Search Results (24)

Rice spikelet size, spikelet length and spikelet width, are very important traits directly related to a rice crop’s yield. The accurate measurement of these parameters is quite significant in research such as breeding, yield evaluation and variety improvement for rice crops. Traditional measurement methods still mainly rely on manual labor, which is time-consuming, labor-intensive and error-prone. In this study, a novel method, dubbed the “SSM-Method”, based on convolutional neural network and traditional image processing technology has been developed for the efficient and precise measurement of rice spikelet size parameters on rice panicle structures. Firstly, primary branch images of rice panicles were collected at the same height to build an image database. The spikelet detection model using convolutional neural network was then established for spikelet recognition and localization. Subsequently, the calibration value was obtained through traditional image processing technology. Finally, the “SSM-Method” integrated with a spikelet detection model and calibration value was developed for the automatic measurement of spikelet sizes. The performance of the developed SSM-Method was evaluated through testing 60 primary branch images. The test results showed that the root mean square error (RMSE) of spikelet length for two rice varieties (Huahang15 and Qingyang) were 0.26 mm and 0.30 mm, respectively, while the corresponding RMSE of spikelet width was 0.27 mm and 0.31 mm, respectively. The proposed algorithm can provide an effective, convenient and low-cost tool for yield evaluation and breeding research. Full article

Rice varieties with high anthocyanin content are often recognized for their vibrant colors and health benefits. The demand for rice with high anthocyanin is increasing domestically and internationally due to consumers becoming more health-conscious. However, the current increase in yield might not raise the anthocyanin content due to its location in the grain pericarp and seed coat, which are relative to the grain surface area. This study aims to develop rice lines to increase anthocyanin yield per production area by improving rice varieties with small, black, and three grains per spikelet. Accordingly, six rice recombinant inbred lines (RILs) were bred by crossing Niaw Dam Chaw Mai Pai 49 (NDCMP49) with Khao Nok (LLR059). The grain color, size, and number of grains per spikelet were selected from the F₁ to the F₄ population through the pedigree selection method. Six RILs and their parents were assigned in a randomized complete block design (RCBD) with three replications under field conditions during the rainy season of 2021 and 2022 in four locations. The results showed statistically significant differences in environmental conditions, affecting productivity and the yield components of rice lines. Consequently, the rice lines adapted to a specific environment, and there were significant differences in genotype. This study identified three RILs with higher yield performance (13-1 (3842 kg/ha), 374-1 (3699 kg/ha), and 903-3 (3550 kg/ha)) compared with the parent NDCMP49 (1996 kg/ha). However, the grain yields were unstable in the three top-yielding RILs due to varying environmental conditions, indicating that selective breeding requires a specific, narrow environment. Based on grain yield and grain size, the RILs performed better in the grain surface area than in the parent NDCMP49. Moreover, only two RILs (374-1 and 903-3) produced the highest anthocyanin content and yield, although this was lower than in the parent NDCMP49. However, the 374-1 and 903-3 RILs produced more grains, black grains, and three grains per spikelet with high yield and moderate anthocyanin content. They can, therefore, be backcrossed to the parent NDCMP49 to increase the accumulated anthocyanin content with a stable, high yield. This work provides a resource of small grains, black grains, and three grains per spikelet in the rice breeding line for breeding programs in the future. Full article

