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Summary: Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild‐type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars. [ABSTRACT FROM AUTHOR]

Research indicates that, owing to the enhanced grain-filling rate of tetraploid rice, its yield has notably improved compared to previous levels. Studies conducted on diploid rice have revealed that optimal planting density and fertilization rates play crucial roles in regulating rice yield. In this study, we investigated the effects of different nitrogen application and planting density treatments on the growth, development, yield, and nitrogen utilization in tetraploid (represented by T7, an indica–japonica conventional allotetraploid rice) and diploid rice (Fengliangyou-4, represented by FLY4, a two-line super hybrid rice used as a reference variety for the approval of super rice with a good grain yield performance). The results indicated that the highest grain-filling rate of T7 could reach 77.8% under field experimental conditions due to advancements in tetraploid rice breeding. This is a significant improvement compared with the rate seen in previous research. Under the same conditions, T7 exhibited a significantly lower grain yield than FLY4, which could be attributed to its lower grain-filling rate, spikelets per panicle, panicle number m−2, and harvest index score. Nitrogen application and planting density displayed little effect on the grain yield of both genotypes. A higher planting density significantly enhanced the leaf area index and biomass accumulation, but decreased the harvest index score. Compared with T7, FLY4 exhibited a significantly higher nitrogen use efficiency (NUEg), which was mainly due to the higher nitrogen content in the straw. Increasing nitrogen application significantly decreased NUEg due to its minimal effect on grain yield combined with its significant enhancement of nitrogen uptake. Our results suggest that the yield and grain-filling rate of T7 have been improved compared with those of previously tested polyploid rice, but are still lower than those of FLY4, and the yield of tetraploid rice can be further improved by enhancing the grain-filling rate, panicle number m−2, and spikelets per panicle via genotype improvement. [ABSTRACT FROM AUTHOR]

Summary: Diurnal floret opening time (DFOT) is a pivotal trait for successful fertilization and hybrid breeding in rice. However, the molecular mechanism underlying this trait is poorly understood in rice.In this study, we combined the cytological, genetic and molecular studies to demonstrate that jasmonic acid (JA) regulates DFOT in rice through modulating the turgor and osmotic pressure of the lodicules.We show that lodicules undergo dramatic morphologic changes, accompanied by changes in water and sugar contents during the process of floret opening. Consistently, a large set of genes associated with cell osmolality and cell wall remodeling exhibits distinct expression profiles at different time points in our time‐course transcriptomes of lodicules. Notably, a group of JA biosynthesis and signaling genes is continuously upregulated, accompanied by a gradual increase in JA accumulation as floret opening approaching. Furthermore, we demonstrate that the JA biosynthesis gene OsAOS1 is required for endogenous JA biosynthesis in lodicules and promoting rice DFOT. Moreover, OsMYC2, a master regulator of JA signaling, regulates rice DFOT by directly activating OsAOS1, OsSWEET4, OsPIP2;2 and OsXTH9.Collectively, our findings establish a core regulatory network mediated by JA for modulating rice DFOT and provide effective gene targets for the genetic improvement of DFOT in rice. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Introduction: Hybrid rice demonstrated superior performance in enhancing yield and efficiency in rice production compared to inbred rice. Nevertheless, the underlying mechanism responsible for the increased yield and efficiency of hybrid rice in South China's double-cropping rice region remains understudied. Methods: Field experiments over two consecutive years were conducted. Firstly, yield variations among 20 inbred and 15 hybrid rice cultivars prevalent in South China's double-cropping rice system were examined. Secondly, selecting representative hybrid and inbred rice cultivars with significant yield disparities were carried out on further analyzing dry-matter production, source-sink relationships, and nutrient absorption and utilization in both rice types. Results: Hybrid rice displayed an average grain yield of 8.07 and 7.22 t hm-2 in the early and late seasons, respectively, which corresponds to a 12.29% and 13.75% increase over inbred rice with statistically significant differences. In comparison to inbred rice, hybrid rice exhibited enhanced nitrogen concentration in leaves at the heading stage (15.48-16.20%), post-heading dry matter accumulation (52.62-73.21%), post-heading dry matter conversion rate (29.23-34.12%), and harvest index (17.31-18.37%). Additionally, grain nitrogen and phosphorus uptake in hybrid rice increased by 11.88-22.50% and 16.38-19.90%. Hybrid rice mainly improved post-heading nitrogen and phosphorus uptake and transport, while not total nitrogen and phosphorus uptake. Internal nitrogen and phosphorus use efficiency enhanced by 9.83%-14.31% and 10.15%-13.66%, respectively. Postheading dry matter accumulation, harvest index, grain nitrogen and phosphorus uptake, and internal nitrogen and phosphorus use efficiency exhibited significant positive linear correlations with grain yield. Discussion: The period from heading to maturity is critical for enhancing hybrid rice yield and efficiency. Improving photosynthetic capacity during this period and promoting nutrient transport to grains serve as crucial pathways for increasing grain yield and efficiency. This study is of great significance for further improvement grain yield and breeding rice cultivars with high-yield and high nutrients use efficiency for South China's double-cropped rice system. [ABSTRACT FROM AUTHOR]

