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Deterioration of rice (Oryza sativa L.) affects grain quality and seed viability during storage. Lipoxygenase (LOX), a key enzyme in lipid metabolism, directly affects the rate of ageing. Here, we found that knock-out of lipoxygenase gene OsLOX1 by CRISPR/Cas9 delayed loss of seed viability and quality. Transcriptome analysis showed that during storage, OsLOX1 affected transcription of multiple genes, including genes related to lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase, which may regulate the seed storability. The genes significantly down- and up-regulated only in Ningjing 4 after NA for 13 months and 3 days of AA suggesting that OsLOX1 likely promoted seed viability in rice by balancing ageing and storage related genes, and regulated the seed storability through the amino acid synthesis and metabolic pathways. Moreover, knock-out of OsLOX1 without CRISPR/Cas9 not only improved the seed viability, but also had little impact on agronomic traits. More importantly, the OsLOX1 knock-out lines were approved in 2019 (Agricultural Foundation of China Report No. 770). Collectively, our study showed that knock-out of OsLOX1 is beneficial for prolongation of seed viability and can be directly applied to agricultural production. [ABSTRACT FROM AUTHOR]

Summary: Endosperm is the main storage organ in cereal grain and determines grain yield and quality. The molecular mechanisms of heat shock proteins in regulating starch biosynthesis and endosperm development remain obscure.Here, we report a rice floury endosperm mutant flo24 that develops abnormal starch grains in the central starchy endosperm cells. Map‐based cloning and complementation test showed that FLO24 encodes a heat shock protein HSP101, which is localized in plastids. The mutated protein FLO24T296I dramatically lost its ability to hydrolyze ATP and to rescue the thermotolerance defects of the yeast hsp104 mutant.The flo24 mutant develops more severe floury endosperm when grown under high‐temperature conditions than normal conditions. And the FLO24 protein was dramatically induced at high temperature. FLO24 physically interacts with several key enzymes required for starch biosynthesis, including AGPL1, AGPL3 and PHO1. Combined biochemical and genetic evidence suggests that FLO24 acts cooperatively with HSP70cp‐2 to regulate starch biosynthesis and endosperm development in rice.Our results reveal that FLO24 acts as an important regulator of endosperm development, which might function in maintaining the activities of enzymes involved in starch biosynthesis in rice. [ABSTRACT FROM AUTHOR]

The formation and development of chloroplasts play a vital role in the breeding of high-yield rice (Oryza sativa L.). Porphobilinogen deaminases (PBGDs) act in the early stage of chlorophyll and heme biosynthesis. However, the role of PBGDs in chloroplast development and chlorophyll production remains elusive in rice. Here, we identified the spotted leaf 42 (spl42) mutant, which exhibited a reddish-brown spotted leaf phenotype. The mutant showed a significantly lower chlorophyll content, abnormal thylakoid morphology, and elevated activities of reactive oxygen species (ROS)-scavenging enzymes. Consistently, multiple genes related to chloroplast development and chlorophyll biosynthesis were significantly down-regulated, whereas many genes involved in leaf senescence, ROS production, and defense responses were upregulated in the spl42 mutant. Map-based cloning revealed that SPL42 encodes a PBGD. A C-to-T base substitution occurred in spl42, resulting in an amino acid change and significantly reduced PBGD enzyme activity. SPL42 targets to the chloroplast and interacts with the multiple organelle RNA editing factors (MORFs) OsMORF8-1 and OsMORF8-2 to affect RNA editing. The identification and characterization of spl42 helps in elucidating the molecular mechanisms associated with chlorophyll synthesis and RNA editing in rice. [ABSTRACT FROM AUTHOR]

