Progress 01/01/24 to 12/31/24
Outputs
Target Audience:Plant breeding, genetics, and genomics community, growers, and other small grain stakeholders. Changes/Problems:PI had hired three postdoc scientists to work on this project. Two previous postdoc scientists got good-paying jobs in industry, so they left. This created some delays in the project, and PI has requested a no-cost extension from the program officer. What opportunities for training and professional development has the project provided?Over the project's three-year cycle, we have trained nine new scientists.This year, the project has trained three postdocs, three PhD students, and four undergraduate students. Ithas also trained a high school student, Mr. Joseph Huang. How have the results been disseminated to communities of interest?The results have been disseminated to communities of interest through several publications, talks, book chapters, extension talks, and field day events. 1. Tiwari VK: Exploring resistance in winter barley through two independent EMS-induced mutant populations. In: Invited talk at GDER-PBG Virtual conference under Wheat Barley Scab Initiative. (April 27th, 2023) 2. Tiwari VK: Feeding the 10 billion. In: Invited talk at Plant Science and Landscape Architecture Seminar series, University of Maryland, College Park. (April 10th, 2023) 3. Tiwari VK: Plant Breeding Partnership to improve bread wheat. In: Invited talk at Plant and Animal Genome Conference San Diego California USA. (January 14th, 2023) 4.Sharma PK, Ayyappan D, Lazo G, Tiwari V. Towards a Comprehensive Wheat Pangenome with Web-Based Visualization and Introductory AI. InPlant and Animal Genome Conference/PAG 31 (January 12-17, 2024) 2024 Jan 16. PAG. 5. Schoen, A.W., Mahlandt, A., Meier, N., Chen, A., Yadav, I., Kajla, A., Paulson, C., Datla, R., Uauy, C., Murphy, A. and Rawat, N., 2024, January. Elucidation of the Genetic Components behind a Novel Gene Controlling Grains per Spike. InPlant and Animal Genome Conference/PAG 31 (January 12-17, 2024). PAG. 6. Kajla A, Schoen AW, Yadav IS, Sharma PK, Paulson C, Kumari N, Riera-Lizarazu O, Gill BS, Datla R, Rawat N, Tiwari V. Genetic Control of Spike Length in Wheat. InPlant and Animal Genome Conference/PAG 31 (January 12-17, 2024) 2024 Jan 14. PAG. 7. Yadav I, Saripalli G, Sharma PK, Ahmed H, Abrouk M, Adhikari L, Heuberger M, Wicker T, Sanchez-Martin J, Keller B, Kolmer JA. Combining Reference Genomes and Population Genomics to Discover and Validate Novel Genes for Disease Resistance in Wheat. InPlant and Animal Genome Conference/PAG 31 (January 12-17, 2024) 2024 Jan 13. PAG. 8. Tiwari VK, Saripalli G, Moot I, Kajla A, Schoen AW, Chhabra B, Rawat N, Poland J. Genomics Enabled Gene Discovery for Climate Resilient Traits in Wheat. InPlant and Animal Genome Conference/PAG 31 (January 12-17, 2024) 2024 Jan 13. PAG. What do you plan to do during the next reporting period to accomplish the goals?We have made excellent progress on the project. We have assembled four reference genomes in a GWAS panel and performed high-quality marker-trait association analysis. In the next reporting season we will complete the candidate gene validation experiments and will report the results in high impact journals.
Impacts
What was accomplished under these goals?
