include a complete chromosome set of Ae. tauschii. These SOWs occasionally lose chromosomes. The ND-FISH probes oligo-pSc119.2 (green), oligo-pTa535 (red), oligo-(GAA)10 (yellow) are used.
Extended Data Fig. 3 Comparison of karyotype pattern and subspecies index (SI) of different groups in Ae. tauschii.
a, The probe oligo-(GAA)10 showed diverse signal patterns among different sublineages of Ae. tauschii. b, A sequential ND-FISH using the probe oligo-pTa535 was conducted to distinguish the 1D-7D chromosomes of Ae. tauschii. Chinese Spring was used as a representative of wheat. c, Clustering based on the karyotype pattern. The red and blue square indicates the presence and absence signal, respectively. The ND-FISH signals are transferred into the digital matrix for cluster analysis. The green dot indicates Ae. tauschii AY61. The oligo-(GAA)10 probe can divide Ae. tauschii into L1 and L2. d, Distribution of subspecies index values of spikelet. The panel’s upper right corner shows the measurement points for spikelet glume width (G) and rachis segment width (R). SI value is calculated by the formula: SI = G/R. Violin plots illustrate the density distribution of SI. The box is the interquartile range, the horizontal line in the box represents the median value. The dashed line indicates an SI value equal to 1.3. The difference between L1 and L2 is analysed by the two-sided Wilcoxon signed-rank test. P < 2.2 × 10-16 and *** indicates P < 0.001.
Extended Data Fig. 4 Heatmaps represent the chromatin interaction matrix of Hi-C pseudo-chromosomes.
a and b indicated the map of Ae. tauschii AY61 and T093, respectively. The Hi-C heatmaps are shown at a resolution of 1 Mb window.
a, Treemaps indicated the difference of fragmentation between long-read (PacBio) and short-read (Illumina) assemblies of the Ae. tauschii genome. The colored rectangles represent the top longest contigs that account for ~200 Mb of the whole assembly. b) to e) represent the assembly of AY61, T093, AL8/78, CS-D, respectively. Yellow box means contig length is > 3 Mb. The gray box indicates contig length is from 0.5 Mb to 3 Mb. Pink box means contig length between 0.1-0.5 Mb. Orange box represents contig length < 0.1 Mb. f, The distribution of gaps across the gene body, upstream and downstream regions of different assemblies. Each gene body region was divided into ten bins with equal size and normalized gap content for the total gene set in each bin.
Extended Data Fig. 6 L1 of Ae. tauschii has no significant introgression to wheat at the population level.
a, D-statistics based on ABBA and BABA SNP frequency differences. We found significant infiltration events from wheat to L2, L2 to wheat, and L1 to L2. However, no significant incident was detected between L1 to wheat. AdmixTools calculated the D statistic of the whole genome. If there is no introgression happened from the population P3 to P2, the expected D statistic would be zero. If there existed introgression from P3 to P2, the D statistic would be significantly smaller than zero, while the significant positive value indicating introgression happed from P3 to P1. We divided the chromosome into 500 kb bins and then performed a block jackknife for calculating Z-score. D statistic was taken as significant if the absolute Z-score was greater than 3. b and c, The distribution and overlap of introgression blocks from L1 to wheat D genome with three independent methods. The introgression blocks from L1 to wheat were identified through the phylogenetic topology (Gene tree), identical by descent (IBD), and fd methods. 500 kb window was used for the analysis. Single copy genes of Ae. tauschii T093, AY61, CS-D, and CS-A were used to construct gene tree in the window of 500 kb. The region with the phylogenetic topology of ((AY61, (CS-D, T093)), CS-A) was supposed to introgression blocks from D1 to CS-D. IBD was identified in the wheat, L1 and L2, the number of recorded IBD tracts between wheat and the two groups was computed in 500 kb window. According to the previous reported method106, the putative introgression segments from L1 to each of the wheat accessions were identified. At the population level, infiltration fragments detected in more than half of wheat individuals were considered candidate fragments. The fd statistic was performed under a given four-taxon topologies ((L2, wheat), L1, SS) in 500 kb window, fd statistic value between 0 and 1 indicates introgression proportion from population L1 to wheat. All three methods detected less than 6% of the area detected by any detections and none of the region.
a, A 5-kb PAV example of the presence-and-absence of Sr13-like genes, a member of NB-ARC gene family. b, An example of tandem-repeat variations of P450 genes involved in positively regulating salt stress resistance in wheat. c, Heatmap showed the expression diversification of tandem-repeat genes mentioned in b at Ae. tauschii and CS, the expression level of tandem-repeat genes was significantly higher in response to ABA, Salt, and PEG stress treatment than that of the wheat genome. d, Genetic variation of Ppd1 in Ae. tauschii and wheat population. In the heatmap, red indicates polymorphic sites (1/1), pink indicates heterozygous sites (0/1), gray indicates no polymorphism (0/0), and light green indicates missing (./.). Circled numbers 1 to 4 indicate the variations reported in previous studies114. Circles 1 and 2 indicate 24 bp and 15 bp insertions in the upstream, respectively. Circles 3 and 4 indicate the 5 bp deletion in the seventh exon and the 18 bp insertion in the eighth exon. The two sites marked by red asterisks can cause amino acid changes and are significantly related to the flowering date. e, Using the two loci mentioned in d, Ae. tauschii can be divided into three haplotypes, and the flowering date of haplotype 1 (n = 53) is significantly earlier than that of haplotype 2 (n = 97) and 3 (n = 15). The middle bars represent the median, while the bottom and top of each box represent the 25th and 75th percentiles, respectively, and the whiskers extend to 1.5 times the interquartile range. Two-tailed Wilcox test was used to assess the statistical significance between each group.
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Zhou, Y., Bai, S., Li, H. et al. Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. Nat. Plants (2021). https://doi.org/10.1038/s41477-021-00934-w