Grain size is a key agronomic trait that determines the yield in plants. Regulation of grain size by brassinosteroids (BRs) in rice has been widely reported. However, the relationship between the BR signaling pathway and grain size still requires further study. Here, we isolated a rice mutant, named small grain2 (sg2), which displayed smaller grain and a semi‐dwarf phenotype. The decreased grain size was caused by repressed cell expansion in spikelet hulls of the sg2 mutant. Using map‐based cloning combined with a MutMap approach, we cloned SG2, which encodes a plant‐specific protein with a ribonuclease H‐like domain. SG2 is a positive regulator downstream of GLYCOGEN SYNTHASE KINASE2 (GSK2) in response to BR signaling, and its mutation causes insensitivity to exogenous BR treatment. Genetical and biochemical analysis showed that GSK2 interacts with and phosphorylates SG2. We further found that BRs enhance the accumulation of SG2 in the nucleus, and subcellular distribution of SG2 is regulated by GSK2 kinase activity. In addition, Oryza sativa OVATE family protein 19 (OsOFP19), a negative regulator of grain shape, interacts with SG2 and plays an antagonistic role with SG2 in controlling gene expression and grain size. Our results indicated that SG2 is a new component of GSK2‐related BR signaling response and regulates grain size by interacting with OsOFP19. [ABSTRACT FROM AUTHOR]

Key message: Knock out OsABA8ox helps improve pre-harvest spouting resistance and do not affect rice yield. Pre-harvest sprouting(PHS) is a phenomenon that the seeds of crops germinate preharvest, which reduces the yield and quality of rice. Abscisic acid(ABA) is one of the phytohormones that promotes seed dormancy. ABA8' hydroxylase is the main enzyme that can catabolism ABA in plant. There are three genes that encode ABA8' hydroxylase in rice, named OsABA8ox1, OsABA8ox2 and OsABA8ox3. In this study, we use CRISPR/Cas9 gene editing technology to target these three genes in Ningjing6 and find that the knockout transgenic lines are all significantly strengthen in seed dormancy and have no effect on the yield. By a series of quantitative experiments, we consider that after knock out OsABA8ox, the high endogenous ABA level will influence the ABA signal which suppress the substantial and energy metabolism in the seeds, and finally led to higher dormancy. [ABSTRACT FROM AUTHOR]

Background: The plant chloroplast is essential for photosynthesis and other cellular processes, but an understanding of the biological mechanisms of plant chloroplast development are incomplete. Results: A new temperature-sensitive white stripe leaf 9(wsl9) rice mutant is described. The mutant develops white stripes during early leaf development, but becomes green after the three-leaf stage under field conditions. The wsl9 mutant was albinic when grown at low temperature. Gene mapping of the WSL9 locus, together with complementation tests indicated that WSL9 encodes a novel protein with an HNH domain. WSL9 was expressed in various tissues. Under low temperature, the wsl9 mutation caused defects in splicing of rpl2, but increased the editing efficiency of rpoB. Expression levels of plastid genome-encoded genes, which are transcribed by plastid-coded RNA polymerase (PEP), chloroplast development genes and photosynthesis-related genes were altered in the wsl9 mutant. Conclusion: WSL9 encodes an HNH endonuclease domain-containing protein that is essential for early chloroplast development. Our study provides opportunities for further research on regulatory mechanisms of chloroplast development in rice. [ABSTRACT FROM AUTHOR]

Lack of seed dormancy, a major cause of pre-harvest sprouting in rice and other cereal crops, causes significant reductions in grain yield and quality. Weedy rice is often strongly dormant; therefore, quantitative trait loci (QTLs) related to seed dormancy in weedy rice "Ludao" could be useful for improving pre-harvest sprouting resistance in the important japonica variety "Ninggeng 4." To identify SD QTLs in variety Ludao, we constructed an advanced backcross population (BC6F2) of Ninggeng 4 with Ludao as the donor parent by marker-assisted backcrossing followed by SD phenotyping. The consistently detected QTL qSdr9 on chromosome 9L explained 18.09% of the phenotypic variance, and the Ludao allele decreased germination percentage by 10.78%. qSdr9 was fine-mapped to a 586.60 kb region between markers QNU9–10 and RM5777. Based on the closest linked marker for locus qSdr9, we developed near-isogenic lines with the qSdr9 allele from Ludao in Ninggeng 4 background. The qSdr9 near-isogenic lines with strong SD will be useful as parents in breeding for pre-harvest sprouting resistance. [ABSTRACT FROM AUTHOR]

