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Tiller angle in cereals is a key shoot architecture trait that strongly influences grain yield. Studies in rice (Oryza sativa) have implicated shoot gravitropism in the regulation of tiller angle. However, the functional link between shoot gravitropism and tiller angle is unknown. Here, we conducted a large-scale transcriptome analysis of rice shoots in response to gravistimulation and identified two new nodes of a shoot gravitropism regulatory gene network that also controls rice tiller angle. We demonstrate that HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) is an upstream positive regulator of the LAZY1-mediated asymmetric auxin distribution pathway. We also show that two functionally redundant transcription factor genes, WUSCHEL RELATED HOMEOBOX6 (WOX6) and WOX11, are expressed asymmetrically in response to auxin to connect gravitropism responses with the control of rice tiller angle. These findings define upstream and downstream genetic components that link shoot gravitropism, asymmetric auxin distribution, and rice tiller angle. The results highlight the power of the high-temporal-resolution RNA-seq data set and its use to explore further genetic components controlling tiller angle. Collectively, these approaches will identify genes to improve grain yields by facilitating the optimization of plant architecture.

Current seawater desalination systems on ships face several limitations including outdated concentration detection methods, low detection accuracy, and insufficient real-time monitoring capabilities. This study addresses these issues by developing a concentration measurement device based on two-electrode conductivity measurement principles. The key innovation involves transforming conventional parallel plates into curved electrode plates that can be embedded directly into pipelines, enabling real-time concentration monitoring in shipboard seawater desalination systems. We established an equivalent circuit model and conducted simulation analysis of amplitude–frequency and phase–frequency response characteristics to guide excitation signal frequency selection. Using 3D printing technology, we fabricated pipeline components and manually processed curved electrode plates, then assembled experimental devices and determined optimal working parameters through systematic measurements of solution conductivity versus frequency and concentration. Laboratory testing with known concentration saline solutions demonstrated high measurement accuracy, with the device achieving a relative error of only 1.457% for 3.5% NaCl solution (simulated seawater) and 3.000% for commercial saline (0.9% NaCl) after calibration. Finally, we integrated a PLC control system for automated concentration measurement and display. Compared to traditional devices that require sampling in static water environments, this system can be distributed throughout shipboard desalination systems, providing more convenient, accurate, and efficient monitoring capabilities.

• Rice (Oryza sativa) tiller angle is a key component for achieving ideal plant architecture and higher grain yield. However, the molecular mechanism underlying rice tiller angle remains elusive. • We characterized a novel rice tiller angle mutant lazy2 (la2) and isolated the causative gene LA2 through map-based cloning. Biochemical, molecular and genetic studies were conducted to elucidate the LA2-involved tiller angle regulatory mechanism. • The la2 mutant shows large tiller angle with impaired shoot gravitropism and defective asymmetric distribution of auxin. We found that starch granules in amyloplasts are completely lost in the gravity-sensing leaf sheath base cells of la2, whereas the seed development is not affected. LA2 encodes a novel chloroplastic protein that can interact with the starch biosynthetic enzyme Oryza sativa plastidic phosphoglucomutase (OspPGM) to regulate starch biosynthesis in rice shoot gravity-sensing cells. Genetic analysis showed that LA2 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport. • Our studies revealed that LA2 acts as a novel regulator of rice tiller angle by specifically regulating starch biosynthesis in gravity-sensing cells, and established the framework of the starch-statolith-dependent rice tiller angle regulatory pathway, providing new insights into the rice tiller angle regulatory network.

Root gravitropism is essential for plants to establish proper root system architecture, enabling efficient soil exploration and optimal acquisition of water and nutrients. However, the molecular mechanisms underlying rice root gravitropism remain poorly understood. Here, we demonstrate that LAZY2 (LA2) and LA3, previously identified regulators for shoot gravitropism control, play critical roles in root gravitropism by maintaining starch accumulation in root columella cells. Loss-of-function mutants (CR-la2, CR-la3) exhibited impaired root gravitropism, resulting in a shallow root architecture. Further analysis revealed a significant reduction in starch accumulation within root statocytes of CR-la2 and CR-la3 mutants, causing reduced root gravity sensing. The complementation lines of LA2 or LA3 can rescue the defect in starch accumulation and root gravitropism. Haplotype analysis linked natural LA2 variation to distinct root architectures, with Hap5 accessions showing steeper angles than Hap1. Additionally, we confirmed that LA2 forms homodimers both in vivo and in vitro. Our findings establish LA2 and LA3 as key regulators coupling starch metabolism with root gravitropism, providing both fundamental insights into gravity sensing and genetic targets for optimizing root architecture to increase grain yield in cereal crops.

