Genome editing toward biofortified soybean with minimal trade-off between low phytic acid and yield.

Phytic acid (PA) in grain seeds reduces the bioavailability of nutrient elements in monogastric animals, and an important objective for crop seed biofortification is to decrease the seed PA content. Here, we employed CRISPR/Cas9 to generate a PA mutant population targeting PA biosynthesis and transport genes, including two multi-drug-resistant protein 5 (MRP5) and three inositol pentose-phosphate kinases (IPK1). We characterized a variety of lines containing mutations on multiple IPK and MRP5 genes. The seed PA was more significantly decreased in higher-order mutant lines with multiplex mutations. However, such mutants also exhibited poor agronomic performance. In the population, we identified  two lines carrying single mutations in ipk1b and ipk1c, respectively. These mutants exhibited moderately reduced PA content, and regular agronomic performance compared to the wild type. Our study indicates that moderately decreasing PA by targeting single GmIPK1 genes, rather than multiplex mutagenesis toward ultra-low PA, is an optimal strategy for low-PA soybean with a minimal trade-off in yield performance. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-024-00158-4.

Nitrogen inhibition of nitrogenase activity involves the modulation of cytosolic invertase in soybean nodule.

Legume symbiotic nitrogen fixation (SNF) is suppressed by inorganic N in the soil. High N inhibition of nitrogenase activity is associated with the deprivation of carbon allocation and metabolism in nodules. However, the underlying molecular mechanisms remain unclear. Here, we identify GmCIN1 which encodes a cytosolic invertase, as a gateway for the N-tuning of sucrose utilization in nodules. GmCIN1 is enriched in mature soybean nodules and its expression is regulated by nitrogen status. The knockout of GmCIN1 using genome editing partially mimicks the inhibitory effects of N on nitrogenase activity and sugar content and the impact of high N on nodule transcriptomes. This indicates that GmCIN1 partially mediates the high N inhibition of nodule activity. Moreover, ChIP-qPCR and EMSA reveal that SNAP1/2 transcription factors directly bind to the GmCIN1 promoter. In addition, SNAP1/2 may be involved in the repression of GmCIN1 expression in mature nodules at high N concentrations. Our findings provide insights into the involvement of the transcriptional tuning of C metabolism genes by N-signaling modulators in the N-induced inhibition of nitrogenase activity.

Genetically optimizing soybean nodulation improves yield and protein content.

Symbiotic nitrogen fixation in legume nodules requires substantial energy investment from host plants, and soybean (Glycine max (L.) supernodulation mutants show stunting and yield penalties due to overconsumption of carbon sources. We obtained soybean mutants differing in their nodulation ability, among which rhizobially induced cle1a/2a (ric1a/2a) has a moderate increase in nodule number, balanced carbon allocation, and enhanced carbon and nitrogen acquisition. In multi-year and multi-site field trials in China, two ric1a/2a lines had improved grain yield, protein content and sustained oil content, demonstrating that gene editing towards optimal nodulation improves soybean yield and quality.