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Summary Foods high in amylose content and resistant starch (RS) offer great potential to improve human health and lower the risk of serious noninfectious diseases. Common wheat (Triticum aestivum L.) is a major staple food crop globally. However, the RS contents in the grains of modern wheat varieties are low. Here, we report the generation of high‐amylose wheat through targeted mutagenesis of TaSBEIIa in a modern winter wheat cv Zhengmai 7698 (ZM) and a spring wheat cv Bobwhite by CRISPR/Cas9, respectively. We generated a series of transgene‐free mutant lines either with partial or triple‐null TasbeIIa alleles in ZM and Bobwhite, respectively. Analyses of starch composition, structure and properties revealed that the effects of partial or triple‐null alleles were dosage dependent with triple‐null lines demonstrated more profound impacts on starch composition, fine structures of amylopectin and physiochemical and nutritional properties. The flours of triple‐null lines possessed significantly increased amylose, RS, protein and soluble pentosan contents which benefit human health. Baking quality analyses indicated that the high‐amylose flours may be used as additives or for making cookies. Collectively, we successfully modified the starch composition, structure and properties through targeted mutagenesis of TaSBEIIa by CRISPR/Cas9 in both winter and spring wheat varieties and generated transgene‐free high‐amylose wheat. Our finding provides deep insights on the role of TaSBEIIa in determining starch composition, structure, properties and end‐use quality in different genetic backgrounds and improving RS content with multiple breeding and end‐use applications in cereal crop species through genome editing for health benefits.

Background Two-line hybrid rice with high yield potential is increasingly popular and the photo- and temperature-sensitive male sterile line is one of the basic components for two-line hybrid rice breeding. The development of male sterile lines through conventional breeding is a lengthy and laborious process, whereas developing thermo-sensitive genic male sterile (TGMS) lines for two-line hybrid breeding by editing a temperature-sensitivity gene by CRISPR/Cas9 is efficient and convenient. Results Here, thermo-sensitive genic male sterility (TGMS) was induced by employing the CRISPR/Cas9 gene editing technology to modify the gene TMS5. Two TGMS mutants, tms5–1 and tms5–2 , both lacking any residual T-DNA, were generated in the indica rice cultivar Zhongjiazao17 (cv. YK17) background. When grown at a sub-optimal temperature (22 °C), both mutants produced viable pollen and successfully produced grain through self-fertilization, but at temperatures 24 and 26 °C, their pollen was sterile and no grain was set. F 1 hybrids derived from the crosses between YK17S ( tms5–1 ) and three different restorer lines outperformed both parental lines with respect to grain yield and related traits. Conclusion The YK17S generated by CRISPR/Cas9 system was proved to be a new TGMS line with superior yield potential and can be widely utilized in two-line hybrid breeding of indica rice.

Cereals high in amylose content (AC) and resistant starch (RS) offer potential health benefits. Previous studies using chemical mutagenesis or RNA interference have demonstrated that starch branching enzyme (SBE) plays a major role in determining the fine structure and physical properties of starch. However, it remains a challenge to control starch branching in commercial lines. Here, we use CRISPR/Cas9 technology to generate targeted mutagenesis in and in rice. The frequencies of obtained homozygous or bi-allelic mutant lines with indels in and in T generation were from 26.7 to 40%. Mutations in the homozygous T lines stably transmitted to the T generation and those in the bi-allelic lines segregated in a Mendelian fashion. Transgene-free plants carrying only the frame-shifted mutagenesis were recovered in T generation following segregation. Whereas no obvious differences were observed between the mutants and wild type, mutants showed higher proportion of long chains presented in debranched amylopectin, significantly increased AC and RS content to as higher as 25.0 and 9.8%, respectively, and thus altered fine structure and nutritional properties of starch. Taken together, our results demonstrated for the first time the feasibility to create high-amylose rice through CRISPR/Cas9-mediated editing of .

