The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos

TY - JOUR

T1 - The annotated blueprint

T2 - integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos

AU - Seong, Kyungyong

AU - Kumar, Rakesh

AU - Prigozhin, Daniil M

AU - Lunde, China

AU - Cherubino Ribeiro, Thales Henrique

AU - Bélanger, Sébastien

AU - Hsieh, Jo-Wei Allison

AU - Tang, McCree

AU - Meyers, Blake C

AU - Krasileva, Ksenia V

N1 - © 2026 The Author(s). New Phytologist © 2026 New Phytologist Foundation.

PY - 2026/5

Y1 - 2026/5

N2 - Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. 3000 exome-capture (EC) and promoter-capture (PC) datasets linked to mutagenized seed stocks, along with extensive transcriptomic and phenotypic resources. However, the absence of a reference genome has constrained their full utility. We assembled a chromosome-scale reference genome for Kronos, with high-confidence annotations, including manual curation of over 1000 disease resistance (nucleotide-binding leucine-rich repeat (NLR)) genes and genome-wide identification of microRNAs and phasiRNAs. We additionally reanalyzed EC and PC data to capture mutational landscapes across ethyl methane sulphonate-mutagenized Kronos populations. We revealed previously hidden NLR diversity and resolved their genomic organization at chromosomal ends. Re-analysis of capture datasets enabled high-resolution mutation discovery in genes and regulatory regions, providing a more comprehensive view of the variations detectable in the Kronos mutant populations. Collectively, these resources provide a reference-quality genomic framework for Kronos and position it as a versatile platform for functional and translational wheat research.

AB - Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. 3000 exome-capture (EC) and promoter-capture (PC) datasets linked to mutagenized seed stocks, along with extensive transcriptomic and phenotypic resources. However, the absence of a reference genome has constrained their full utility. We assembled a chromosome-scale reference genome for Kronos, with high-confidence annotations, including manual curation of over 1000 disease resistance (nucleotide-binding leucine-rich repeat (NLR)) genes and genome-wide identification of microRNAs and phasiRNAs. We additionally reanalyzed EC and PC data to capture mutational landscapes across ethyl methane sulphonate-mutagenized Kronos populations. We revealed previously hidden NLR diversity and resolved their genomic organization at chromosomal ends. Re-analysis of capture datasets enabled high-resolution mutation discovery in genes and regulatory regions, providing a more comprehensive view of the variations detectable in the Kronos mutant populations. Collectively, these resources provide a reference-quality genomic framework for Kronos and position it as a versatile platform for functional and translational wheat research.

KW - Triticum/genetics

KW - Genomics

KW - Genome, Plant

KW - Tetraploidy

KW - Molecular Sequence Annotation

KW - Mutation/genetics

KW - Genes, Plant

KW - Chromosomes, Plant/genetics

KW - Disease Resistance/genetics

U2 - 10.1111/nph.71006

DO - 10.1111/nph.71006

M3 - Article

C2 - 41724714

SN - 0028-646X

VL - 250

SP - 1389

EP - 1410

JO - New Phytologist

JF - New Phytologist

IS - 3

ER -