SUMMARY: Diurnal flower‐opening time (DFOT), the time of spikelet opening during the day, is an important trait for hybrid rice (Oryza sativa L.) seed production. Hybrids between indica and japonica rice varieties have strong heterosis, but the parental lines usually have different, nonoverlapping DFOTs. This reduces the success of hybrid seed production in crosses between indica and japonica subspecies, thus hindering the utilization of indica and japonica inter‐subspecies heterosis. However, little is known about the molecular mechanisms regulating DFOT in rice. Here, we obtained japonica rice lines with a DFOT 1.5 h earlier than the wild type by overexpressing OsMYC2, a gene encoding a key transcription factor in the jasmonate (JA) signaling pathway. OsMYC2 is activated by JA signaling and directly regulates the transcription of genes related to JA biosynthesis and cell wall metabolism. Overexpressing OsMYC2 led to significantly increased JA contents and decreased cellulose and hemicellulose contents in lodicule cells, as well as the softening of lodicule cell walls. This may facilitate the swelling of lodicules, resulting in early diurnal flower‐opening. These results suggest that the OsMYC2–JA feedback loop regulates DFOT in rice via cell wall remodeling. These findings shed light on the understanding of regulatory mechanism of the DFOT of plants, which should promote the development of indica and japonica varieties suitable for hybrid rice breeding. Significance Statement: OsMYC2 regulates diurnal flower‐opening time by directly regulating the transcription of JA biosynthesis genes and cell wall remodeling genes. This study not only elucidates the mechanism of JA regulating diurnal flower‐opening time but also helps reduce the cost of hybrid seed production and promote the development of indica and japonica rice hybrid breeding. [ABSTRACT FROM AUTHOR]

The nuclear factor Y (NF‐Y) has been shown to be involved in plant growth and development in response to various environmental signals. However, the integration of these mechanisms into breeding practices for new cultivars has not been extensively investigated. In this study, the Arabidopsis gene AtNF‐YB1 was introduced into rice, including inbred Kasalath and the hybrids Jinfeng × Chenghui 727 and Jinfeng × Chuanhui 907. The obtained transgenic rice showed early flowering under both natural long day (NLD) and natural short day (NSD) conditions. For the inbred Kasalath, the transgenic lines clearly showed a shorter plant height and lower grain yield, with a decrease in spike length and grain number but more productive panicles. However, the hybrids with AtNF‐YB1 had much smaller or even zero reduction in spike length and grain number and more productive panicles. Thus, maintained or even increased grain yields of the transgenic hybrids were recorded under the NLD conditions. Quantitative PCR analysis indicated that the rice flowering initiation pathways were early activated via the suppression of Ghd7 induction in the transgenic rice. RNA‐Seq further demonstrated that three pathways related to plant photosynthesis were markedly upregulated in both Jinfeng B and the hybrid Jinfeng × Chuanhui 907 with AtNF‐YB1 expression. Moreover, physiological experiments showed an upregulation of photosynthetic rates in the transgenic lines. Taken together, this study suggests that AtNF‐YB1 expression in rice not only induces early flowering but also benefits photosynthesis, which might be used to develop hybrid varieties with early ripening. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2LOC_Os05g09520. These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor. [ABSTRACT FROM AUTHOR]