Tiller angle, a key agronomic trait for achieving ideal plant architecture and increasing grain yield, is regulated mainly by shoot gravitropism. Strigolactones (SLs) are a group of newly identified plant hormones that are essential for shoot branching/rice tillering and have further biological functions as yet undetermined. Through screening for suppressors of lazy1 (sols), a classic rice mutant exhibiting large tiller angle and defective shoot gravitropism, we identified multiple SOLS that are involved in the SL biosynthetic or signaling pathway. We show that SL biosynthetic or signaling mutants can rescue the spreading phenotype of lazy1 (la1) and that SLs can inhibit auxin biosynthesis and attenuate rice shoot gravitropism, mainly by decreasing the local indoleacetic acid content. Although both SLs and LA1 are negative regulators of polar auxin transport, SLs do not alter the lateral auxin transport of shoot base, unlike LA1 , which is a positive regulator of lateral auxin transport in rice. Genetic evidence demonstrates that SLs and LA1 participate in regulating shoot gravitropism and tiller angle in distinct genetic pathways. In addition, the SL-mediated shoot gravitropism is conserved in Arabidopsis . Our results disclose a new role of SLs and shed light on a previously unidentified mechanism underlying shoot gravitropism. Our study indicates that SLs could be considered as an important tool to achieve ideal plant architecture in the future.

Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited. Methods: Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members. Results: The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings. Conclusions: CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight.

Soil salinization constitutes a major constraint on global agricultural production, with marked divergence in salt adaptation strategies between salt-tolerant barley (Hordeum vulgare) and salt-sensitive rice (Oryza sativa). This study systematically investigated the evolution and functional specialization of the C3HC4-type RING zinc finger gene family, known to mediate abiotic stress responses through E3 ubiquitin ligase activity, in these contrasting cereal species. Through comparative genomics, we identified 123 HvC3HC4 genes and 90 OsC3HC4 genes, phylogenetically classified into four conserved subgroups. Differences in C3HC4 genes in phylogenetic relationships, chromosomal distribution, gene structure, motif composition, gene duplication events, and cis-elements in the promoter region were observed between barley and rice. Moreover, HvC3HC4s in barley tissues preferentially adopted an energy-conserving strategy, which may be a key mechanism for barley’s higher salt tolerance. Additionally, we found that C3HC4 genes were evolutionarily conserved in salt-tolerant species. The current results reveal striking differences in salt tolerance between barley and rice mediated by the C3HC4 gene family and offer valuable insight for potential genetic engineering applications in improving crop resilience to salinity stress.

Background Expanding noninvasive prenatal testing (NIPT) to include the detection of fetal subchromosomal copy number variations (CNVs) significantly decreased the sensitivity and specificity. Developing analytic pipeline to achieve high performance in the noninvasive detection of CNVs will largely contribute to the application of CNVs screening in clinical practice. Methods We developed the Noninvasively Prenatal Subchromosomal Copy number variation Detection (NIPSCCD) method based on low‐pass whole‐genome sequencing, and evaluated its efficacy in detecting fetal CNVs and chromosomal aneuploidies with 20,003 pregnant women. Results Totally, NIPSCCD identified 36 CNVs, including 29 CNVs consistent and 7 CNVs inconsistent with amniocytes tests. Additionally, seven fetal CNVs identified by amniocytes testing were undetected by NIPSCCD. The sensitivities for detecting CNVs > 10 Mb, 5 Mb–10 Mb, and CNVs < 5 Mb were 91.67%, 100.00%, and 68.42%, respectively. Moreover, NIPSCCD identified 103/ true positive trisomy 21/18/13 cases and 21 false positives, producing an overall 100.00% sensitivity and 99.89% specificity. Conclusion NIPSCCD showed a good performance in detecting fetal subchromosomal CNVs, especially for CNVs >10 Mb, and can be incorporated into the routine NIPT chromosomal aneuploidies screening with high sensitivity and specificity. We developed the Noninvasively Prenatal Subchromosomal Copy number variation Detection (NIPSCCD) method based on low‐pass whole‐genome sequencing (WGS) in this study. Evaluation of NIPSCCD with clinical samples showed good performance on prenatal testing of fetal CNVs, and high sensitivity and specificity in the detection of trisomy 21/18/13.

Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M(2) mutants in a common wheat cultivar 'Jinmai 47'. Numerous phenotypes with altered morphological and agronomic traits were observed from the M(2) and M(3) lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.

Low-light has emerged as a primary environmental factor limiting rice production, yet there is currently limited research on relevant regulatory measures. In this study, a low-light-intolerant RGA1 gene mutant d1 , and its wild type (Zhonghua 11, WT), along with RGA1 overexpression line OE-1, were used to investigate the effects of nitrogen levels on rice yield formation under low-light condition during anthesis, using field shading treatment. Our results showed that low-light significantly decreased spikelet fertility, with inhibited pollen tube elongation leading to spikelet abortion. We found that RGA1 could promote pollen tube elongation resulted from low-light stress at low nitrogen (60 kg N·ha − 1 , LN) and medium nitrogen (160 kg N·ha − 1 , MN) levels. Under low-light condition, the MN treatment notably increased the ratio of pollen tube entering into the ovule and spikelet fertility compared to the LN treatment, while the high nitrogen treatment (260 kg N·ha − 1 , HN) decreased spikelet fertility and yield in WT and OE-1 plants. For the d1 mutant, except for the LN treatment, other nitrogen treatments had minimal effects on spikelet fertility and yield. Furthermore, compared to the LN treatment, the activities of invertase and sucrose synthase, as well as the content of ATP, and ATPase in the spikelets of WT and OE-1 significantly increased when treated with MN under low-light condition. In conclusion, moderately increasing nitrogen levels can enhance sucrose metabolism, maintain energy balance thus alleviating inhibition of pollen tube elongation resulted from low-light stress and improving spikelet fertility.