Objective 1: Generate high-quality assemblies of T. monococcum accessions We assembled the genomes of two einkorn wheat accessions: a wild T. monococcum ssp. aegilopoides (TA391) and a domesticated T. monococcum ssp. monococcum (TA10868) using Pacbio HiFi sequencing. The assembled contigs consisted of 5.18Gb and 5.15Gb of sequences with an N50 of 47Mb and 35Mb for the TA391 and TA10868, respectively. Reference-based scaffolding of the primary assembly performed with previously published genomes of T. monococcum spp. aegilopoides (TA299) (Ahmed et al., 2023) using Ragtag (Alonge et al., 2022) generated 7 pseudomolecules and 65Mb and 35Mb of unassigned sequences in TA391 and TA10868, respectively. BUSCO analysis of conserved genes identified 97% complete BUSCO genes in both assemblies. Additionally, merqury Click or tap here to enter text. was used for reference-free assembly evaluation, revealing the completeness of 97% solid k-mer between the raw reads and the assembled sequences. The methods confirm the high level of completeness achieved in our assemblies. Objective 2: Whole-genome sequencing of diverse T. monococcum accessions To perform the GWAS we sequenced a diverse association panel of 282 selected T. monococcum accessions. These were chosen to optimally represent diversity based on geographical origin and genotyping data with 202 wild (167 α race, 10 β race and 25 γ race) and 80 domesticated einkorn accessions. We generated a diversity panel's whole-genome sequencing data (around tenfold coverage). The panel was aligned to the wild einkorn (TA299), and 121,459,674 high-quality single-nucleotide polymorphisms (SNPs) were retained. We observed a low false-positive error rate of variant calling. Nucleotide diversity (π) was highest in the γ races (π = 0.0023) and similar across the other three groups (α, π = 0.0011; β, π = 0.0018; domesticated, π = 0.0014). Phylogeny confirmed wild einkorn clusters into α, β and γ races. The domesticated einkorn accessions clustered with race β, most of which were collected in the Karacada? area in the southeastern. This supports the hypothesis that einkorn was domesticated from a small and restricted wild population closely related to presentday β accessions. Objective 3: Association genetics to identify important genes and alleles for wheat improvement. Gene bank germplasm collection is a good resource for identifying genes conferring resistance to diseases and pests. We used the GWAS panel comprised of 220 T. monococcum accessions to identify the novel sources of resistance for powdery mildew (Blumeria graminis f. sp. tritici ) , leaf rust (Puccinia triticina) , stem rust (Puccinia graminis f. sp. tritici ) and stripe rust (Puccinia striiformis f. sp. tritici) using kmer-GWAS method. The Kmer presence/absence matrix was created following the protocol described by (Gaurav et al., 2022) with some modifications in the process. Jellyfish (jellyfish-2.3.0) was used to count the kmers of size 51 from the filtered fastq files. k-mers with a count of less than two in an accession were discarded immediately. Changes in the original protocol involve developing a Jellyfish database for the accessions using "-disk" parameter to make databases of similar sizes. Later on, the utility script (count_in_file) was provided with jellyfish, and it was used to create a composite matrix with kmers (https://github.com/gmarcais/Jellyfish/tree/master/examples/count_in_file).Association mapping plots were generated by mapping the associated kmer to one of the reference assemblies: TA391 (powdery mildew) and TA10868 (leaf rust, stem rust, and stripe rust). The primary output of this objective includes: • Identification of potential candidate genes for 5 of the devastating powdery mildew races. • Potential resistant candidate genes for leaf rust and stem rust. • These candidates present a novel reservoir for disease resistance. • We identified other resistant gene classes and RGAs: Helix loop helix, protein kinases, and lectin receptors. Moving forward, we have recently positionally cloned a broad-spectrum resistant gene against powdery mildew after validating it using transgenic approaches. We are also validating resistance genes against leaf rust and stem rust, and the work requires a little more time as we just sent the gene sequences for the genetic transformation at UC Davis. Objective 4: Develop, characterize, and deploy introgressions from T. monococcum in wheat. We have generated introgressive derivatives of 4 accessions using bridge crosses (through T. durum) in bread wheat. Eight hundred introgressive derivatives from these crosses had been advanced to BC3F1 generation. These are being selfed this year. All the fertile and bread wheat-like lines will be genotyped using skim sequencing, and sequence data will aligned back to the respective einkorn reference genomes. Since all these einkorn genotypes are sources of resistance genes against several wheat diseases, and our association genetics data has already identified diagnostic markers, the identified introgression lines will be shared with relevant information with the breeders. We have developed KASP assays for the agronomically essential genes identified from the GWAS panel. We have also developed introgressive derivatives from resistant einkorn accessions from six independent accessions. The last two recent accessions show excellent FHB resistance, which is critical for US wheat breeding programs.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Heuberger, M.; Koo, D.-H.; Ahmed, H. I.; Tiwari, V. K.; Abrouk, M.; Poland, J.; Krattinger, S. G.; Wicker, T. Evolution of Einkorn Wheat Centromeres Is Driven by the Mutualistic Interplay of Two LTR Retrotransposons. Mob. DNA 2024, 15 (1), 16. https://doi.org/10.1186/s13100-024-00326-9.
(2) Origin and evolution of the bread wheat D genome | Nature. https://www.nature.com/articles/s41586-024-07808-z (accessed 2024-12-03).
(3) Tiwari, V. K.; Saripalli, G.; Sharma, P. K.; Poland, J. Wheat Genomics: Genomes, Pangenomes, and Beyond. Trends in Genetics 2024, 40 (11), 982992. https://doi.org/10.1016/j.tig.2024.07.004.
