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ARS Home » Pacific West Area » Logan, Utah » Forage and Range Research » Research » Publications at this Location » Publication #425585
Research Project: Improved Plant Genetic Resources and Methods to ensure Resilient and Productive Rangelands, Pastures, and Turf Landscapes

Location: Forage and Range Research

Title: Haplotype-resolved genome assembly of ‘Manhattan’ perennial ryegrass (Lolium perenne L.) and characterization of drought responsive late embryogenesis abundant genes

Author
item Robbins, Matthew
item Bushman, Bradley
item Gallagher, Joseph
item MAUGHAN, JEFFERY - Brigham Young University
item Hayes, Ryan

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2025
Publication Date: 11/20/2025
Citation: Robbins, M.D., Bushman, B.S., Gallagher, J.P., Maughan, J., Hayes, R.J. 2025. Haplotype-resolved genome assembly of ‘Manhattan’ perennial ryegrass (Lolium perenne L.) and characterization of drought responsive late embryogenesis abundant genes. BMC Genomics. 26. Article 1125. https://doi.org/10.1186/s12864-025-12144-1.
DOI: https://doi.org/10.1186/s12864-025-12144-1

Interpretive Summary: Perennial ryegrass is a premier forage and turf grass but has relatively poor persistence under drought stress. To improve turf-type perennial ryegrass genetic resources for the identification of genetic loci that contribute to its persistence under drought stress, we sequenced and assembled a Manhattan reference genome and extracted genes in the late embryogenesis abundant (LEA) gene families. The perennial ryegrass genome was complex, with 80% of the genome being repeats and approximately 43,000 genes. Seventy-two LEA genes were mapped onto the chromosomes and fitted into eight gene families, with 38 being induced upon drought stress. Three dehydrin genes in particular were highly induced by drought and provide candidates for genetic improvement of perennial ryegrass.

Technical Abstract: Perennial ryegrass is a premier forage and turf grass, a genomic model organism for cool-season perennial grasses, but has relatively poor persistence under drought stress. The cultivar Manhattan is an heirloom turf-type cultivar, and ancestral to many current turf cultivars and breeding lines in the USA. To improve turf-type perennial ryegrass genome resources, we assembled and compared two haplotypes of Manhattan and extracted late embryogenesis abundant (LEA) gene families. Both haplotypes resolved into 2.3 Gb genome assemblies of 7 chromosomes each, with Gypsy-like retrotransposon concentrations in putative centromere regions. Repeat content was 80%, and the two haplotypes were syntenic with each other as well as published forage-type perennial ryegrass genomes. Annotations resulted in 43,000 genes for each haplotype, over 95% coverage, 89% as single copy genes, and 86% with functional annotation. Seventy-two LEA genes were identified in haplotype-1 and fitted into 8 Pfam-based families, with 46 exhibiting expression evidence in vegetative tissues and 39 showing differential expression upon drought stress. Broad synteny but high heterozygosity characterized the Manhattan perennial ryegrass genome haplotypes. Repeat content, including LTR genes with annotation support, were high and indicative of cool-season Poaceae grasses. The numbers and percentages of differentially expressed LEA genes upon drought stress provide candidate genes for further drought tolerance studies.