Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement

Authors: SINGH, JATINDER - North Dakota State University; GUDI, SANTOSH - North Dakota State University; MAUGHAN, JEFF - Brigham Young University; LIU, ZHAOHUI - North Dakota State University; Kolmer, James; Chen, Xianming; Rouse, Matthew; SEHGAL, SUNISH - South Dakota State University; Gupta, Rajeev; UPINDER, GILL - North Dakota State University; Fiedler, Jason; CHOULET, FREDERIC - Inland Northwest Research Alliance, Inra; ACEVEDO, MARICELIS - Cornell University

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/26/2024
Publication Date: 9/18/2024
Citation: Singh, J., Gudi, S., Maughan, J., Liu, Z., Kolmer, J.A., Chen, X., Rouse, M.N., Sehgal, S., Gupta, R., Upinder, G., Fiedler, J.D., Choulet, F., Acevedo, M. 2024. Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.14470.
DOI: https://doi.org/10.1111/pbi.14470

Interpretive Summary: Wheat is one of the most consumed staple foods by the human population. Significant production losses are incurred annually in wheat due to various abiotic and biotic stresses, and newly emerging patterns of stresses in climate change scenarios pose an even greater threat to wheat production. During the evolution of cultivated wheat, hybridization between tetraploid wheat and a small number of wild plants led to a bottleneck in its genetic diversity. Wheat genetic diversity can be enriched by bringing back valuable stress tolerance traits from wheat progenitors and related wild species. In this study we developed genomic resources which include platinum standards reference genome and resequencing of 20 additional global accessions for one of the wheat wild relative, Aegilops umbellulata. These genomics resources along with high levels of resistance in the resequenced accessions against five devastating wheat diseases presented in this study affirmed the genetic potential of this wheat wild relative for future wheat improvement programs.

Technical Abstract: Aegilops spp. serve as an important reservoir for novel biotic and abiotic stress tolerance. To harness this reservoir, we have generated a platinum standard chromosome-level genome assembly of an accession “PI 554389” of Aegilops umbellulata using a combination of PacBio HiFi, Oxford nanopore, and chromosome conformation capture (Hi-C) sequencing technologies and resequenced 20 Ae. umbellulata genomes using Illumina sequencing. Our platinum standard U-genome assembled into 4.20 Gb genome spanned over seven chromosomes, rich in repetitive elements (~84%), achieving a QV of 59.54 with 98.14% completeness. The phylogenetic analysis places the U-genome with D-lineage but major and distinct rearrangements were revealed in the U-genome by the comparative genomics analysis. Unique transposable elements landscape and complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, of diploid U-genome uncovered a distinct evolutionary trajectory of Ae. umbellulata. Additionally, the resequencing of geographically and morphologically diverse Ae. umbellulata accessions revealed high genetic diversity distributed in three sub-populations. Resequencing also identified six new haplotypes for Lr9, the first leaf rust resistance gene introgressed and cloned from Ae. umbellulata. These genomics resources along with high levels of resistance in the resequenced accessions against five devastating wheat diseases presented in this study affirmed the genetic potential of Ae. umbellulata for wheat improvement.