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.
Abstract
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.
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.
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
This comprehensive review demonstrates that shifting from reactive field evaluation to marker-driven, genomics-assisted precision design provides the definitive molecular framework required to engineer high-yielding, climate-resilient, and disease-proof cacao cultivars, thereby permanently safeguarding the long-term economic sustainability of global cocoa supply chains.
Atharva Gangurde, Adesina Christiana, Franc Olivier Nzogang· International Journal of Inn...· 0 citations
The results suggest that flax morphotype divergence is driven primarily by selection on pre-existing allelic variation within a conserved gene repertoire, highlighting the importance of standing genetic variation as a key resource for flax breeding and improvement.
Frank M. You, C. Zheng, T. Edwards et al.· bioRxiv· 0 citations
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.
Lotus (Nelumbo) is an ancient aquatic plant of major ecological, economic, and cultural importance, yet its genomic architecture and domestication history remain incompletely resolved. Here, we generate telomere-to-telomere reference genomes for the two extant species, Asian lotus (N. nucifera) and American lotus (N. lutea). Comparative genomics analysis reveals divergence in centromeric regions and chromosomal structural variation between the two species. Population analysis of 832 globally distributed lotus accessions supports tropical Asia as the primary dispersal cradle of Asian lotus. We detect historical introgression events contributing to modern cultivated gene pools, and identify key loci regulating flower color variation and rhizome enlargement. To support research and breeding, we develop the Nelumbo Multi-omics Genome Platform (NMGP; http://182.92.235.125:18888/lotus/home/), integrating multi-omics data with a Pearson correlation-weighted Fusion of machine learning Models for Genomic Prediction (PFMGP) framework. These resources provide foundation for studying lotus evolution and genome-informed breeding. Lotus (Nelumbo) genomic architecture and domestication history remained incompletely resolved. Here, the author report the genome assembly of Asian lotus and American lotus and reveal domestication history through population genetics analysis of 832 globally distributed lotus accessions.
Heng Sun, J. Xin, Yuye Yu et al.· Nature Communications· 0 citations
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