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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Improvement Research » Research » Publications at this Location » Publication #410122

Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

Title: Telomere-to-telomere genome assembly and resequencing of 20 Aegilops umbellulata genomes reveals broad genetic and phenotypic diversity for novel disease resistance traits

Author
item SINGH, JATINDER - NORTH DAKOTA STATE UNIVERSITY
item GUDI, SANTOSH - NORTH DAKOTA STATE UNIVERSITY
item MAUGHAN, JEFF - BRIGHAM YOUNG UNIVERSITY
item LIU, ZHAOHUI - NORTH DAKOTA STATE UNIVERSITY
item KOLMER, JAMES
item Chen, Xianming
item ROUSE, MATTHEW
item SEHGAL, SUNISH - SOUTH DAKOTA STATE UNIVERSITY
item Fiedler, Jason
item CHOULET, FREDERIC - INRAE
item ACEVEDO, MARICELIS - CORNELL UNIVERSITY
item Gupta, Rajeev
item UPINDER, GILL - NORTH DAKOTA STATE UNIVERSITY

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/9/2023
Publication Date: 1/12/2024
Citation: Singh, J., Gudi, S., Maughan, J., Liu, Z., Kolmer, J.A., Chen, X., Rouse, M.N., Sehgal, S., Fiedler, J.D., Choulet, F., Acevedo, M., Gupta, R., Upinder, G. 2024. Telomere-to-telomere genome assembly and resequencing of 20 Aegilops umbellulata genomes reveals broad genetic and phenotypic diversity for novel disease resistance traits (abstract). Poster No. PE0420.

Interpretive Summary:

Technical Abstract: Diversifying the narrow genetic base of cultivated wheat is essential to ensure a sustainable global food supply in the face of impending climate change. Aegilops spp. serve as an important reservoir for novel biotic and abiotic stress tolerance traits. To harness this reservoir, we have generated a platinum standard chromosome-level genome assembly of anaccession “PI 554389” of a Aegilops umbellulata, a diploid grass species (2n=2x=14) with U genome, using a combination of PacBio HiFi, Oxford nanopore, and chromosome conformation capture (Hi-C) sequencing technologies. A total of ~4.2 Gb genome assembled in seven chromosomes, with N50 of 634Mb, and around ~79% of the genome contains repetitive elements. The quality of the genome (QV 59.54) was validated by mapping HiFi reads to the assembled genome with a mapping rate of 99.99%. In total, 48366 high confidence gene models were predicted and 837 of them were predicted to be NLRs. The phylogenetic analysis places Ae. umbellulata with D lineage and comparative genomic analysis with other D lineage species, such as Ae. tauschii (D), Ae. longissima (S), and Ae. sharonensis (S) reveal major rearrangements in the 4U, 6U, and 7U chromosomes of Ae. umbellulata. Further, the resequencing of 20 geographically and morphologically diverse Ae. umbellulata accessions resistant to multiple wheat diseases (wheat rusts, tan spot, and bacterial leaf streak) revealed high genetic and phenotypic diversity in this species. Based on phenotypic and genomic data, we found different haplotypes for Lr9, the first rust resistance gene introgressed and recently cloned from Ae. umbellulata.