OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the ‘Oat-like rice’ mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1^Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1^Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

Salt–alkali stress threatens the resilience to variable environments and thus the grain yield of rice. However, how rice responds to salt–alkali stress at the molecular level is poorly understood. Here, we report isolation of a novel salt–alkali-tolerant rice (SATR) by screening more than 700 germplasm accessions. Using 93-11, a widely grown cultivar, as a control, we characterized SATR in response to strong salt–alkali stress (SSAS). SATR exhibited SSAS tolerance higher than 93-11, as indicated by a higher survival rate, associated with higher peroxidase activity and total soluble sugar content but lower malonaldehyde accumulation. A transcriptome study showed that cell wall biogenesis-related pathways were most significantly enriched in SATR relative to 93-11 upon SSAS. Furthermore, higher induction of gene expression in the cell wall matrix polysaccharide biosynthesis pathway, coupled with higher accumulations of hemicellulose and pectin as well as measurable physio-biochemical adaptive responses, may explain the strong SSAS tolerance in SATR. We mapped SSAS tolerance to five genomic regions in which 35 genes were candidates potentially governing SSAS tolerance. The 1,4-β-D-xylan synthase gene OsCSLD4 in hemicellulose biosynthesis pathway was investigated in details. The OsCSLD4 function-disrupted mutant displayed reduced SSAS tolerance, biomass and grain yield, whereas the OsCSLD4 overexpression lines exhibited increased SSAS tolerance. Collectively, this study not only reveals the potential role of cell wall matrix polysaccharides in mediating SSAS tolerance, but also highlights applicable value of OsCSLD4 and the large-scale screening system in developing SSAS-tolerant rice.

Terrestrialization is an important evolutionary process that plants experienced. However, little is known about how land plants acquired aquatic growth behaviors. Here, we integrate multiproxy evidence to elucidate the evolution of the aquatic plant duckweed. Three genera of duckweeds show chronologically gradual degeneration in root structure and stomatal function and a decrease in lignocellulose content, accompanied by the contraction of relevant gene families and/or a decline in their transcription levels. The number of genes in main phytohormone pathways is also gradually decreased. The coordinated action of genes involved in auxin signaling and rhizoid development causes a gradual decrease in adventitious roots. Additionally, the significant expansion of the flavonoid pathway is related to the adaptation of duckweeds to floating growth. This study reconstructs the evolutionary history of duckweeds, tracing its journey from land back to water — a reverse trajectory of early land plants.

Duckweeds, recognized as the fastest growing aquatic flowering plants, exhibit substantial biomass production. Recently, they have been emerged as a potential industrial crop for efficient and eco-friendly protein production and nutrient recovery compared to conventional crops. The objective of the study was to determine the biomass accumulation rate, protein content and amino acid analysis of duckweeds (Lemna minor D0158).We cultured L. minor D0158 from its preserved state in the gene bank into both aseptic (in-vitro) and open condition at controlled room. The medium was Hoagland Solution (HS) mixed with sucrose in in-vitro condition while 1/5 concentration of HS (without sucrose) was in the open condition. Subsequently, we determined the dry biomass growth by calculating the weight difference adopting the Bergmann Method, and then calculated the protein percentage following the Kjeldahl Method. Moreover, the amino acid profiling was obtained using the Hydrolysis and Liquid Chromatography Technique. Later on, we compared the results with those of the other duckweeds and soybean together with the FAO requirements. We found that L. minor D0158 possessed the dry biomass growth rate of 6.72 g/m2/d with 33.13% protein content within 7-day cultivation period. Moreover, it exhibited significantly higher levels of branched chain amino acids (BCCAs) than soybean and met the FAO requirements. However, methionine (Met) content was found to be slightly low. The study suggested that L. minor D0158 might offer a sustainable solution for protein food security in future.

Polyploid rice and its reverted diploid show rich phenotypic variation and strong heterosis, showing great breeding value. However, the genomic differences among tetraploids, counterpart common diploids, tetraploid-revertant diploids, and hybrid descendants are unclear. In this work, we bred a new excellent two-line hybrid rice variety, Y Liang You Duo Hui 14 (HTRM12), using Haitian tetraploid self-reverted diploid (HTRM2). Furthermore, we comparatively analyzed the important agronomic traits and genome-wide variations of those closest relatives, Haitian diploid (HT2), Haitian tetraploid (HT4), HTRM2, and HTRM12 in detail, based on multiple phenotypic investigations, genome resequencing, and bioinformatics analysis. The results of agronomic traits analysis and genome-wide variation analysis of single nucleotide polymorphism (SNP), insertion–deletion (InDel), and copy number variation (CNV) show that HT4 and HTRM2 had abundant phenotypic and genomic variations compared to HT2. HTRM2 can inherit important traits and variations from HT4. This implies that tetraploid self-reverted diploid has high potential in creating excellent breeding materials and in breeding breakthrough hybrid rice varieties. Our study verifies the feasibility that polyploid rice could be used as a mutation carrier for creating variations and provides genomic information, new breeding materials, and a new way of application for tetraploid rice breeding.