The mechanical strength of rice culm, an essential factor for lodging resistance and yield maintenance, is influenced by the composition and structure of the cell wall. In this study, we characterized a rice brittle culm mutant 22 (bc22), derived from LR005 through ethyl methanesulfonate (EMS) mutagenesis. The bc22 culm exhibited increased fragility and reduced mechanical strength compared to LR005. The mutant displayed pleiotropic effects, including a shorter plant height and panicle length, a smaller grain size, and the absence of the glume hairs. Scanning electron microscopy revealed a decrease in cell density and a looser structure in the bc22 culms. Biochemical analysis demonstrated a significant increase in hemicellulose content and a marked reduction in lignin content in the culm of bc22. Genetic analysis indicated that the brittle culm trait was governed by a single recessive gene. After employing bulked segregant analysis (BSA), whole-genome resequencing, and MutMap methods, LOC_Os02g25230 was identified as the candidate gene responsible for bc22. In bc22, a point mutation from proline (Pro) to leucine (Leu) in its coding region led to the pleiotropic phenotype. A complementation test further confirmed that the missense mutation causing the proline to leucine amino acid substitution in LOC_Os02g25230 was causative of the observed bc22 phenotype. Additionally, gene expression analysis showed that BC22 had higher expression levels in the culms, leaves, and spikelets compared to the roots. Taken together, our findings indicate that BC22 is a pleiotropic gene, and the influence of BC22 on brittleness may be associated with cell wall biosynthesis in rice culm. Full article

Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin–proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function. Full article

Dry direct seeding rice (DSR) is an emerging production system because of increasing labor and water scarcity in rice cultivation. The limited availability of rice cultivars suitable for dry direct seeding hampers the widespread adoption of this cultivation method in Northeast China. This study aimed to investigate grain production and plant characteristics associated with dry direct seeding rice. We conducted a field experiment on 79 japonica rice cultivars in Shenyang City, Liaoning Province, Northeast China, in 2020 and 2021. This study found that the grain yield of the tested rice cultivars ranged from 5.75–11.00 t ha⁻¹, with a growth duration lasting between 144–161 days across the cultivars. These cultivars were then categorized into high yielding (HY), medium yielding (MY), and low yielding (LY) based on daily yield by using Ward’s hierarchical clustering method. The higher grain yield for HY compared to MY and LY was attributed to more spikelets per unit area. The HY alleviated the conflict between higher panicle density and larger panicle size by improving the seedling emergence rate and productive stem rate. It also significantly increased shoot biomass at maturity. The HY reduced the period between seeding and beginning of heading (BBCH 51) and the proportion of dry matter partitioned to the leaf at the heading stage. However, it also increased the accumulation of dry matter in the grain and the proportion of dry matter partitioned to the grain at maturity. Furthermore, the HY markedly increased the harvest index and grain-leaf ratio, which are beneficial to coordinate the source–sink relationship. A quadratic function predicted that 98 days is the optimum growth duration before heading (BBCH 51) for achieving maximum yield. In conclusion, for dry direct seeding rice, it is appropriate to select high-yielding japonica inbred rice cultivars with shorter growth duration before heading (about 93–102 day), higher panicle number (about 450–500 × 10⁴ ha^–1), more spikelet number per panicle (about 110–130), higher seedling emergence rate (about 70–75%), higher productive stem rate (about 60–70%), and greater harvest index (about 50–55%). Full article

The source strength and sink demand as well as their interaction have been demonstrated to co-regulate the synthesis of starch and determine the grain quality, but the knowledge of the underlying physiological mechanisms is limiting. An indica variety, Yangdao 6, and a japonica variety, Jinxiangyu 1, were planted with three treatments, including normal growth plant (CK), leaf-cutting (LC) and spikelet-thinning (ST). The transcript levels of starch metabolic genes, physicochemical characteristics of starch and appearance, milling, cooking and tasting qualities of rice under different treatments were determined. The ST treatment increased the relative expression of genes related to the synthesis of short branch-chains of amylopectin (SSI, BEI, BEIIb) and amylose (GBSSI) and reduced the relative expression of medium-long to long branch-chains of amylopectin synthesis genes (SSIIa, SSIIIa, SSIIIb, ISA1). When comparing ST with the CK treatment, starch granules became smoother with higher contents of short branch-chains and lower ratios of medium-long and long branch-chains of amylopectin; the crystallinity and the value of 1045/1022 cm⁻¹ was decreased; for pasting properties, the setback and pasting temperature were decreased; the peak viscosity, hot viscosity, breakdown and final viscosity were significantly increased. Meanwhile, the ST treatment improved the appearance, milling and cooking and tasting qualities. The opposite results were observed under the LC treatment. These results indicated that source strength and sink size would regulate expression levels of starch metabolic genes, which is pivotal for the contents of amylose and short/long branch chains ratio of amylopectin, thus changing the structure and physicochemical properties of starch and grain quality. Here, we speculated that the improved source strength in terms of higher leaf/canopy photosynthesis and small sink size, such as small panicle size, would be preferred traits in high grain quality rice breeding. Full article

