Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

Between the two major rice subspecies, indica varieties generally exhibit higher nitrate (NO₃^‒) uptake and nitrogen (N)-use efficiency (NUE) than japonica varieties. Introducing efficient NO₃^‒ utilization alleles from indica into japonica could improve NUE, and at the same time uncover unknown regulators of NO₃^‒ metabolism. Here, we identify OsWRKY23 as a key regulator of NO₃^‒ uptake and NUE differences between indica and japonica rice. The OsWRKY23^indica allele exhibits reduced transcriptional activation of a negative regulator of auxin accumulation, DULL NITROGEN RESPONSE1 (DNR1). The resultant increase in auxin level improves NO₃^‒ uptake and assimilation, which ultimately enhances grain yield. Geographical and evolutionary analyses reveal overlapping distribution of OsWRKY23^indica and DNR1^indica, particularly in low-fertility soils, suggesting their involvement in the adaptation to low N conditions to improve NUE and grain yield. Incorporating the OsWRKY23-DNR1 module from indica rice represents a promising strategy to enhance japonica NUE, which is crucial for sustainable agriculture.

Nitrogen (N) deficiency–induced increases in the root-to-shoot biomass ratio in plants are adaptive in nature but suboptimal for agriculture. Understanding the regulatory mechanisms governing this developmental plasticity could help improve crop performance while reducing fertilizer application. We identified OsWRI1a (WRINKLED1a) as a regulatory hub coordinating rice root and shoot growth in response to external N supply, thereby stabilizing the root-to-shoot ratio. In roots, OsWRI1a enhances N-responsive development by promoting auxin accumulation. Meanwhile, shoot OsWRI1a stimulates tiller development and therefore shoot growth. We identified an elite OsWRI1a haplotype that minimizes root-to-shoot ratio fluctuation under N deficiency, improving N-use efficiency and grain yield. Our findings reveal a central mechanism coordinating N-responsive growth allocation for sustainable agriculture.