(4) Wallace, S.; Chhabra, B.; Dong, Y.; Ma, X.; Coleman, G.; Tiwari, V.; Rawat, N. Exploring Fusarium Head Blight Resistance in a Winter Triticale Germplasm Collection. Journal of Plant Registrations 2024, 18 (3), 457465. https://doi.org/10.1002/plr2.20392.
(5) Boyles, R. E.; Ball�n-Taborda, C.; Brown-Guedira, G.; Costa, J.; Cowger, C.; DeWitt, N.; Griffey, C. A.; Harrison, S. A.; Ibrahim, A.; Johnson, J.; Lyerly, J.; Marshall, D. S.; Mason, R. E.; Mergoum, M.; Murphy, J. P.; Santantonio, N.; Saripalli, G.; Sutton, R.; Tiwari, V.; van Sanford, D.; Winn, Z. J. Approaching 25 Years of Progress towards Fusarium Head Blight Resistance in Southern Soft Red Winter Wheat ( L.). Plant Breeding 2024, 143 (1), 6681. https://doi.org/10.1111/pbr.13137.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Origin and evolution of the bread wheat D genome | Nature. https://www.nature.com/articles/s41586-024-07808-z (accessed 2024-12-03).
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Tiwari, V. K.; Saripalli, G.; Sharma, P. K.; Poland, J. Wheat Genomics: Genomes, Pangenomes, and Beyond. Trends in Genetics 2024, 40 (11), 982992. https://doi.org/10.1016/j.tig.2024.07.004.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Wallace, S.; Chhabra, B.; Dong, Y.; Ma, X.; Coleman, G.; Tiwari, V.; Rawat, N. Exploring Fusarium Head Blight Resistance in a Winter Triticale Germplasm Collection. Journal of Plant Registrations 2024, 18 (3), 457465. https://doi.org/10.1002/plr2.20392.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Boyles, R. E.; Ball�n-Taborda, C.; Brown-Guedira, G.; Costa, J.; Cowger, C.; DeWitt, N.; Griffey, C. A.; Harrison, S. A.; Ibrahim, A.; Johnson, J.; Lyerly, J.; Marshall, D. S.; Mason, R. E.; Mergoum, M.; Murphy, J. P.; Santantonio, N.; Saripalli, G.; Sutton, R.; Tiwari, V.; van Sanford, D.; Winn, Z. J. Approaching 25 Years of Progress towards Fusarium Head Blight Resistance in Southern Soft Red Winter Wheat ( L.). Plant Breeding 2024, 143 (1), 6681. https://doi.org/10.1111/pbr.13137.
|
Progress 01/01/23 to 12/31/23
Outputs
Target Audience:Plant breeding, genetics, and genomics community, growers, and other small grain stakeholders. Changes/Problems:PI had hired three postdoc scientists to work on this project. Two previous postdoc scientists got good-paying jobs in industry, so they left. This created some delays in the project, and PI has requested a no-cost extension to the program officer. What opportunities for training and professional development has the project provided?The project has trained 3 postdocs, 3 PhD students, and 4 undergraduate students. In addition, the project has also trained a high school student, Mr. Joseph Huang. How have the results been disseminated to communities of interest?The results have been disseminated to communities ofinterest throughseveral publications, talks, book chapters, extension talks and field day events. Tiwari VK: Exploring resistance in winter barley through two independent EMS-induced mutant populations. In: Invited talk at GDER-PBG Virtual conference under Wheat Barley Scab Initiative. (April 27th, 2023) Tiwari VK: Feeding the 10 billion. In: Invited talk at Plant Science and Landscape Architecture Seminar series, University of Maryland, College Park. (April 10th, 2023) Tiwari VK: Plant Breeding Partnership to improve bread wheat. In: Invited talk at Plant and Animal Genome Conference San Diego California USA. (January 14th, 2023) What do you plan to do during the next reporting period to accomplish the goals?We are working on generating more robust data on objectives 3 and 4 to validate some essential candidate genes and precise mapping of some novel genes for the stem, stripe rusts, and FHB diseases. We plan to develop introgressive derivatives for two more accessions showing promising responses against wheat blast. We will use the majority of the time next year to start preparing some high-quality and high-impact research articles.
Impacts
What was accomplished under these goals?
