A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning all 10 recognized tetraploid wheat subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
Abstract
Tetraploid wheat (Triticum turgidum L., BBAA), a key pasta crop, serves as an untapped genetic resource with rich genomic diversity for hexaploid bread wheat improvement. Here we de novo assembled 12 genomes spanning all 10 recognized tetraploid wheat (genome BBAA) subspecies, and a graph-based pangenome was constructed. Chromosome rearrangements drove subgenome asymmetry and shaped genomic divergence, with an average of 0.25 million structural variations per accession, predominantly attributable to transposon activity. Using 736 globally distributed tetraploid wheat accessions, we identified locally adapted subgroups with untapped breeding potential and discovered a novel retrotransposon‑induced loss‑of‑function Btr1-A allele responsible for convergent adaptation of non-brittle rachis. Genome-wide association studies identified 287 loci associated with 32 traits. A homeodomain-leucine zipper transcription factor HAT14-B that enhances both spikelet number and grain size was identified. This subspecies-wide pangenome enriches Triticeae AB subgenome resources and facilitates the discovery and application of agronomically important genetic variations. A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning 10 subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication. Silphium species native to North American prairies show strong drought tolerance. This study presents a haplotype-phased genome of a hybrid between S. integrifolium (oilseed crop) and S. perfoliatum (biomass/fiber crop), identifying loci linked to environmental adaptation and domestication.
Renan Souza, J. Clevenger, Jerry W. Jenkins et al.· Nature Communications· 0 citations
Cucumber (Cucumis sativus L.) is a global vegetable crop and powerful model for sex determination, fruit development and vascular biology. We present high-quality genome assemblies for 125 cultivated and wild accessions, capturing worldwide genetic diversity. Syntenic gene family analysis characterized 37,897 gene families and revealed haplotype diversity shaped by geographic expansion. Comparative analyses uncovered copy-number variations linked to local adaptation, including a CsFT tandem duplication promoting early flowering at higher latitudes. This resource reduces reference bias, enabling the annotation of resistance loci and the discovery of CsCcu, a nucleotide-binding leucine-rich repeat-type R gene conferring scab resistance. We cataloged 135,597 structural variations and quantified their regulatory effects, with ~30% driving trait diversification among geographic groups. Integrating structural variations into genome-wide association studies identified 172 quantitative trait loci for 38 agronomic traits, including a rare long terminal repeat insertion regulating fruit length via CsSPL1. Our findings provide a genomic toolkit for cucumber evolution research and precision breeding. Pangenome analyses of chromosome-scale genome assemblies for 125 diverse cucumber accessions highlight structural variation shaped by selection for geographical adaptation, fruit-length diversification and disease resistance.
Jiantao Guan, Xiangsheng Li, H. Miao et al.· Nature Genetics· 1 citation
Canola breeding has been shaped by strong selection for oil quality, yet the origins of the known oil quality alleles and genomic consequences of their selection are not fully resolved. By integrating pedigree reconstruction with graph pan-genomics we trace inheritance of ancestral genomic regions across historical and contemporary germplasm. Surrounding the low erucic acid allele in BnA08.FAE1, we identify a 17.23 Mb haplotype that approached fixation in Australian canola in the early 2000s. Contradicting the prevailing model, this haplotype predates modern breeding and was likely widespread in ancestral B. napus in the early 1900s. Genomic analyses implicate centromeric recombination suppression and structural variation in its long-term persistence, which has led to megabase-scale diversity loss through hitchhiking of neighbouring alleles. The haplotype contains extensive structural variation and multiple alleles associated with polygenic disease resistance. Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement.
NC White, KK Gagalova, TE Newman et al.· bioRxiv· 0 citations
The "Tropical-Temperate Integration" strategy, which involves the introgression of robust stress resistance from tropical germplasm into elite temperate lines, is a genomic imperative for stabilizing maize yields under climate change. Here, we investigated the genomic architecture of this strategy using KNY8009, a representative elite hybrid of the Huang-Huai-Hai summer maize region, by generating platinum-quality, pedigree-resolved genome assemblies across its lineage. We identified massive knob180 tandem repeat arrays as primary drivers of maize genome size plasticity and as hotspots for organellar DNA capture, while also demonstrating that these regions were a major source of error in reference-guided scaffolding. Furthermore, we identified hyperdivergent regions (HDRs) as punctate hotspots of extreme genetic diversity, whose boundaries were enriched for known regulatory motifs. Intensive functional genomics and novel genome-wide association studies across 38 traits confirm that targeted tropical introgressions reshaped specific genomic landscapes, conferring broad-spectrum resistance while preserving the elite temperate backbone. Finally, an alignment-free k-mer analysis provided an unbiased atlas of tropical-temperate divergence, valuable for further integration. Our study elucidated the genetic basis of Tropical-Temperate Integration, and established a rigorous, structural-aware framework for decoding the hidden variations that drive modern crop improvement.
Rye (Secale cereale L.) is an important cereal crop known for its high yield potential and tolerance to biotic and abiotic stresses. However, its large, repeat-rich, and heterozygous genome has posed challenges for assembly compared to related species such as wheat and barley. Here, we present a high-quality, chromosome-scale genome assembly of the inbred line Lo7, generated using PacBio HiFi, Oxford Nanopore, Hi-C, and BioNano technologies with the TRITEX pipeline. The resulting Lo7_V3 assembly spans 6.76 Gb with a contig N50 of 128 Mb, correcting previous misorientations and fully assembling all seven centromeres. Repetitive clusters containing rye-specific satellite sequences (pSc200 and pSc250) are contiguously assembled. Their chromosomal positions are validated using FISH. Centromeric retrotransposon analysis reveals RLG_Abia and RLG_Abigail as abundant, recently active elements, unlike in wheat. Collectively, the Lo7_V3 genome assembly provides an improved genomic resource for future genomic research in rye and related cereal species. The large, repeat-rich, and highly heterozygous rye (Secale cereale L.) genome has posed significant challenges for genome assembly. Here, the authors present an improved rye genome assembly and uncover unique retrotransposon organizations within its centromeres.
Erwang Chen, Carlotta Marie Wehrkamp, Srijan Jhingan et al.· Nature Communications· 0 citations