The rhizosphere microbiome plays a crucial role in determining plant performance and fitness. Nevertheless, regulatory mechanisms linking host genetic variation, root gene regulation and microbiome assembly—and their collective influence on plant nutritional traits—remain poorly understood. Here we generated and integrated 1,341 paired datasets, including root transcriptomes, rhizosphere bacterial 16S rRNA profiles and root ionomes, across 175 resequenced Brassica napus ecotypes grown at two contrasting field sites. We identified 203 highly heritable bacterial amplicon sequence variants (ASVs), many of which were significantly associated with root nitrogen (N) levels. Host transcriptome-wide gene expression and these microbial features together explained up to 45% of natural variation in N uptake while genome-wide association analyses revealed host loci regulating ASV abundance, many of which were under the control of eQTL hotspots linked to carbon and N metabolism. Isolate-level inoculation, whole-genome sequencing, metabolite profiling and confocal imaging demonstrated that the dominant, genetically regulated bacterial genus Sphingopyxis modulates auxin biosynthesis and promotes lateral root development to enhance N acquisition under stress. This study therefore identifies Sphingopyxis as a functionally relevant taxon with potential for microbiome-assisted breeding of nutrient-efficient crops.

Hybrid wheat offers significant benefits such as increased yield and high yield stability. Despite these benefits, the commercial adoption of wheat hybrids has been limited, primarily due to the high cost of hybrid seed production. Improving the efficiency of seed production requires a deeper understanding of key traits influencing hybrid seed set and their genetic bases. This study examined traits contributing to seed set beyond anther extrusion. Field trials were conducted across six environments using two European winter wheat cultivars, PIKO and HERMANN, and their derived double haploid population. Traits such as flowering time, visual anther extrusion, and plant height were measured. Field assessments of pollen shed were conducted to identify effective male pollen donors. Furthermore, traits including the interaction between male and female lines were examined. A quantitative trait locus on chromosome 1B was found for seed set, paving the way for marker-assisted selection. Our findings underscore the importance of considering traits beyond anther extrusion and pollen shed for cost-efficient hybrid seed production. Preselecting lines based on the beginning and duration of male flowering, nicking, and plant height promise to be particularly effective. Consequently, breeders can significantly increase seed set by focusing on a reduced number of key traits.

To meet the growing global demand for food, increasing yields through heterosis in agriculture is crucial. A deep understanding of the genetic basis of heterosis has led to the development of a quantitative genetic framework that incorporates both dominance and epistatic effects. However, incorporating all pairwise epistatic interactions is computationally challenging due to the large sequencing depth and population sizes needed to uncover the genes behind complex traits. In this study, we develop hQTL-ODS, a one-dimensional scanning method that directly assesses the net contribution of each quantitative trait locus to heterosis. Simulations show that hQTL-ODS reduces computational time while offering higher power and lower false-positive rate. We apply this method to a population of 5243 wheat hybrids with whole-genome sequenced profile, revealing key epistatic hubs that play a critical role in determining heterosis.

The dominance model of heterosis explains the superiority of F ₁ -hybrids via the complementation of unfavorable by beneficial alleles in many genes. Consistent with this model, genes active in only one parent and the hybrid display single-parent expression (SPE) complementation. Here we demonstrated, that SPE can explain up to 29% of heterotic variance in maize ( Zea mays L.). Moreover, expression quantitative trait loci (eQTL) revealed, that the genotype of the active parent determines the regulation mode of SPE patterns in cis or trans , which might explain how phylogenetic distance translates to transcriptomic diversity and heterosis in hybrids. Furthermore, we showed that most eQTL are located in heterozygous regions of the genome and that a trans eQTL controls the activity of a SPE gene which regulates lateral root density in hybrids. We anticipate that our study will stimulate further research elucidating the regulation and molecular mechanisms underlying heterosis.