Objective 1:Generate high-quality assemblies ofT. monococcum accessions We assembled the complete genomes of two einkorn wheat accessions: a wild T. monococcum ssp. aegilopoides (TA391) and a domesticated T. monococcum ssp. monococcum (TA10868) using Pacbio HiFi sequencing. The assembled contigs consisted of 5.18Gb and 5.15Gb of sequences with an N50 of 47Mb and 35Mb for the TA391 and TA10868, respectively. Reference-based scaffolding of the primary assembly performed with previously published genomes of T. monococcum spp. aegilopoides (TA299) (Ahmed et al., 2023) using Ragtag (Alonge et al., 2022) generated 7 pseudomolecules and 65Mb and 35Mb of unassigned sequences in TA391 and TA10868, respectively. BUSCO analysis of conserved genes identified 97% complete BUSCO genes in both assemblies. Additionally, merqury Click or tap here to enter text. was used for reference-free assembly evaluation, revealing the completeness of 97% solid k-mer between the raw reads and the assembled sequences. The methods confirm the high level of completeness achieved in our assemblies. Objective 2:Whole-genome sequencing of diverseT. monococcumaccessions To perform the GWAS we sequenced a diverse association panel of 282 selected T. monococcum accessions. These were selected to optimally represent diversity based on geographical origin and genotyping data with 202wild (167α race, 10β race and 25 γ race) and 80 domesticated einkorn accessions. We generated a diversity panel's whole-genome sequencing data (around tenfold coverage). The panel was aligned to the wild einkorn (TA299) and a total, 121,459,674 high-quality single-nucleotide polymorphisms (SNPs) were retained and we observed a low false-positive error rate of variant calling. Nucleotide diversity (π) was highest in the γ races (π = 0.0023) and similar across the other three groups (α, π = 0.0011; β, π = 0.0018; domesticated, π = 0.0014). Phylogeny confirmed wild einkorn clusters into α, β and γ races. The domesticated einkorn accessions clustered with race β, most of which were collected in the Karacada? area in the southeastern. This supports the hypothesis that einkorn was domesticated from a small and restricted wild population closely related to present-day β accessions. Objective 3:Association genetics to identify important genes and alleles for wheat improvement Gene bank collection of germplasm is a good resource for identifying genes conferring resistance to diseases and pests. We used the GWAS panel comparized of 220 T. monococcum accessions to identify the novel sources of resistance for powdery mildew (Blumeria graminis f. sp. tritici ) , leaf rust (Puccinia triticina) , stem rust (Puccinia graminisf. sp.tritici ) and stripe rust (Puccinia striiformisf. sp. tritici) using kmer-GWAS method. The Kmer presence/absence matrix was created following the protocol described by (Gaurav et al., 2022) with some modifications in the process. Jellyfish (jellyfish-2.3.0) was used to count the kmers of size 51 from the filtered fastq files. k-mers with a count of less than two in an accession were discarded immediately.Changes in the original protocol involve developing a Jellyfish database for the accessions using "-disk" parameter to make databases of similar sizes. Later on, the utility script (count_in_file) provided with jellyfish (https://github.com/gmarcais/Jellyfish/tree/master/examples/count_in_file) was used to create a composite matrix of the kmers. A custom Python script was used to convert the matrix into a presence/absence matrix by replacing the occurrence of kmer with 1 and absence with 0. Matrix was further filtered for kmers occurring in less than two or all but one accession. The rest of the analysis protocol discussed by (Gaurav et al., 2022) was used. Association mapping plots were generated by mapping the associated kmer to one of the reference assemblies: TA391 (powdery mildew), and TA10868 (leaf rust, stem rust and stripe rust). The major output of this objective includes: Identification of potential candidate genes for 5 of the devastating powdery mildew races. Potential resistant candidate genes for leaf rust and stem rust. These candidates present a novel reservoir for disease resistance. We identified other resistant gene classes along with RGAs, namely Helix loop helix, protein kinases, and lectin receptors. Objective 4:Develop, characterize, and deploy introgressions fromT. monococcum in wheat We have generated introgressive derivatives of 4 accessions using bridge crosses (through T. durum) in bread wheat. Eight hundred introgressive derivatives from these crosses had been advanced to BC3F1 generation. These are being selfed this year. All the fertile and bread wheat-like lines will be genotyped using skim sequencing, and sequence data will aligned back to the respective einkorn reference genomes. Since all these einkorn genotypes are sources of resistance genes against several wheat diseases, and our association genetics data has already identified diagnostic markers, the identified introgression lines will be shared with relevant information with the breeders.