Genetic improvement has been devoted to increasing rice yield by increasing the spikelet number per panicle and the spikelet/leaf ratio. As a result, indica-japonica hybrid rice “Yongyou” varieties with large panicles and superhigh yield potential have been developed. These varieties exhibit significantly higher grain yield and nitrogen use efficiency for grain (NUEg) under moderate and high N supply conditions due to their large sink size, but their yield performance remains obscure under low N input and low soil fertility conditions. In the present study, we investigated four varieties including Yongyou2640 (YY2640, large-panicle india-japonica hybrid variety), Yangliangyou6 (YLY6, two-line indica hybrid variety), Quanyou6 (QY6, three-line indica hybrid variety), and Huanghuazhan (HHZ, indica inbred variety) under two low soil fertility treatments [LF (removing half of soil depth) and CK] and two N fertilizer rates (0 and 100 kg N ha⁻¹) in Central China. The results showed that the grain yield of YY2640 was more responsive to fertility than that of other varieties, which was 19.4–42.3% higher than that of the other three varieties under CK N100 treatment, but it was 14.5–19.4% lower than that of YLY6 and QY6 under LF N0 and LF N100. A higher spikelet/leaf ratio resulted in more biomass and N partition to panicles rather than to leaves under LF N0 and N100. Slightly more post-flowering dry matter obtained from higher leaf N content and crop growth rate failed to compensate for the adverse effects of reduced pre-flowering dry matter accumulation and stem-to-grain translocation during grain filling. This led to the lower NUEg of YY2640 than YLY6 and QY6 under low soil fertility conditions. Based on these findings, the present study suggested that the source–sink relationship of the super hybrid varieties should be optimized according to the soil N supply condition. Full article

Pyramiding of quantitative trait loci (QTLs) is a powerful approach in breeding super-high-yield varieties. However, the performance of QTLs in improving rice yield varies with specific genetic backgrounds. In a previous study, we employed the CRISPR/Cas9 system to target three yield-related genes, gn1a, gs3, and ipa1 in japonica ‘Zhonghua 11’, mutants of which featured large panicle, big grain, few sterile tillers, and thicker culm, respectively. In this paper, four pyramided lines, including gn1a-gs3, gn1a-ipa1, gs3-ipa1, and gn1a-gs3-ipa1, were further generated by conventional cross-breeding to be tested. Agronomic traits analysis showed that: (1) the stacking lines carried large panicles with an increased spikelet number in the main panicle or panicle; (2) the grain weight of the stacking lines, especially gs3-ipa1 and gn1a-gs3-ipa1, were heavier than those in single mutants; (3) both gn1a-gs3 and gs3-ipa1 produced more grain yield per plant than single mutant lines; (4) pyramided lines were higher than single mutants and transcriptome analysis found improved expression levels of genes related to lipid, amino acid, and carbohydrate transport and metabolism in lines pyramiding three mutant alleles, possibly as a result of complementary and additive effects. Accordingly, the alteration of gene-expression patterns relating to hormone signaling, plant growth, and seed size control was characterized in pyramided lines. The present study not only investigates the effects of pyramiding genes, but also may provide an efficient strategy for breeding super-high-yield rice by reducing the time cost of developing pyramided lines. Full article

