Soil cadmium (Cd) contamination poses significant risks to human health and environmental sustainability. Despite advances in bioremediation, effective bioagents with clear mechanistic insights for Cd detoxification are lacking. We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance. In five independent pot and field trials, we revealed the T32781-induced alleviation mechanisms of plant–microbe–soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic, physiological, microbiome and metabolome approaches. We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels. T32781 predominantly colonized soils, mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites. These beneficial effects were further validated in the field, where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley. This work highlights the potential of T32781 to enhance plant‒microbe–soil interactions and support sustainable and safe crop production in Cd-contaminated soils, addressing the increasing global demand for cereal production for food and feed.

Soybean is an important source of oil, protein, and feed. However, its yield is far below that of major cereal crops. The green revolution increased the yield of cereal crops partially through high-density planting of lodging-resistant semi-dwarf varieties, but required more nitrogen fertilizers, posing an environmental threat. Genes that can improve nitrogen use efficiency need to be integrated into semi-dwarf varieties to avoid the overuse of fertilizers without the loss of dwarfism. Unlike cereal crops, soybean can assimilate atmospheric nitrogen through symbiotic bacteria. Here, we created new alleles of GmGID1-2 (Glycine max GIBBERELLIN INSENSITIVE DWARF 1-2) using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) editing, which improved soybean architecture, yield, seed oil content, and nitrogen fixation, by regulation of important pathways and known genes related to branching, lipid metabolism, and nodule symbiosis. GmGID1-2 knockout reduced plant height, and increased stem diameter and strength, number of branches, nodes on the primary stem, pods, and seeds per plant, leading to an increase in seed weight per plant and yield in soybean. The nodule number, nodule weight, nitrogenase activity, and nitrogen content were also improved in GmGID1-2 knockout soybean lines, which is novel compared with the semi-dwarf genes in cereal crops. No loss-of-function allele for GmGID1-2 was identified in soybean germplasm and the edited GmGID1-2s are superior to the natural alleles, suggesting the GmGID1-2 knockout mutants generated in this study are valuable genetic resources to further improve soybean yield and seed oil content in future breeding programs. This study illustrates the pleiotropic functions of the GID1 knockout alleles with positive effects on plant architecture, yield, and nitrogen fixation in soybean, which provides a promising strategy toward sustainable agriculture.

Dissecting quantitative traits into Mendelian factors is a great challenge in genetics. Apple fruit storability is a complex trait controlled by multi-genes with unequal effects. We previously identified 62 quantitative trait loci (QTLs) associated with apple fruit storability and genomics-assisted prediction (GAP) models were trained using 56 QTL-based markers. Here, three candidate genes, MdNAC83, MdBPM2, and MdRGLG3, were screened from the regions of QTLs with large G’ value and large genetic effects. Both a 216-bp deletion and an SNP934 T/C at the promoter of MdNAC83 were associated with higher MdNAC83 expression but an SNP388 G/A at the coding region significantly reduced the activity to activate the expression of the target genes MdACO1, MdMANA3, and MdXTH28. MdBPM2 and MdRGLG3 participated in the ubiquitination of MdNAC83. SNP657 T/A of MdBPM2 and SNP167 C/G of MdRGLG3 caused a reduction in the activity to ubiquitinate MdNAC83. By the addition of functional markers to the GenoBaits SNP array, the prediction accuracy of the updated GAP models increased to 0.7723/0.6231 and 0.5639/0.5345 for flesh firmness/crispness at harvest and flesh firmness/crispness retainability, respectively. The variation network involving eight simple Mendelian variations in six genes helps to gain insight into the molecular quantitative genetics, to improve breeding strategy, and to provide targets for future genome editing.

Lignified stone cells are a unique feature of pear fruit, significantly affecting fruit texture. Even though some research efforts have already been made, the stone cell formation mechanism is complex, with many aspects yet to be elucidated. Here, through a genome-wide association analysis of stone cell traits, we identified PbrMADS1, a member of the SEPALLATA3 (SEP3) subfamily, as a candidate gene specifically expressed in stone cells during early fruit development. Functional studies confirmed that PbrMADS1 promotes stone cell formation; however, it does not directly activate lignin-related genes. Instead, PbrMADS1 interacts with PbrMYB169, enhancing PbrMYB169's binding to AC elements and amplifying downstream gene activation. Notably, homologous MADS1 and MYB169 proteins from closely related species such as apple and loquat do not form a similar complex. Sequence analysis revealed that the protein sequence of PbrMADS1 contains methionine (M) at the 63^rd amino acid position, while apple and loquat homologs carry threonine (T) at the same site. Substituting M with T (PbrMADS1^M63T) weakened its interaction with PbrMYB169 and impaired its function in regulating stone cell formation. This study offers new insights into MADS gene-mediated stone cell formation and highlights functional divergence within the SEP3 subfamily among apple tribe species of the Rosaceae family.

Chitin and its deacetylated derivative chitosan are the major components of fungal cell walls and are recognized by plant pattern-recognition receptors (PRRs) as pathogen-associated molecular patterns that induce innate immunity. Recognition of chitin oligosaccharide (CTOS) in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) requires the membrane-localized lysin-motif (LysM)-domain-containing receptors AtLYK5 and OsCEBiP, respectively. However, the mechanism underlying chitosan oligosaccharide (CSOS)-induced plant immunity remains unclear. In this study, we determined that CTOS and CSOS trigger immune responses and boost disease resistance in soybean (Glycine max) through the LysM-domain-containing protein GmNRF5a and its co-receptor GmCERK1. Surprisingly, both GmNFR5a and GmCERK1 bind directly to CTOS and CSOS, with distinct binding sites. The receptor-like kinase GmCAK1 acts downstream of GmCERK1 and is essential for CTOS/CSOS-mediated immune activation. Overall, these findings uncovered how soybean plants respond to CSOS and initiate immune signaling, demonstrating that soybean exploits shared immune sectors to transduce immune signals triggered by CTOS/CSOS, paving the way for the development of disease-resistant crops with broad-spectrum resistance.