The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement. Currently available genome-editing tools have a limited number of targets, restricting their application in genetic research. In this study, we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors, eight donor vectors, four destination vectors, and one primer-design software package. By combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombination to assemble large fragments and by changing the structure of the amplicons used to assemble sgRNA expression cassettes, the plant ultra-multiplex genome editing system can assemble a single binary vector targeting more than 40 genomic loci. A rice knockout vector containing 49 sgRNA expression cassettes was assembled and a high co-editing efficiency was observed. This plant ultra-multiplex genome editing system advances synthetic biology and plant genetic engineering.

Chloroplasts are the center of plant life activities including photosynthesis, growth and development, and abiotic stress response. Chloroplast development and biogenesis in rice have been studied in detail, but how does abiotic stress affect chloroplasts is less studied. We obtained an albino mutant, alm1, whose chlorophyll content was greatly decreased. Transmission electron microscopy showed that chloroplast development in alm1 was blocked, especially in thylakoid-like structures, which could not form normally. The ALM1 gene encodes a chloroplast-localized superoxide dismutase. Full-length ALM1 successfully restored the non-albino phenotype, and in knockout lines, the albino phenotype reappeared. The ALM1 gene is expressed mainly in young leaves. alm1 plants died as a consequence of excessive reactive oxygen accumulation after the third-leaf stage. A series of biochemical assays verified that ALM1 interacted with the OsTrxz protein, which is one of the components of plastid-encoded RNA polymerase (PEP) complexes. A western blot experiment indicated that ALM1 played an important role in stabilizing OsTrxz in rice. An overexpression test of ALM1 revealed that ALM1 can increase drought resistance by removing excess reactive oxygen in rice seedlings. This study suggests that ALM1 not only participates in rice chloroplast biogenesis, but also increases rice stress resistance by scavenging excess reactive oxygen.