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Parva Kumar Sharma, Hanin Ibrahim Ahmed, Matthias Heuberger, Dal-Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, St�phane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Inderjit Singh Yadav, Nagarajan Kathiresan, Naveenkumar Athiyannan, Ricardo H Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Michael Abrouk, Yong Q Gu, Jesse Poland, Simon G Krattinger, Gerard R Lazo, Vijay K Tiwari, An online database for einkorn wheat to aid in gene discovery and functional genomics studies, Database, Volume 2023, 2023, baad079, https://doi.org/10.1093/database/baad079
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Ahmed, H.I., Heuberger, M., Schoen, A. et al. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 620, 830838 (2023). https://doi.org/10.1038/s41586-023-06389-7
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Saripalli, G., Adhikari, L., Amos, C. et al. Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits. Commun Biol 6, 835 (2023). https://doi.org/10.1038/s42003-023-05189-z
- Type:
Other Journal Articles
Status:
Published
Year Published:
2023
Citation:
Evolutionary history of worlds oldest domesticated crop. (2023). Nature. https://doi.org/10.1038/d41586-023-02375-1
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
DeWitt, N.; Lyerly, J.; Guedira, M.; Holland, J. B.; Ward, B. P.; Murphy, J. P.; Boyles, R. E.; Mergoum, M.; Babar, M. A.; Shakiba, E.; Sutton, R.; Ibrahim, A.; Tiwari, V.K.; Santantonio, N.; Sanford, D. A. V.; Howell, K.; Smith, J. H.; Harrison, S. A.; Brown-Guedira, G. Bearded or Smooth? Awns Improve Yield When Wheat Experiences Heat Stress during Grain Fill in Southern United States. Journal of Experimental Botany 2023 erad318. https://doi.org/10.1093/jxb/erad318
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Arora, S.; Steed, A.; Goddard, R.; Gaurav, K.; OHara, T.; Schoen, A .; Rawat, N.; Elkot, A. F.; Chinoy, C.; Nicholson, M. H.; Asuke, S.; Steuernagel, B.; Yu, G.; Awal, R.; Forner-Mart�nez, M.; Wingen, L.; Baggs, E.; Clarke, J.; Krasileva, K. V.; Tosa, Y.; Jones, J. D. G.; Tiwari, V. K.; Wulff, B. B. H.; Nicholson, P. A Wheat Kinase and Immune Receptor Form the Host-Specificity Barrier against the Blast Fungus. Nature Plants 2023, 9, 385392
https://doi.org/10.1038/s41477-023-01357-5
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Yadav, I.S .; Rawat, N.; Chhuneja, P.; Kaur, S.; Uauy, C.; Lazo, G.; Gu, Y.Q.; Dole~el, J.; and Tiwari, V.K.*. Comparative Genomic Analysis Of 5Mg Chromosome of Aegilops geniculata and 5Uu chromosome of Aegilops umbellulata Reveal Genic Diversity In The Tertiary Gene Pool. Frontiers in Plant Science. 2023 14 doi: 10.3389/fpls.2023.1144000
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Tiwari V, and Springer N. Comparative Genomics workshop. Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024)
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Yadav, I. S .; Singh, N.; Wu, S.; Raupp, J.; Wilson, D. L.; Rawat, N.; Gill, B. S.; Poland, J.; Tiwari, V. K*. Exploring Genetic Diversity of Wild and Related Tetraploid Wheat Species Triticum turgidum and Triticum timopheevii. Journal of Advanced Research 2022. https://doi.org/10.1016/j.jare.2022.08.020.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Boyles, RE.: Brown-Guedira, Gina.; Costa.; Cowger, C.; DeWitt, N.; Griffey, C.; Harrison, S.A.; Ibrahim, A.; Johnson, J.; Lyerly, J.; Marshall, D.S.; Mason, E.R; Mergoum, M.; Murphy, J.P.; Winn, Z.; Santantonio, N.; Sutton, R.; Sarripalli, G^.; Tiwari, V.K.; van Sanford, D. 25 Years of Progress Toward Fusarium Head Blight Resistance In Soft Red Winter Wheat. Plant Breeding 2023. https://doi.org/10.1111/pbr.13137
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Kajla, A .; Schoen, A .; Paulson, C .; Kumari, N.; Gill, B.S.; Datla, R.; Coleman, G.; Riera-Lizarazu, O.; Leonard, J.; Rawat, N.; and Tiwari V.K*. High-Resolution Mapping of the C-Locus In Wheat By Combining Radiation Hybrid (RH) And Recombination-Based Mapping Approaches. Theoretical and applied genetics 2023, 136, 159.
- Type:
Other Journal Articles
Status:
Published
Year Published:
2023
Citation:
Schoen, A .; Yadav, I.S .; Poland, J.; Rawat, N.; Tiwari V.K*. Genomics Assisted Identification of a Novel Tillering Inhibition Locus tin6 In Hexaploid Wheat. Functional and Integrated Genomics 2023, 12; 23 (2):157
https://doi..org/10.1007/s10142-023-01084-2
|
Progress 01/01/22 to 12/31/22
Outputs
Target Audience:Plant breeding, genetics, and genomics community, growers, and other small grain stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Combining all the project partners, we are training three postdoc scientists, two graduate students, and one undergraduate student. How have the results been disseminated to communities of interest?The project's output has been disseminated through peer-reviewed publications in Journals, including Nature and Communication Biology,as well as through more than 12 PowerPoint presentations at various scientific meetings, conferences, and symposia. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1:We generated reference assemblies of two einkorn accessions using a combination of PacBio circular consensus sequencing, optical mapping,and chromosome conformation capture. TA10622 is a domesticated einkorn landrace and TA299 is a wild einkorn accession. Assembly integrities were verified using an Einkorn genetic map. We observed high collinearity across the two sets of pseudomolecules and between the einkorn assemblies and the bread wheat A subgenome. We annotated 32,230 and 32,090 high-confidence gene models on the seven pseudomolecules of TA299 and TA10622, respectively (BUSCO scores of 99.2% for TA299 and 99.4% for TA10622).In addition to these, we further generated two high-quality chromosome-scale assemblies of accessions T. monococcum accessions TA4342-L95 and TA4342-L96. We used PacBio circular consensus sequencing (CCS), and genomes were assembled using hifiasm. These contig level assemblies were anchored and ordered using reference level assemblies of (TA299 and TA10622) using RaGOO. For L95, we assembled the genome's 5.18 Gb (5.5 Gb) in 1236 contigs with N50 of 47.6 Mb. For domesticated accession L96, the total length of the assembled genome was estimated as 5.15 Gb (out of 5.4 Gb), and the entire genome was completed in 887 contigs with N50 of 35.1Mb.For each accession (L95 and L96), we sampled root and leaf tissues at multiple growth stages along with immature spikes and performed RNAseq and Iso-Seq methods. Gene annotation analysis indicated ~32,000 high-confidence gene models in these two accessions with (BUSCO scores of 99.1% for L95 and 99.3% for L96). Assemblies are now frozen for critically analyzing genomics features and comparative genomics studies. Objective 2:We investigated einkorn genetic diversity and evolutionary history using a diversity panel comprising 219 einkorn fully sequenced accessions with tenfold coverage. We selected the constituent accessions of the panel to optimally represent diversity based on geographical origin and genotyping data, with 158 wild and 61 domesticated einkorn accessions. In total, 121,459,674 high-quality single-nucleotide polymorphisms (SNPs) were retained, and we observed a low false-positive error rate of variant calling43,44,45,46. Nucleotide diversity (π) was highest in the γ races (π = 0.0023) and similar across the other three groups (α, π = 0.0011; β, π = 0.0018; domesticated, π = 0.0014). Notably, but consistent with previous observations, we did not observe a considerable reduction in nucleotide diversity in domesticated einkorn. Phylogeny and principal component analysis (PCA) confirmed wild einkorn clusters into α, β and γ races. The domesticated einkorn accessions clustered with race β, most of which were collected in the Karacada? area in southeastern Turkey. This supports the hypothesis that einkorn was domesticated from a small and restricted wild population closely related to present-day β accessions. To test for admixture and whether specific genomic segments contributed to the split of domesticated einkorn, we estimated genetic differentiation (FST) between the two domesticated einkorn groups in sliding windows across the seven chromosomes, revealing two large segments that were highly differentiated between the two groups. These two blocks spanned the centromeric and pericentromeric regions of chromosomes 2A (around 266 Mb) and 5A (around 329 Mb). Divergence analyses across these two segments confirmed a strong separation of domesticated einkorn accessions. We performed PCA considering only variants within these two diverged segments, revealing the clustering of some domesticated einkorn accessions with wild γ rather than β accessions. These results suggest an introgression of genetic material from race γ into the domesticated-einkorn gene pool. Pericentromeric regions show low recombination frequency in wheat 24,47,48, explaining why they can persist as large blocks.To obtain a more complete estimate of the proportions of γ introgressions in domesticated einkorn, we performed pairwise comparisons of nucleotide diversity across chromosomes between one γ accession and each domesticated einkorn accession. In addition to the two large segments on chromosomes 2A and 5A, we determined that most (92%) domesticated einkorn accessions carry an approximately 150 Mb γ genomic element in the pericentromeric region of chromosome 7A. Objective 3:We have made exciting progress on this objective as well. The entire einkorn panel and four fully assembled genomes were phenotyped for wheat diseases, including leaf rust, stem rust, stripe rust, powdery mildew, wheat blast and FHB. As discussed in the project, we collaborated with global experts for wheat diseases, which allowed us to obtain high-quality, reproducible phenotypic data on the Einkorn association panel.In the next step, we generated K-mers from the 221 sequenced (tenfold, using Illumina Hi-Seq) einkorn accessions from the TmGWAS panel. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance. We demonstrated their functional transfer into wheat using the diverse einkorn genomes. Exploiting the genomic diversity of the einkorn wheat will allow rapid trait discovery and functional genetic Validation. K-mer-based GWAS has allowed us to identify genomic regions providing resistance against our targeted diseases as well as other agronomic traits such as grain number /spike, grain weight, spikelet number/spike, tiller number, flowering time, grain color, trichome length, and brittle rachis. Work is progressing to add more traits and validate QTL and candidate genes. Objective 4:We started with the direct crossing of 4 einkorn accessions with available reference genomes but did not see any seed set in any of those crosses. We then adapted the crossing scheme described in the proposed research (using a bridge crossing scheme). We crossed two einkorn accessions, L95 and L96, with tetraploid wheat cultivar Svevo (with reference genome available). The F1 plants were crossed with a soft red winter wheat cultivar MD315, and backcrossed progenies were fertile. The backcrossing of these plants is in progress, and for the next generation, these crosses will be selfed for two consecutive generations. Then, we will use a skim sequencing approach to detect the A-genome introgressions in the progenies of these lines. Our Co-PI, Dr. Dal-Hoe Koo, made crosses of two einkorn accessions, TA299 and TA10622, with tetraploid wheat Altar and Svevo to transfer valuable genes using a bridge cross scheme. In addition to these, we have requested A-genome introgression lines from Dr. Jorge Dubcovsky and Dr. Parveen Chhuneja for their critical phenotyping and genotyping studies.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Saripalli, G.; Adhikari, L.; Amos, C.; Kibriya, A.; Ahmed, H.A.; Heuberger, M.; Raupp, J.; Athiyannan, N.K.; Wicker, T.; Abrouk, M.; Wallace, S.; Hosseinirad, S.; Chhuneja, P.; Livesay, J.; Rawat, N.; Krattinger, S.G.; Poland, J.; and Tiwari, V.K. Integration of Genetic and Genomics Resources In Einkorn Wheat Enables Precision Mapping of Key Domestication And Agronomic Traitscommunication Biology. https://doi.org/10.1038/s42003-023-05189-z
- Type:
Journal Articles
Status:
Accepted
Year Published:
2023
Citation:
Sharma, P.; Ahmed, H.A.; Adhikari, L.; Yadav, I.S.; Heuberger, M.; Raupp, J.; Athiyannan, N.K.; Wicker, T.; Abrouk, M.; Rawat, N.; Gu, Y.Q.; Krattinger, S.G.; Lazo, G.; Poland, J.; and Tiwari, V.K. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Accepted with minor edits).
