A constitutively active cortical nitrate-uptake cell state underlies nitrogen-use efficiency in perennial ryegrass
- 1Norwegian University of Life Sciences, Norway
Abstract
Perennial ryegrass (Lolium perenne) is the most widely sown forage grass of temperate agriculture and a major sink for fertiliser nitrogen, yet the cellular basis of its nitrogen-use efficiency (NUE) is unknown. We built a single-nucleus atlas of 76,684 root nuclei from a high- and a low-NUE genotype under matched nitrogen resupply. High-affinity nitrate uptake is concentrated in one cortical cell state that co-expresses nine NRT2 transporters and all three NAR2 partner proteins, a state that whole-root RNA-seq of the same tissue cannot resolve. Under reduced nitrogen the low-NUE genotype induces this state, whereas the high-NUE genotype does not; it expresses NRT2.3 at a higher baseline and uses different NRT2 paralogs, with one array member nearly silent. Across 44 annual and perennial Pooideae genomes, the same gene families show no life-history difference in copy number, evolutionary rate or selection intensity. Their regulation, however, varies in the same direction as between the two genotypes: the perennial Brachypodium sylvaticum expresses the NRT2.3 ortholog at the level that the annual B. distachyon reaches only under nitrogen deprivation, and an N-efficient barley genotype does not induce the transporters that an N-sensitive genotype induces. NUE differences are therefore associated with constitutive versus inducible deployment of a conserved toolkit, and the expression and presence/absence variants we identify are candidate breeding markers. The atlas, the first for a forage grass, is released as an open web resource.
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BibTeX
@misc{kovi2026constitutively,
title = {{A constitutively active cortical nitrate-uptake cell state underlies nitrogen-use efficiency in perennial ryegrass}},
author = {M. R. Kovi and P. Guevarra and S. Thu and E. T. M. Kragholm and A. R. Pashapu and F. H. Nohr and I. F. da Costa and M. Steinkopf and K. H. Gylstrom and H. Amdahl and P. Manishankar and J. M. Alcantara and S. Windju and M. Veerabagu and M. Alsheikh and S. Fjellheim and R. S. Sobral and O. A. Rognli},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.12.758384},
url = {https://www.biorxiv.org/content/10.64898/2026.10.12.758384v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A constitutively active cortical nitrate-uptake cell state underlies nitrogen-use efficiency in perennial ryegrass
AU - M. R. Kovi
AU - P. Guevarra
AU - S. Thu
AU - E. T. M. Kragholm
AU - A. R. Pashapu
AU - F. H. Nohr
AU - I. F. da Costa
AU - M. Steinkopf
AU - K. H. Gylstrom
AU - H. Amdahl
AU - P. Manishankar
AU - J. M. Alcantara
AU - S. Windju
AU - M. Veerabagu
AU - M. Alsheikh
AU - S. Fjellheim
AU - R. S. Sobral
AU - O. A. Rognli
PY - 2026
DA - 2026/10/12
PB - bioRxiv
DO - 10.64898/2026.10.12.758384
UR - https://www.biorxiv.org/content/10.64898/2026.10.12.758384v1
AB - Perennial ryegrass (Lolium perenne) is the most widely sown forage grass of temperate agriculture and a major sink for fertiliser nitrogen, yet the cellular basis of its nitrogen-use efficiency (NUE) is unknown. We built a single-nucleus atlas of 76,684 root nuclei from a high- and a low-NUE genotype under matched nitrogen resupply. High-affinity nitrate uptake is concentrated in one cortical cell state that co-expresses nine NRT2 transporters and all three NAR2 partner proteins, a state that whole-root RNA-seq of the same tissue cannot resolve. Under reduced nitrogen the low-NUE genotype induces this state, whereas the high-NUE genotype does not; it expresses NRT2.3 at a higher baseline and uses different NRT2 paralogs, with one array member nearly silent. Across 44 annual and perennial Pooideae genomes, the same gene families show no life-history difference in copy number, evolutionary rate or selection intensity. Their regulation, however, varies in the same direction as between the two genotypes: the perennial Brachypodium sylvaticum expresses the NRT2.3 ortholog at the level that the annual B. distachyon reaches only under nitrogen deprivation, and an N-efficient barley genotype does not induce the transporters that an N-sensitive genotype induces. NUE differences are therefore associated with constitutive versus inducible deployment of a conserved toolkit, and the expression and presence/absence variants we identify are candidate breeding markers. The atlas, the first for a forage grass, is released as an open web resource.
ER -