Simple Summary: Chalk5 is an important gene used in rice breeding to improve rice chalkiness, which greatly affects rice quality. For this study, the first exon of Chalk5 was edited, and two different knockout mutants were obtained. These two lines showed a decreased percentage of grains with chalkiness, chalkiness degree, and seed setting ratio. Moreover, their chalkiness was insensitive to temperature during the grain-filling stage, and the head milled rice rate was improved even under high-temperature conditions. The two lines showed significantly reduced PGWC and DEC without changes in other agronomic traits in the hybrid background. These results indicate that Chalk5 gene-edited lines are useful in indica hybrid rice breeding for a high yield and superior grain quality in high-temperature growing environments. Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H+-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions. [ABSTRACT FROM AUTHOR]

Summary: Inter‐subspecific indica–japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra‐subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica–japonica hybrid rice breeding. Diurnal flower‐opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1‐ and 2‐h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM‐DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50‐min and 1.5‐h earlier DFOT respectively. The yields of FHSP using japonica male‐sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica–japonica hybrid rice breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Hybrid rice is grown by millions of Asian farmers and has normally higher yields compared to inbred varieties. However, hybrid rice has been associated with high damage from herbivores. This susceptibility could be due to the physiology of the hybrid plant type or due to a limited availability of male sterile parents that are necessary for hybrid seed production. We examined how plant type and breeding affect the relative susceptibilities of hybrid and inbred rice by exposing 32 rice genotypes to the brown planthopper, whitebacked planthopper, and yellow stemborer in controlled environments and field plots. We compared insect fitness on the plants and related this to the type and genetic similarity of genotypes. Despite their diverse origins (China, Colombia, India, and the Philippines), the hybrids and inbreds formed two distinct genetic groups, thereby confounding plant type and phylogeny. Hybrids were generally more susceptible to stemborers but not to planthoppers. Relative herbivore fitness was strongly influenced by plant origin (i.e., breeding program) with one group of related genotypes being relatively susceptible to all three herbivores. Our results indicate that hybrids are not inherently more susceptible than inbreds to insect herbivores and that careful screening with the elimination of the most susceptible genotypes is necessary to reduce herbivore damage to hybrid and inbred rice in Asia. Several studies have reported higher damage from insect herbivores to hybrid compared to inbred (pure line) rice. We used a collection of 20 hybrid and 12 inbred genotypes from diverse origins to test the hypotheses that hybrid rice susceptibility is due to (a) the hybrid plant type and/or (b) rice phylogeny. We challenged the genotypes with Nilaparvata lugans (BPH), Sogatella furcifera (WBPH) and Scirpophaga incertulas (YSB) in greenhouse and screenhouse bioassays and monitored herbivores in field plots. We used single nucleotide polymorphic (SNP) markers to assess genetic similarities between the genotypes and found that the hybrids and inbreds formed two distinct clusters regardless of origin. In the screenhouse, hybrids were more susceptible than inbreds to YSB; however, resistant hybrids and susceptible inbreds were also apparent from both the screenhouse and field plots. Plant biomass was the best predictor of susceptibility to YSB. Plant origin had a greater effect than plant type on susceptibility to BPH and WBPH. WBPH was the most abundant planthopper in the field plots where numbers were highly correlated with planthopper fitness in the greenhouse bioassays. Our results provide evidence that high-yielding hybrids that are relatively resistant to herbivores can be achieved through careful breeding. The avoidance of susceptible genotypes during breeding should remain a key element of integrated rice pest management. [ABSTRACT FROM AUTHOR]

Panicle-type structure is an important factor affecting rice yield, and an excellent panicle type has become a key indicator in rice breeding. In this study, the indica rice variety R766, which has an open panicle type, was obtained through natural mutation and hybrid selection. Through analyzing differences in panicle structure, panicle yield, and chemical composition between open panicle rice R766 and conventional panicle rice R2928, we found that the angles of the middle and lower branches in R766 were 186.99% and 135.93% greater than those in R2928, respectively. By comparing the grain-filling characteristics of different panicle positions in the two rice varieties, we found that the grain filling at the middle and lower panicle positions of R2928 was significantly lower, accompanied by an increase in the percentage of empty spikelets. However, in R766, the grain-filling rates in the middle and lower panicle positions were consistent with those in the upper panicle position, with significantly higher rates of grain filling and grain plumpness in the middle and lower panicle positions than in R2928. The empty grain rate at the lower panicle position of R766 was 15.25% lower than that of R2928, and the grain filling was 24.75% higher than that of R2928. Additionally, the variation in the 1000-grain weight of grains at different panicle positions in R766 was relatively small, with decreases of 1.55% and 0.38% in the middle and lower panicle positions, respectively, compared with the upper position, whereas R2928 showed decreases of 5.99% and 7.12% in the 1000-grain weight of grains at the middle and lower panicle positions, respectively, compared with the upper position. The cellulose content in the stems of R766 was 7.51% higher than that of R2928, with no significant difference in the cellulose content in the panicle axis and primary branches compared to R2928. The lignin content of the panicle axis in R766 was 8.03% higher than that in R2928, whereas there was no significant difference between the lignin content of the stems and primary branches. This preliminary study revealed the open panicle characteristics of R766 and the reasons for its high basal grain setting rate. This study provides a reference for promoting this open panicle-type indica rice variety to improve yield and disease resistance in environments with high humidity and low sunlight levels. [ABSTRACT FROM AUTHOR]