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Ahmed, H.A.; Heuberger, M.; Schoen, A.; Koo, Dal-Hoe.; Quiroz-Chavez, J.; Adhikari, L.; Sharma, P.K.; Raupp, J.; Cauet, S.; Nathalie Rodde, N.; Cravero, C.; Callot, C.; Lazo G.R.; Kathiresan, N.; Athiyannan, N.K.; Yadav I.S., Moot, I., Saripalli, G.; Ramirez-Gonzalez, R.H.; Uauy, C.; Wicker, T.; Abrouk, M.; Tiwari V.K.; Poland, J.; Krattinger, S.G. Einkorn Genomics Sheds Light on the Evolutionary History of The Oldest Domesticated Wheat. Nature. https://doi.org/10.1038/s41586-023-06389-7
- Type:
Book Chapters
Status:
Accepted
Year Published:
2023
Citation:
Saripalli G, Hosseinirad S, Yadav IS, Kajla A, Schoen AW, Tiwari VK. 2023. Allele mining for improvement of plant architecture, grain quality, and abiotic stress tolerance traits in wheat. In: Allele Mining for Genomic Designing of Cereal Crops. CRC Press. Taylor & Francis (In production)
- Type:
Book Chapters
Status:
Accepted
Year Published:
2023
Citation:
Schoen AW, Saripalli G, Hosseinirad S, Yadav IS, Kajla A, Tiwari VK. 2023. Genome sequences from diploids and wild relatives of wheat for comparative genomics and alien introgressions. In: Genome book. Springer Nature. (Accepted)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Tiwari VK: Exploring resistance in winter barley through two independent EMS-induced mutant populations. In: Invited talk at GDER-PBG Virtual conference under Wheat Barley Scab Initiative. (April 27th, 2023)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Tiwari VK: Feeding the 10 billion. In: Invited talk at Plant Science and Landscape Architecture Seminar series, University of Maryland, College Park. (April 10th, 2023)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Tiwari VK: Plant Breeding Partnership to improve bread wheat. In: Invited talk at Plant and Animal Genome Conference San Diego, California, USA. (January 14th, 2023)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Einkorn Genomics for Gene Discovery and Validation. In: Invited talk at Crop and Soil Science Society of America meeting, Baltimore. (September 6, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Combining germplasm, genetics, and genomics tools to enhance FHB resistance in wheat. In: invited talk at the US Wheat Barley Scab Initiative Meeting, Tampa, Florida. (December 5, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Speeding up gene discovery in wheat by integrating genomes and germplasm. In: Invited talk at the School of Computational and Integrative Sciences, Jawahar Lal Nehru University, New Delhi, India. (August 1, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Integrating forward and reverse genetics tools to develop next-generation wheat cultivars. In: Invited talk at the School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India. (August 2, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Combining Genetics and Genomic Tools for Translational Research in Wheat. In: Invited talk at the National Agricultural Biotechnology Institute Mohali, India. (August 4, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Kajla, A., Chhabra, B., Schoen, A., Rawat, N., Tiwari, V. K. (2022, November 6-9). Identification of novel dwarfing genes in wheat using MutMap approach [Short oral presentation]. ASA, CSSA, SSSA Annual Meeting, Baltimore, MD, United States.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Integrating genetics and genomics tools to improve wheat for the global grand challenges. In: Invited talk at the department of Biotechnology, Indian Institute of Technology Roorkee, India. (April 25, 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Simplifying gene discovery in wheat using diploid forward and reverse genetics Resources. In: International seminar on "Biotechnological Interventions to Overcome the Challenges of Covid/Post-Covid Era (BIOCoPE-2022)" at Amity University Rajasthan, Jaipur, India. (24-25 March 2022)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Tiwari VK: Genomics assisted breeding for improving soft red winter wheat cultivars. In: 2022 SWQL-ARR/SWQC/C&G virtual meeting. USDA-ARS-CSWQRU, Wooster, Ohio. March 15, 2022.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Saripalli G., Adhikari L., Wallace S., Hosseinirad S., Livesay, J., Ahmed, H. I., Kratinger, S., Rawat, N., Poland, J., Tiwari, V. K. (2023, May 24) Identification of a novel candidate gene controlling spikelet number per spike in wheat for grain yield improvement [Conference presentation]. MAS-ASPB & UMD Plant Symposium, College Park, MD.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Saripalli G, Adhikari L, Amos C, et al. (2023) High-density bin-mapping in einkorn wheat and its application in QTL mapping for domestication and agronomic traits. A talk delivered at PAG 30 2023, held in San Diego, California, United States during January 13-18, 2023.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Schoen, A., Yadav I. S., Kajla A., Poland, J., Wu S., Gill B. S., Rawat, N., Tiwari, V. K. (2023, January 13-18). Advancements in wheat genomic resources allow for efficient gene mapping of agronomic traits using the mutmap approach [Conference presentation]. PAG30 2023, San Diego, CA, United States.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Schoen, A., Yadav, I. S., Poland, J., Wu, S., Rawat, N., Tiwari, V. K. (2022, November 6-9) discovering agronomically important genes in wheat using forward genomics tools [Conference presentation]. ASA, CSSA, SSSA International Annual Meeting, Baltimore, MD, United States.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Saripalli G, Adhikari L, Poland J, Tiwari V.K. (2022) Genetic dissection of Triticum mononoccum for important agronomic and domestication traits. A talk delivered at Joint MA-ASPB and UMD Plant Mini-symposium 2022 held at the University of Maryland, College Park, MD held May 25-26, 2022.
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