Oryza longistaminata is an African wild rice species with valuable agronomic traits and the donor parent of perennial rice. Endophytic bacteria play an important role in host health, adaptive evolution and stress tolerance. However, endophytic bacterial communities in O. longistaminata and their plant growth-promoting (PGP) effects on the perennial rice of O. longistaminata offspring are poorly understood. In this study, the endophytic bacterial diversity, composition and network structures in the root, stem, and leaf tissues of O. longistaminata were characterized using Illumina sequencing of the 16S rRNA gene. The results suggested that O. longistaminata contains a multitude of niches for different endophytic bacteria, among which the root endosphere is more complex and functionally diverse than the stem and leaf endospheres. Tissue-specific biomarkers were identified, including Paludibaculum, Pseudactinotalea and Roseimarinus and others, for roots, Blautia for stems and Lachnospiraceae NK4A136 for leaves. The endophytic bacterial network of O. longistaminata was reassembled for various functions, including degradation/utilization/assimilation, detoxification, generation of precursor metabolites and energy, glycan pathways, macromolecule modification and metabolism. A total of 163 endophytic bacterial strains with PGP traits of potassium release, phosphate solubilization, nitrogen fixation, siderophore activity, indole-3-acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity were isolated from O. longistaminata. Eleven strains identified as Enterobacter cloacae, Enterobacter ludwigii, Stenotrophomonas maltophilia, Serratia fonticola, and Bacillus velezensis showed stable colonization abilities and PGP effects on perennial rice seedlings. Inoculated plants generally exhibited an enhanced root system and greater photosynthesis, biomass accumulation and nutrient uptake. Interestingly, two strains of E. cloacae have host genotype-dependent effects on perennial rice growth. The results of this study provide insights into the endophytic bacterial ecosystems of O. longistaminata, which can potentially be used as biofertilizers for sustainable perennial rice productivity.

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart, irrigated rice. Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations. A nonsynonymous mutation (C to T, from irrigated to upland rice) may have led to functional variation fixed by artificial selection, but the exact biological function in dryland adaptation is unclear. In this study, transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2, increasing ABA levels, root development, and drought tolerance in upland rice under dryland conditions. OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance. OsNCED2^T-NILs showed a denser root system and drought resistance, promoting the yield of rice under dryland conditions. OsNCED2^T may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted, water-saving rice.

Rice yield is an important and complex agronomic trait controlled by multiple genes. In recent decades, dozens of yield-associated genes in rice have been cloned, many of which can increase production in the form of loss or degeneration of function. However, mutations occurring randomly under natural conditions have provided very limited genetic resources for yield increases. In this study, potentially yield-increasing alleles of two genes closely associated with yield were edited artificially. The recently developed CRISPR/Cas9 system was used to edit two yield genes: Grain number 1a (Gn1a) and DENSE AND ERECT PANICLE1 (DEP1). Several mutants were identified by a target sequence analysis. Phenotypic analysis confirmed one mutant allele of Gn1a and three of DEP1 conferring yield superior to that conferred by other natural high-yield alleles. Our results demonstrate that favorable alleles of the Gnla and DEP1 genes, which are considered key factors in rice yield increases, could be developed by artificial mutagenesis using genome editing technology.