The performance of novel genetic combinations under untested environmental scenarios and management practices can be virtually examined using process‐based crop models. Indeed, there has been a long‐standing interest in the crop modeling community to expand the utility of process‐based models to broader germplasm panels (e.g., breeding lines or diversity panels). Yet, there is often a misalignment between data needed to parameterize process‐based crop models and data routinely collected by breeding programs. To address this gap, we leverage a dataset from a long‐term trial on advanced experimental lines and released varieties from the Louisiana rice breeding program to calibrate and evaluate the decision support for agrotechnology transfer (DSSAT) CSM‐CERES‐Rice model. Next, we use data collected by the same program on a large collection of breeding lines to generate numerous in silico genotypes and evaluate their performance across different management practices (different planting dates) and three climatic conditions (current climate and two future scenarios based on CMIP6‐SSP5‐8.5 climate projections). Our simulations indicate that shifting the current planting date (i.e., March) back by 1–2 months (to January) under moderate warming conditions (+1.3°C warmer and 41% higher CO2 level), and 2–3 months (to December) under extreme warming conditions (+4.1°C warmer and 133% higher CO2 level) could potentially offset the negative impacts of the increased future temperature. Given earlier planting, shorter duration varieties (i.e., those with shorter growing degree day requirements during the vegetative and grain filling periods) are found to be more favorable for supporting high yields. Such varieties with a shorter thermal time to anthesis are found to remain just outside of the current pool of variation for this trait. Opportunities and challenges for leveraging breeding data in process‐based modeling to derive insights into adaptation strategies for future climates are further discussed. Core Ideas: There has been a long‐standing interest in the crop modeling community to extend the utility of process‐based models to breeding.Data required for models are often misaligned with data routinely collected from applied breeding programs.Parameterization of the CERES‐Rice model was informed using historical and recent data collected from the Louisiana rice breeding program.The impact of future climate, planting dates, and novel genetic combinations on the yield and phenology was tested.The range of genetic variability for phenology in the current breeding program to adapt varieties to future conditions was assessed. [ABSTRACT FROM AUTHOR]

SUMMARY: Rice (Oryza sativa L.) is a short‐day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late‐maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker‐assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1‐NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability. Significance Statement: We identified the genetic basis of transgressive late maturation in hybrid rice, which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired photoperiod sensitivity. Our study lays an important foundation for improving the breeding efficiency and latitude adaptability of hybrid rice. [ABSTRACT FROM AUTHOR]

Hybrid rice needs to prevent lodging due to excessive grain weight during maturity, which can lead to yield loss, grain quality deterioration and difficulty in harvesting. Breeding excellent parents (restorer and male-sterile lines) is the foundation for cultivating lodging-resistant hybrid rice. However, there is still limited information about restorers with improved lodging resistance. To identify a new restorer with significantly enhanced resistance to lodging, the restorer line Huazhan, which has been used for many years in hybrid rice breeding in China, was used as the control, to evaluate the lodging resistance of the new restorer R382. A two-year field experiment was executed to investigate the difference on lodging-related traits of the basal two internodes above-ground, such as out diameters of stems with or without leaf sheath (DWS, DWOS), culm thickness (CT), the section modulus (SM), bending stress (BS), and bending moment at break (M). The results indicated that DWS, CT, BS, M of R382 was at least 19.9%, 13.3%, 36.5% and 52.6% higher than that of Huazhan. However, the negative indicator lodging index of R382 was over 17.5% lower. The number and area of vascular bundles, and the contents of the chemical components of the cell wall including cellulose, lignin, and hemicellulose, together with the accumulation of starch granules, were significantly greater in R382. Furthermore, in the basal stems during the jointing stage, a series of genes that promote cell wall formation exhibited significantly higher expression levels in R382. Meanwhile, there was no significant difference in the yield of R382 and Huazhan. Thus, this new restorer could be a valuable donor in the future hybrid rice breeding programs for improving lodging resistance. [ABSTRACT FROM AUTHOR]