Summary Identification of seed development regulatory genes is the key for the genetic improvement in rice grain quality. NF‐Ys are the important transcription factors, but their roles in rice grain quality control and the underlying molecular mechanism remain largely unknown. Here, we report the functional characterization a rice NF‐Y heterotrimer complex NF‐YB1‐YC12‐bHLH144, which is formed by the binding of NF‐YB1 to NF‐YC12 and then bHLH144 in a sequential order. Knock‐out of each of the complex genes resulted in alteration of grain qualities in all the mutants as well as reduced grain size in crnf‐yb1 and crnf‐yc12. RNA‐seq analysis identified 1496 genes that were commonly regulated by NF‐YB1 and NF‐YC12, including the key granule‐bound starch synthase gene Wx. NF‐YC12 and bHLH144 maintain NF‐YB1 stability from the degradation mediated by ubiquitin/26S proteasome, while NF‐YB1 directly binds to the ‘G‐box’ domain of Wx promoter and activates Wx transcription, hence to regulate rice grain quality. Finally, we revealed a novel grain quality regulatory pathway controlled by NF‐YB1‐YC12‐bHLH144 complex, which has great potential for rice genetic improvement.

Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 ( SDR3.1 ) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs . In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy. Seed dormancy is the preferred trait in rice production as it can prevent preharvest sprouting. Here, the authors report that MODD (mediator of OsbZIP46 deactivation and degradation) negatively regulates seed dormancy by inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVES (ABIs).

Polycomb group (PcG) proteins have been shown to affect growth and development in plants. To further elucidate their role in these processes in rice, we isolated and characterized a rice mutant which exhibits dwarfism, reduced seed setting rate, defective floral organ, and small grains. Map-based cloning revealed that abnormal phenotypes were attributed to a mutation of the Fertilization Independent Endosperm 2 (OsFIE2) protein, which belongs to the PcG protein family. So we named the mutant as osfie2-1. Histological analysis revealed that the number of longitudinal cells in the internodes decreased in osfie2-1, and that lateral cell layer of the internodes was markedly thinner than wild-type. In addition, compared to wild-type, the number of large and small vascular bundles decreased in osfie2-1, as well as cell number and cell size in spikelet hulls. OsFIE2 is expressed in most tissues and the coded protein localizes in both nucleus and cytoplasm. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that OsFIE2 interacts with OsiEZ1 which encodes an enhancer of zeste protein previously identified as a histone methylation enzyme. RNA sequencing-based transcriptome profiling and qRT-PCR analysis revealed that some homeotic genes and genes involved in endosperm starch synthesis, cell division/expansion and hormone synthesis and signaling are differentially expressed between osfie2-1 and wild-type. In addition, the contents of IAA, GA3, ABA, JA and SA in osfie2-1 are significantly different from those in wild-type. Taken together, these results indicate that OsFIE2 plays an important role in the regulation of plant height and grain yield in rice.

Long grain geng/japonica rice has a higher market preference due its excellent appearance quality. The dense and erect-panicle 1 (dep1) gene has been widely used in the breeding of high-yielding geng/japonica rice cultivars in China. However, this gene causes short and round grain shape thus making it less attractive in global rice markets. Therefore, breeding of high-yielding long-grain geng/japonica rice cultivars by incorporating dep1 with major-effect grain shape gene is of high priority in rice industry. Up to now, multiple grain shape genes’ effect mechanism has been clearly elaborated, however, under the background of erect-panicle geng/japonica rice, the effect of major grain shape genes on the appearance quality need to be further clarified, as detailed reports are limited. Utilizing CRISPR/Cas9 technology, a series of near-isogenic lines (NILs) (YF47dep1-gw8, YF47dep1-gs3, YF47dep1-gl7, YF47dep1-qgl3 and YF47dep1-tgw6) in Yanfeng 47(YF47dep1) background were created. Grain appearance and yield components analysis showed that: (1) All NILs’ grain length to width ratio was significantly increased compared to that of YF47dep1, excepted YF47dep1-gs3, (2) The chalkiness degree was significantly reduced in all of the NILs, (3) In all of the NILs, YF47dep1-gw8 grains exhibited the greatest length to width ratio and the lowest chalkiness degree, (4) The composition of glume cells and filling characteristics of the endosperm were two key factors contributing grain shape and grain chalk variations, respectively, and v) Owning to a substantial increase in the thousand grain weight, the yields of YF47dep1-gs3 and YF47dep1-tgw6 were significantly higher than that of YF47dep1, whereas YF47dep1-qgl3 exhibited the lowest yield because of a dramatic decrease in the effective panicle number and thousand grain weight. All the results revealed that pyramiding dep1 with major-effect grain shape alleles was an effective approach to improving the appearance quality of erect-panicle geng/japonica rice, owning to both of the appearance quality and yield improvement, GS3 and TGW6 alleles can be applied directly for breeding long-grain shape geng/japonica rice, and editing GW8 resulted in excellent appearance quality but low yield, therefore, this gene would be difficult to use directly but can be considered as the core germplasm resource.

