Map-based cloning of a gene underlying grain shape in wheat suggests that modest genetic changes induce dramatic phenotypic variations associated with a new whe

Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified single-nucleotide polymorphism densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of “Green Revolution” genes and can guide allele mining and dissect the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multi-scale network.

Semi-dwarf varieties of wheat (Triticum aestivum L.) carrying Reduced height (Rht) genes revolutionized wheat production. Rht8, a widely deployed semi-dwarfing allele, encodes RNHL1 (Ribonuclease H-Like 1), yet the molecular mechanisms underlying its growth regulation remain unclear. Here, we uncover a liquid-liquid phase separation (LLPS)-mediated transcriptional pathway by which RNHL1 controls plant height. We show that RNHL1 forms nuclear biomolecular condensates via its intrinsically disordered regions (IDR1 and IDR3) and physically interacts with the ethylene signaling transcription factor TaEIL1 (Ethylene insensitive3-like 1) to establish functional transcriptional hubs. These RNHL1–TaEIL1 condensates directly bind and repress the ethylene response factor gene TaERF1 (Ethylene response factor 1), and TaERF1 suppresses the gibberellin (GA) biosynthetic gene TaGA3ox2 (Gibberellin 3-beta dioxygenase 2). Genetic analyses demonstrate that both RNHL1 and TaEIL1 positively regulate plant height, with loss-of-function mutants exhibiting similar dwarf phenotypes and convergent transcriptomic profiles. Importantly, we establish TaERF1 as a direct repressor of TaGA3ox2, completing a regulatory cascade in which RNHL1–TaEIL1 condensates modulate GA-mediated internode elongation. Our findings reveal an integration point between ethylene and GA signaling orchestrated by RNHL1–TaEIL1 phase separation and highlight RNHL1’s roles in nucleic acid metabolism and transcriptional regulation. This study provides fundamental insights into LLPS-mediated growth control in crops and identifies specific protein domains as potential targets for wheat improvement.