Rice is a staple food for nearly two-thirds of China's population. As socio-economic development continues, there is a growing demand for high-quality rice. This study collected grain quality traits for 17,785 rice varieties approved throughout China, and categorized them into the following five types: indica inbred (II), indica hybrid (IH), japonica inbred (JI), japonica hybrid (JH), and indica-japonica hybrid (IJ). Comprehensive analyses were conducted to assess the differences and trends in rice quality across these varieties. We found that JI and JH excel in processing and cooking qualities, featuring higher brown rice and head milled rice rates, coupling with longer gel consistency. Inbred varieties display lower chalky rice rates than hybrids. Over several decades, head milled rice rates have notably increased across all types except for IJ. Transparency grade has decreased in nearly all types except for IJ, with similar declines observed in chalky rice rates and chalkiness degree, suggesting an overall progress in appearance quality. In terms of cooking and taste attributes, amylose content has decreased in most varieties except for IJ, and gel consistency has improved in indica varieties. Generally, the rice quality of varieties approved in China has shown a clear trend of improvement over the past 40 years. This study provides significant data support and theoretical backing for ongoing rice breeding efforts. [ABSTRACT FROM AUTHOR]

Summary: The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR‐Cas9, which accounted for approximately 34.1%–47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene‐edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two‐line hybrid rice Guang‐liang‐you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene‐modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three‐line hybrid rice Quan‐you‐si‐miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR‐Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield‐related heterosis and provided a promising strategy for breeding higher‐yielding rice varieties above what is currently achievable. [ABSTRACT FROM AUTHOR]

Summary: Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq‐1 and qMq‐2, represent allelic variants of Waxylv/Waxyb (hereafter Wx) encoding Granule‐Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc/ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc. Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY. [ABSTRACT FROM AUTHOR]

Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding. [ABSTRACT FROM AUTHOR]

Huamoxiang 3 (HMX3) is a new variety of whole grain black rice that has been bred for its superior taste and nutritional benefits. Whole grain black rice is rich in anthocyanins, which have antioxidant and anti-inflammatory properties. Despite the health benefits of whole grain rice, its consumption remains low worldwide. HMX3 was developed through a breeding program and has been certified as a new variety. It has shown good performance in terms of yield and quality and has received positive feedback from consumers. The nutritional composition of HMX3 is superior to milled grain rice, with higher levels of protein, dietary fiber, amino acids, oil, vitamins, minerals, and bioactive compounds. HMX3 is recommended for late rice cropping in Hubei Province. The research was supported by various grants. [Extracted from the article]

The aim of this study was to explore the characteristics essential for a maintainer line to effectively complement the A lines in hybrid rice production. The experiment was conducted at the Regional Agricultural Research Station, Jagtial and Telangana, India during kharif, 2016 (June-October). A total of 40 genotypes were raised in Randomized Block Design (RBD) with two replications. PCA identified five principal components (PCs) with Eigen values over 1, collectively accounting for approximately 75.50% of the total variance. PC1 predominantly representing yield and related features (number of tillers per plant, panicle length, length-to-breadth ratio, grain yield per plant), while the other PCs corresponded to unique aspects like grain numbers, morphological and quantitative traits. The study also utilized biplot analysis to elucidate the relationships among these traits, revealing significant correlations and interactions crucial for rice breeding. It indicated a negative correlation between 1000 grain weight, kernel breadth, and the number of grains per panicle, while showing positive correlations among traits influencing grain yield. This method also proved assistance in identifying superior genotypes for specific traits, as exemplified by genotypes JMS18B and JMS20B excelling in grain numbers per panicle and genotype B18 standing out in grain yield and other yield-related traits. [ABSTRACT FROM AUTHOR]