Taste is crucial for the economic value of rice ( Oryza sativa L.) and determines consumer preference. However, the mechanisms underlying taste formation have remained unclear. Here, we show that OsGATA7 contributes to desirable taste quality by affecting the swelling properties, texture, and taste value of cooked rice. OsGATA7 binds to the promoter of SMOS1 , and activates its expression, thereby regulating taste quality. Furthermore, SMOS1 binds to the promoter of the protein biosynthesis gene OsGluA2 , and recruits the PRC2 complex to repress its expression, leading to increased protein content. The overexpression of both OsGATA7 and SMOS1 reduces protein content and enhances taste quality. The haplotypes OsGATA7 Hap1 and SMOS1 Hap1 maintain low protein content and improve taste scores. Collectively, these findings reveal a regulatory mechanism for taste quality formation mediated by the OsGATA7–SMOS1 protein content module, and identify the elite haplotypes OsGATA7 Hap1 and SMOS1 Hap1 as a means to improve taste quality. Rice taste is a crucial trait that determines consumer preference, but how it is established has been unclear. Here, the authors report that the formation of taste quality is mediated by the OsGATA7-SMOS1 protein content module and identify elite haplotypes for improving rice taste quality.

Rice growth and development occur in several distinct stages: a seedling stage, a vegetative stage, a reproductive stage, and maturity [...].Rice growth and development occur in several distinct stages: a seedling stage, a vegetative stage, a reproductive stage, and maturity [...].

The head rice rate, defined as the proportion of milled grains retaining at least three-quarters of their original length, has become a limiting factor that restricts the improvement of rice quality in China in recent years. Here, we characterized the role of ETHYLENE RESPONSIVE FACTOR34 (OsERF34), an APETALA2 (AP2/ERF) family TF, in the grain morphology, physiochemical properties, and processing quality of rice. Through CRISPR/Cas9-mediated knockout (Oserf34) and overexpression (OsERF34-OE) in the japonica cultivar ZH11, we demonstrate that OsERF34 exerts dose-dependent effects on grain morphology and processing traits. Oserf34 mutants exhibited significantly elevated chalkiness levels, with a 52.0% increase in percentage of grains with chalkiness(PGWC) and a 65.4% enhancement in chalkiness degree, with disordered and enlarged starch granules, reduced amylose content and skewed chain-length distribution (A/B1 chains increased but B2/B3 chains decreased), and displayed heightened starch solubility and swelling power but diminished milling resistance (shear hardness having fallen by 12.7–16.1% and compression hardness having fallen by 11.2–16.4%), culminating in doubled breakage rates and lower head rice rate (decreased by 6.7–9.0%) during processing. Strikingly, both mutants and OE lines showed analogous grain narrowing, yet the processing quality diverged. Mutants suffered structural fragility, while the OE lines enhanced mechanical robustness (compression hardness increased by 11.4–12.1%). The OsERF34-OE lines achieved 6.5–7.1% higher head rice rates. Our work positions OsERF34 as a dual-function regulator that governs grain morphology, regulating appearance and processing quality. These insights suggest that an overexpression of OsERF34 could improve processing efficiency, potentially laying a foundation for precision breeding.