Seed dormancy is a complex agronomic trait that is not only controlled by genetics but also influenced by environmental conditions. Novel seed dormancy genes could improve rice yield and quality by preventing losses due to pre-harvest sprouting (PHS). Although there have been many reported studies related to seed dormancy in rice, little is known about seed dormancy genes derived from weedy rice. We used a weedy rice line 'Ludao' (with strong seed dormancy) as the donor parent and elite japonica variety 'Ninggeng 4' (with weak seed dormancy) as a recurrent parent for backcrossing. A BC4F2 population was developed for gene mapping, and germination percentage was used as the phenotype. Four quantitative trait loci (QTLs), qSdr7-1, qSdr7-2, qSdr7-3, and qSdr7-4, were identified on chromosome 7. Seed dormancy alleles of the QTLs were all derived from 'Ludao.' Located between markers RM21103 and RM5672, qSdr7-2 had the largest effect and explained 27.2% of the phenotypic variation with a LOD score of 14.5. Based on the closest linked marker for locus qSdr7-2, we developed near-isogenic lines (NILs) with the qSdr7-2 allele from 'Ludao' in 'Ninggeng 4' background. The qSdr7-2-NILs, which have strong seed dormancy and elite agronomic traits, should be useful as a parent in breeding for PHS resistance. [ABSTRACT FROM AUTHOR]

Seed dormancy and germination in rice (Oryza sativa L.) are complex and important agronomic traits that involve a number of physiological processes and energy. A mutant named h470 selected from a60Co-radiated indica cultivar N22 population had weakened dormancy that was insensitive to Gibberellin (GA) and Abscisic acid (ABA). The levels of GA 4 and ABA were higher in h470 than in wild-type (WT) plants. The gene controlling seed dormancy in h470 was cloned by mut-map and transgenesis and confirmed to encode an ADP-glucose transporter protein. A 1 bp deletion in Os02g0202400 (OsBT1) caused the weaker seed dormancy in h470. Metabolomics analyses showed that most sugar components were higher in h470 seeds than the wild type. The mutation in h470 affected glycometabolism. • We identified a new allele of OsBT1 regulating seed dormancy in rice. • The germination phenotype of h470 was not regulated by GA or ABA. • The OsBT1 protein regulates seed dormancy through the glycometabolism pathway. [ABSTRACT FROM AUTHOR]

• The N22 OsDOG1L-3 allele is a candidate gene for the seed dormancy in QTL qSd-1-1. • OsbZIP75 and OsbZIP78 promote OsDOG1L-3 expression through binding to its promoter. • OsDOG1L-3 promotes the expression of ABA-related genes consistently with up-regulate ABA content. Seed dormancy is closely related to pre-harvest sprouting resistance. Both plant hormone abscisic acid (ABA) and DELAY OF GERMINATION 1 (DOG1) protein are key regulators of seed dormancy. Their relationship is well reported in Arabidopsis, but little is known in rice. Here, we show that a quantitative trait locus, qSd-1-1 contributes significantly to seed dormancy differences between the strongly dormant indica variety N22 and non-dormant japonica variety Nanjing35. It encodes a DOG1-like protein named OsDOG1L-3 with homology to Arabidopsis DOG1. There were evident promoter and expression differences in OsDOG1L-3 between N22 and Nanjing35, and overexpression or introduction of the N22 OsDOG1L-3 allele in Nanjing35 enhanced its seed dormancy. OsDOG1L-3 expression was positively correlated with seed dormancy and induced by ABA. OsbZIP75 and OsbZIP78 bound directly with the promoter of OsDOG1L-3 to induce its expression. Overexpression of OsbZIP75 increased OsDOG1L-3 protein abundance and promoted seed dormancy. OsDOG1L-3 upregulated expression of ABA-related genes and increased ABA content. We propose that the N22 OsDOG1L-3 allele is a candidate gene for the seed dormancy in QTL qSd-1-1 , and that it participates in the ABA pathway to establish seed dormancy in rice. [ABSTRACT FROM AUTHOR]