Structural and deleterious burdens and their effects on yield traits in foxtail millet domestication.

Crop domestication typically accumulates structural and deleterious variants through genetic bottlenecks and selection hitchhiking. However, the structural and deleterious variant burden has not been investigated in the foxtail millet (). Integrating comparative genomics, pangenomics, population genetics, and quantitative genetics, we identified 6,713 gene gains and 2,802 losses during domestication, affecting flowering time and developmental processes.

The genomic design of fruit metabolomes.

As a major source of vitamins, minerals and dietary fibers, fruits are critical elements for ensuring global dietary sufficiency. Domestication and improvement boosted fruit yield and disease resistance but reduced flavor and aroma. With the rapid development of multiomics and gene editing, such as genomics, metabolomics and CRISPR-Cas9, improving fruit quality through genome design has become feasible.

The cytonuclear interactions during grapevine domestication.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan-mitogenome, pan-plastome, and haplotype-resolved nuclear genomes, all assembled from long-read sequences across 33 wild and domesticated grapevine accessions.

Major Facilitator Superfamily transporters balance sugar metabolism in peach.

Sugar content is a key determinant of peach (Prunus persica) fruit quality, influencing taste, consumer preferences, and market value. However, the roles of Major Facilitator Superfamily (MFS) transporters in sugar metabolism and regulation remain largely unexplored. This study employed a combination of spatial metabolomics, quantitative genetics, transcriptomics, comparative genomics, and functional genomics to investigate the role of 67 MFS members in balancing sugar metabolism during peach fruit development.

Grapevine pangenome facilitates trait genetics and genomic breeding.

Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.

The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes.

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar 'Yan73' was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi)， Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads.