Aug 2026· Plant Communications· pp.
102079
· 0 citations
Medicine
TL;DR
This 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.
Abstract
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.
Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement and trace inheritance of ancestral genomic regions across historical and contemporary germplasm.
NC White, KK Gagalova, TE Newman et al.· bioRxiv· 0 citations
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.
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, providing a genomic toolkit for cucumber evolution research and precision breeding.
Jian-Tao Guan, Xiangsheng Li, H. Miao et al.· Nature Genetics· 1 citation
Amid escalating water scarcity and groundwater depletion, halophytes such as Salicornia (Amaranthaceae) represent valuable models for extreme salt tolerance and hold promise for saltwater-based agriculture. Here, we show chromosome-scale genome assemblies for six Salicornia species, revealing four distinct subgenomes, reconciling our assemblies with two existing reference genomes (S. ramosissima UK and S. europaea China), correcting chromosome numbering and orientation. Comparative analyses across ploidy levels demonstrate genome expansion in North American lineages driven by Gypsy retrotransposons, and lineage-specific expansions of two gene families implicated in stress metabolism. Phylogenetic and population-structure analyses of a global resequencing panel of 318 accessions resolve interspecific relationships and establish curated germplasm collections for future crop breeding. Genetic analyses uncover a contrasting population-genetic signal on chromosome 6A between two species, highlighting an OSCA calcium-permeable channel gene as a candidate locus for osmotic adaptation. Together, these resources establish a genomic framework for Salicornia that supports evolutionary studies of halophyte adaptation and crop development. Salicornia is a halophytic flowering plants in the family Amaranthaceae. Here, the authors report chromosome-scale genome assemblies for six Salicornia species and reveal subgenome diversity, species boundaries and signatures of halophyte adaptation.
Yun-Chuan Wang, Laxman Adhikari, Lina María Cáceres Leal et al.· Nature Communications· 0 citations
Chromosomal rearrangements are hypothesized to facilitate speciation by suppressing recombination in locally adapted genomic regions, yet how they shape evolutionary rates during rapid divergence remains poorly understood. Here, we investigate the genomic architecture of two sister Carex (Cyperaceae) species on Réunion Island, which rapidly diverged (∼0.5 Mya) to occupy contrasting tropical-montane and dry-subalpine habitats. Using chromosome-level assemblies and population genomics, we show that genomic divergence is not uniform across the genome but is concentrated within specific large-scale inversions. Crucially, genes within these structural variants exhibit significantly accelerated rates of protein evolution, as evidenced by elevated ω, compared to the collinear genome. This is consistent with recombination suppression and subsequent relaxation of purifying selection driving these patterns, which may complement or even outweigh the signal of positive selection. Functional analysis and environmental associations reveal that these "genomic accelerators" include key adaptive loci: Inversions on chromosomes 14 and 28 are enriched for mechanosensitive ion channels and auxin transport, which is consistent with facilitating the interspecific physiological shift to aridity. Partial redundancy analyses reveal that ongoing intraspecific ecological adaptation is highly polygenic across the collinear genome. Our results demonstrate that genomic architecture actively dictates evolutionary speed, suggesting that certain lineages boosted by structural variants may bypass the typical constraints of purifying selection to rapidly exploit vacant ecological opportunities.
Inés Gómez-Ramos, Rogelio Sánchez-Villegas, A. Mohan et al.· Proceedings of the National...· 0 citations
Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding.
Yang Lv, Hao Wu, M. Asad et al.· Plants· 0 citations
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