Inbred rice has been grown more and more widely, while the planting area of hybrid rice has decreased by approximately 25% in China since 1995. This study aimed to assess the changes in grain yield and yield attributes due to cultivar development in indica (Oryza sativa ssp. indica) inbred rice in China. Field experiments were conducted in 2019 and 2020 to determine the performance of grain yield and yield attributes of an indica super inbred rice cultivar Jinnongsimiao (JNSM) released in 2010 by comparing it with an indica high-yielding inbred rice cultivar Guichao 2 (GC2) released in 1978 and an indica super hybrid rice cultivar Y-liangyou 900 (YLY900) released in 2016. Results showed that JNSM produced 18% higher grain yield than GC2 but 6% lower grain yield than YLY900. Compared with GC2, JNSM had higher spikelets per panicle, spikelet-filling percentage, and harvest index by 67%, 4%, and 11%, respectively. Compared with YLY900, JNSM had 14% lower grain weight and 19% lower biomass production during the pre-heading period. The difference in biomass production during the pre-heading period between JNSM and YLY900 was explained more by crop growth rate than growth duration. This study suggests that (1) the recently released indica super inbred rice cultivar JNSM outyields the old indica high-yielding inbred rice cultivar GC2 as a result of increasing panicle size, spikelet-filling percentage, and harvest index, and (2) further improvement in grain yield in indica inbred rice can be achieved by improving biomass production through promoting pre-heading crop growth. Full article

APETALA2/ethylene response factor (AP2/ERF) is widely found in the plant kingdom and plays crucial roles in transcriptional regulation and defense response of plant growth and development. Based on the research progress related to AP2/ERF genes, this paper focuses on the classification and structural features of AP2/ERF transcription factors, reviews the roles of rice AP2/ERF genes in the regulation of growth, development and stress responses, and discusses rice breeding potential and challenges. Taken together; studies of rice AP2/ERF genes may help to elucidate and enrich the multiple molecular mechanisms of how AP2/ERF genes regulate spikelet determinacy and floral organ development, flowering time, grain size and quality, embryogenesis, root development, hormone balance, nutrient use efficiency, and biotic and abiotic response processes. This will contribute to breeding excellent rice varieties with high yield and high resistance in a green, organic manner. Full article

Manganese (Mn) is a mineral element essential for plant growth and development. In agronomy reality, Mn deficiency or overload in crops disturbs metal homeostasis, photosynthesis, and many other biological processes. Mining genetic resources linking Mn acquisition and homeostasis is vitally important to help understand plant adaptation to Mn stress and breeding genetically improved crops for sustainable agriculture. Metallic chaperone (metallochaperone) is a class of family proteins playing an essential role in positive responses to metal and abiotic stresses. Here, we report a novel function of a metal chaperone gene OsHIPP56 in regulating Mn accumulation in rice (Oryza sativa) crops. OsHIPP56 was transcriptionally induced by excessive Mn stress but hardly by Mn deficiency. OsHIPP56-expression in a yeast Mn-sensitive mutant pmr1 rescued the Mn-defective phenotype by increasing Mn accumulation in cells. Knocking out OsHIPP56 by Crispr/cas9 protocol did not affect the growth and physiological responses of rice seedlings supplied with normal Mn concentration. However, excess Mn stress moderately retarded growth of the knockout plants compared with the wild-type. A life span field trial was conducted under natural conditions with the two rice varieties. Knocking out OsHIPP56 also distorted rice growth, leading to reduced plant height, stem elongation, panicle length, spikelet fertility, seed size, and grain yield. Mn concentrations in rice straw (leaves and stem/internodes), brown rice, and husk in cas9 plants were much lower than those in wild-type. This was particularly seen in the brown rice where the Mn concentrations in cas9 plants were reduced by 26.7–49.1% compared with the wild-type control. Overall, these lines of evidence point out that OsHIPP56 plays a primary role required for rice growth, seed development, and Mn acquisition. Full article

