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.
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
Incipient reproductive isolation in the presence of gene flow has traditionally been attributed to a small number of major-effect loci under strong selection. Here, using the Heliconius erato adaptive radiation, we apply a pangenome framework to examine how mutational divergence, regulatory variation, and structural variants contribute to genome-wide divergence. In contrast to earlier studies, our high-resolution analyses reveal widespread divergence across the genome, consistent with a multilocus barrier to gene flow. Our findings support a model in which selection acts on regulatory phenotypes under migration-selection balance, with genetic differentiation becoming more pronounced as gene flow declines. By integrating population-level sampling, we show that apparent population-specific structural and regulatory variation inferred from single-reference genomes is overestimated, reflecting pervasive reference bias. While structural variants contribute to genomic variation, in our system, most are shared or polymorphic rather than fixed differences between populations. Together, our results show that the genomic landscape of H. erato divergence reflects the combined contributions of regulatory variation and mutational change, while highlighting the importance of accounting for reference bias when interpreting structural and regulatory divergence. This multilocus framework provides a more accurate view of how reproductive barriers emerge and strengthen under ongoing gene flow.
A. A. Ruggieri, F. Cicconardi, Nicolò Bellin et al.· Science Advances· 0 citations
There is an urgent need to expand groundnut genomics knowledge base to improve yield and adaptability in the target environments. Whole-genome sequencing can discover selective sweeps in the genomic regions distinguishing adaptive from non-adaptive germplasm within target environments. When combined with genome-wide association studies (GWAS), this approach can reveal genes underpinning local adaptability and yield advantage. The objective of this study was to establish a genome-wide quantitative framework form identifying genomic regions under selection, with a particular focus on narrowing down regions associated with important yield and adaptive traits. Moreover, validation of elite haplotype distributions in an independent fully sequenced groundnut panel. A panel of 197 groundnut accessions was subjected to whole-genome sequencing and phenotypic evaluation to dissect the collection into adaptive and non-adaptive subsets to uncover the genomic regions under selection. This was then combined with GWAS to uncover genetic variants governing agronomic traits associated with yield and adaptability. The stringent single and multi-trait analysis identified 60 loci for 12 agronomic traits, of which seven loci controlled multiple yield related traits and were pleiotropic. Within our diversity panel, 48 genomic regions showed signs of selection. Among these selective sweeps, six positively selected loci were co-localized with trait associated loci. A large genomic region on chr2 spanning ∼78 Mb was under divergent selection and harbored genes underpinning yield and 20-pod length. A F-box transcription factor, Arahy.37HYKA, on chr9, and an alanine transferase protein gene, Arahy.E9MTVL, on chr12 carried peak SNPs associated with yield and related traits. We further cross-validated our results in another groundnut355 panel, where the corresponding genes within LD blocks showed significant effects on HKW, pod length and pod weight. The genomic resources developed here provide a high-resolution variation map to delineate the genes underpinning yield and developmental traits in groundnut, improved our understanding of the genetic basis of important agronomic traits, and provide a valuable resource for further functional genomics studies and groundnut improvement programs.
M. Jahanzaib, Kun-Hui He, S. Rehman et al.· bioRxiv· 0 citations
Structural variants (SVs) are a major yet underused source of adaptive variation in aquaculture. We built a genome‐wide SV atlas for 180 Penaeus vannamei from six commercial breeding populations and discovered 1,159,046 SVs, with uneven chromosomal distributions and multi‐type hotspots. Over 63.53% of SVs overlapped repeats—especially simple sequence repeats, DNA transposons, and LINEs. SV and SNP densities were highly correlated. Across populations, 482 k SVs were shared and 145,623 were singletons; the fraction of deletions increased from shared to singleton classes. BMK and KH harbored more singletons than SIS, RH, and CP, indicating greater divergence. PCA and ADMIXTURE recovered three major clusters and revealed the substructure in RH, mirroring SNP analyses. Selection scans identified 78–193 sweep windows per population encompassing 38–161 candidate genes. These genes were predominantly enriched in population‐specific processes such as chromatin regulation, meiotic recombination, membrane‐associated functions, suggesting that structural variants may contribute to divergence in reproductive, metabolic, and structural pathways across breeding programs. Nevertheless, 10 genes showed parallel signals in over 3 populations; many carry short deletions likely affecting regulatory or coding elements. Together, these results show that genome architecture and domestication jointly shape the shrimp SV landscape; that SVs alone robustly resolve population history; and that a small set of recurrent, deletion‐bearing regulatory genes may underpin convergent improvement. The SV map and candidate loci provide diagnostic markers for germplasm tracing and candidate loci for marker‐assisted or genomic selection in P. vannamei breeding.
Ming-Yang Zhao, Hao Wang, Mingxuan Teng et al.· Evolutionary Applications· 0 citations
Quinoa (
Chenopodium quinoa
Willd.) is an allotetraploid crop with extraordinary environmental adaptability. To explore its genetic diversity, evolutionary dynamics, and altitudinal differentiation, we constructed a gene-based pangenome using 11 genomes (7 highland and 4 lowland accessions), comprising 51,298 orthologous groups with 19,653 core pan-genes, suggesting a near-closed pangenome architecture within the sampled accessions. Evolutionary analysis revealed that core pan-genes experienced the strongest purifying selection, whereas private pan-genes exhibited the weakest purifying selection, though the difference was not statistically significant compared to the other three pan-gene sets. Subgenomic asymmetry analysis showed that subgenome A retained fewer single-copy genes than subgenome B, with dosage-sensitive two-copy genes enriched in biotic stress-related domains and tandemly duplicated genes associated with abiotic stress adaptation. Presence/absence variation (PAV) analysis identified 7,477 orthologous groups enriched in highland accessions and 3,549 enriched in lowland accessions. We caution that these counts may be substantially inflated by the uneven sample size (7 highland vs. 4 lowland accessions) and should be interpreted as descriptive enrichment patterns rather than definitive evidence of ecotype divergence. Highland-enriched genes were enriched in transposon-related families and FAR1 domains potentially enhancing genomic plasticity and light signaling, whereas lowland-enriched genes were enriched in nitrogen metabolism and defense-related families. Copy number variation of betalain biosynthetic genes (CqCYP76AD, CqDODA, CqDOPA5-GT) was not the primary driver of seed coat color divergence between highland and lowland ecotypes. Four positively selected genes, including NADH-quinone oxidoreductase and MT-A70, harbor population-specific amino acid substitutions that may contribute to differential adaptation, potentially optimizing photosynthetic metabolism, RNA epigenetic modification, and protein homeostasis. These findings provide insights into the genomic basis of quinoa’s environmental adaptation and altitudinal differentiation, offering a genomic resource for molecular breeding.
Y. Pu, Li-Wen Wang, Yong-Chao Gong et al.· Frontiers in Plant Science· 0 citations
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