Understanding the agronomic and physicochemical characteristics related to grain yield and grain quality is an ongoing hotspot. In 2018 and 2019, high-yielding rice with good palatability (HYGP), high-yielding rice with poor palatability (HYPP), and low-yielding rice with good palatability (LYGP) were grown in paddy fields to explore the main traits underlying the better grain yield and overall palatability of HYGP. HYGP and HYPP demonstrated a 18.1–20.7% higher grain yield (p < 0.05) than LYGP; HYGP and LYGP gave an overall palatability from 75.2 to 77.0, higher (p < 0.05) than HYPP. The higher grain yield of HYGP compared to that of LYGP resulted from a larger sink size because of the spikelets per panicle and the higher total shoot biomass weight (p < 0.05). HYGP exhibited more (p < 0.05) panicles per m² but lower spikelets per panicle and 1000-grain weight than HYPP and maintained a similar grain yield to HYPP. Compared with HYPP and LYGP, HYGP exhibited more (p < 0.05) biomass accumulation from heading to maturity, supported by the higher leaf area index, post-heading leaf photosynthetic rate, and SPAD values. HYGP had higher (p < 0.05) adenosine diphosphate glucose pyrophosphorylase and starch branching enzyme activities at the middle and late grain-filling stages than HYPP and LYGP. HYGP and LYGP had a lower (p < 0.05) chalky area, chalky degree, amylose content, setback, grain protein content, and prolamin content than HYPP, while it had a higher (p < 0.05) gel consistency, breakdown, and ratio of glutelin content to prolamin content. Our results suggested that optimized yield components, more biomass accumulation through improved leaf photosynthetic capacities, a lower amylose content with coordinated enzyme activities involved in starch synthesis, and a lower grain protein content with a better composition were the main traits facilitating the better grain yield and overall palatability of rice in east China. Full article

The remobilization of non-structural carbohydrates (NSCs) in the stem is essential for rice grain filling so as to improve grain yield. We conducted a two-year field experiment to deeply investigate their relationship. Two large-panicle rice varieties with similar spikelet size, CJ03 and W1844, were used to conduct two treatments (removing-spikelet group and control group). Compared to CJ03, W1844 had higher 1000-grain weight, especially for the grain growth of inferior spikelets (IS) after removing the spikelet. These results were mainly ascribed to the stronger sink strength of W1844 than that of CJ03 contrasting in the same group. The remobilization efficiency of NSC in the stem decreased significantly after removing the spikelet for both CJ03 and W1844, and the level of sugar signaling in the T6P-SnRK1 pathway was also significantly changed. However, W1844 outperformed CJ03 in terms of the efficiency of carbon reserve remobilization under the same treatments. More precisely, there was a significant difference during the early grain-filling stage in terms of the conversion of sucrose and starch. Interestingly, the sugar signaling of the T6P and SnRK1 pathways also represented an obvious change. Hence, sugar signaling may be promoted by sink strength to remobilize the NSCs of the rice stem during grain filling to further advance crop yield. Full article

Rice yield is determined by source, sink, and flow and the coordination of these factors. However, the genetic base of the sink-flow is still unknown. We conducted on genome-wide association to detect quantitative trait loci (QTL) related to sink size (the number of rachis branches and spikelet number in rachis branches) and flow vascular bundle (large and small vascular bundles number in panicle neck and second internode) using 440 germplasm resources. The accessions exhibited marked variation in all traits and demonstrated complex phenotypic correlations. A total of 138 QTL affecting the 8 traits were detected using 3,188,500 high-quality single nucleotide polymorphism markers. Sixteen QTL clusters simultaneously affected flow and sink traits, which might explain the genetic base of significant correlations between flow and sink traits. The nine candidate genes in two consistent chromosomal regions simultaneously affecting multiple vascular bundle and sink size traits by performing gene-based association analysis and haplotype analysis. Among them, D2 (LOC_Os01g10040) and Gn1a (LOC_Os01g10110) for qPLVN1.1, qSLVN1.1, and qPRN1.2 and OsPIN5b (LOC_Os08g41720) for qPLVN8, qSLVN8, qSSVN8, and qSTSN8.2 were considered the most likely candidate genes based on functional annotations. The results provide useful information for improving rice yield potential via balancing sink–flow relationships by marker-assisted selection. Full article

Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice. Full article