Grain size and grain weight contribute greatly to the final grain yield in rice. In order to identify QTLs conferring grain size and grain weight, an F2 population derived from a cross between two indica rice accessions, Guangzhan 63-4S (GZ63-4S) and Dodda, and its derived F2:3 population were developed, and were exploited for QTL analysis of the five related traits, namely grain length (GL), grain width (GW), length-to-width ratio (LWR), grain thickness (GT) and thousand-grain weight (TGW). A total of 36 QTLs were detected, and the number of beneficial alleles was contributed roughly equally by the two parents. Among those, 7 QTL regions were repeatedly detected in the two populations. In order to further validate effects of QTLs detected, a BC1F2 population derived from a backcross of a mixture of F2 plants with GZ63-4S was developed and was exploited for QTL selection. Heterozygous regions of 3 QTLs, qGS3, qTGW6.2 and qGT7 were identified respectively, and corresponding near-isogenic lines (NILs) of each QTL were constructed with three rounds of self-crosses. In the background of NILs, qGS3 was responsible for GL, LWR, GT and TGW, qTGW6.2 was for GL and TGW, and qGT7 was for GT and TGW. These results have laid the foundation of further fine mapping work, and could be of great use in breeding and improvement of rice lines with desirable size and yield. [ABSTRACT FROM AUTHOR]

The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three‐line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding. [ABSTRACT FROM AUTHOR]

Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field. [ABSTRACT FROM AUTHOR]

Understanding the yield attributes of the popular rice (Oryza sativa L.) hybrids can provide useful information for developing new hybrid rice varieties. Field experiments were conducted at two subtropical sites (Hengyang and Xingyi) in two years (2021 and 2022) to compare grain yield and yield attributes of three currently popular hybrid rice varieties (Jingliangyouhuazhan, Jingliangyou 534, and Longliangyouhuazhan) with three representative super hybrid rice varieties (Y-liangyou 1, Y-liangyou 2, and Y-liangyou 900). No significant differences in grain yield were observed between the group of popular hybrids and the group of super hybrids at Hengyang and Xingyi in 2021 or at Xingyi in 2022, but at Hengyang in 2022, the group of popular hybrids produced a 15% higher grain yield. The grain yield at Hengyang in 2022 was lower than that at Hengyang and Xingyi in 2021 and at Xingyi in 2022. At Hengyang in 2022, the group of popular hybrids had 9–15% higher panicles per m2, spikelet filling percentage, and harvest index but similar spikelets per panicle and total biomass production and 12% lower grain weight compared to the group of super hybrids. Correlation plot analysis showed that grain yield was significantly related to panicles per m2 but not other yield attributes across six varieties at Hengyang in 2022. These results indicated that the currently popular hybrid rice varieties had higher yield performance than the representative super hybrid rice varieties under the condition of relatively lower productivity, and the key factor for this higher yield performance in the popular hybrids was the higher panicles per m2. This finding highlights that more attention should focus on the yield performance under medium- and low-productivity conditions in hybrid rice breeding programs, and an effective breeding strategy is to select the varieties with high panicle numbers. [ABSTRACT FROM AUTHOR]

Tillering, also known as shoot branching, is a fundamental trait for cereal crops such as rice to produce sufficient panicle numbers. Effective tillering that guarantees successful panicle production is essential for achieving high crop yields. Recent advances in molecular biology have revealed the mechanisms underlying rice tillering; however, in rice breeding and cultivation, there remain limited genes or alleles suitable for effective tillering and high yields. A recently identified quantitative trait locus (QTL) called MORE PANICLES 3 (MP3) has been cloned as a single gene and shown to promote tillering and to moderately increase panicle number. This gene is an ortholog of the maize domestication gene TB1 , and it has the potential to increase grain yield under ongoing climate change and in nutrient-poor environments. This review reconsiders the potential and importance of tillering for sustainable food production. Thus, I provide an overview of rice tiller development and the currently understood molecular mechanisms that underly it, focusing primarily on the biosynthesis and signaling of strigolactones, effective QTLs, and the importance of MP3 (TB1). The possible future benefits in using promising QTLs such as MP3 to explore agronomic solutions under ongoing climate change and in nutrient-poor environments are also highlighted. [ABSTRACT FROM AUTHOR]

Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers' final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (composed of two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test the mapping effects of different methods by using MQ-GS correlation dissection as sample case; (3) to perform genetic and breeding simulation on pyramiding favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci on average for MQ-GS traits. Notably, 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful resources for rice molecular breeding. [ABSTRACT FROM AUTHOR]

This article, published in the Journal of Integrative Plant Biology, discusses the molecular bases for the three-line hybrid rice breeding system. The authors focus on the fertility restoration gene Rf4 and its impact on the Wild Abortive (WA) cytoplasmic male sterility type three-line system. They identify a two-copy haplotype of Rf4 (H1) as the most valuable for future hybrid rice breeding. The study provides insights into the evolutionary trajectory of Rf genes and the origin of cytoplasmic male sterility and fertility restoration systems in rice breeding. The findings contribute to our understanding of the CMS/Rf system and offer guidance for the molecular design breeding of three-line hybrid rice. [Extracted from the article]

The basic requirement for the barnase-barstar-based hybrid-seed production technology is the availability of stable male-sterile barnase and restorer barstar lines. Development of two rice (Oryza sativa) male-sterile barnase lines has been earlier reported from our lab. Complete restoration of male fertility in transgenic male-sterile lines has always been a challenging task for molecular breeders. In the present study, we have reported the successful fertility restoration in male-sterile barnase lines using barstar restorer lines generated through two completely different tapetum-specific promoters. The barstar lines were not able to restore male fertility in one barnase line but did restore it in the other barnase line. The male-sterile barnase line and its corresponding restorer line could be diversified into appropriate combiners for heterosis rice breeding. [ABSTRACT FROM AUTHOR]

Improving quality is an essential goal of rice breeding and production. However, rice quality is not solely determined by genotype, but is also influenced by the environment. Phenotype plasticity refers to the ability of a given genotype to produce different phenotypes under different environmental conditions, which can be a representation of the stability of traits. Seven quality traits of 141 hybrid combinations, deriving from the test-crossing of 7 thermosensitive genic male sterile (TGMS) and 25 restorer lines, were evaluated at 5 trial sites with intermittent sowing of three to five in Southern China. In the Yangtze River Basin, it was observed that delaying the sowing time of hybrid rice combinations leads to an improvement in their overall quality. Twelve parents were identified to have lower plasticity general combing ability (GCA) values with increased ability to produce hybrids with a more stable quality. The parents with superior quality tend to exhibit lower GCA values for plasticity. The genome-wide association study (GWAS) identified 13 and 15 quantitative trait loci (QTLs) associated with phenotype plasticity and BLUP measurement, respectively. Notably, seven QTLs simultaneously affected both phenotype plasticity and BLUP measurement. Two cloned rice quality genes, ALK and GL7, may be involved in controlling the plasticity of quality traits in hybrid rice. The direction of the genetic effect of the QTL6 (ALK) on alkali spreading value (ASV) plasticity varies in different cropping environments. This study provides novel insights into the dynamic genetic basis of quality traits in response to different cropping regions, cultivation practices, and changing climates. These findings establish a foundation for precise breeding and production of stable and high-quality rice. [ABSTRACT FROM AUTHOR]

Appropriate parental selection is the breeder's main concern to exploit the highest genetic diversity and generate superior genotypes for subsequent breeding programs. Hence, the presented investigation proceeded to evaluate 353 breeding lines of rice at three breeding zones (Rajshahi, Cumilla, and Gazipur) in Bangladesh in replicated yield trials during the Boro season of 2018-2019 to identify the best genotypes and utilize them as parental materials. Data recorded on 12 yield-related traits helped to determine the best breeding lines with higher predicted breeding values. The first five principal components (PC1, PC2, PC3, PC4, and PC5) represented more than 70% (75.1%) contribution to the variability of the data. Three hundred fifty-three rice genotypes incurred distribution into five clusters over three environments. Clusters I, II, III, IV, and V comprised 66, 51, 83, 79, and 74 genotypes, respectively. Based on estimated breeding values (EBVs), IR107971-B-B RGA-B RGA-202 showed the highest value (0.395), followed by IR 108000-B-B-B-B-13 (0.329), IR 103309-B-B RGA-B RGA-194 (0.321), IR 107982-B-41-1-2-1 (0.291), IRRI 174 (0.264), and IR 107976-B-B RGA-B RGA-254 (0.234). The lowest EBV (0.022) appeared in IR103309-B-B RGA-B RGA-204 among the top 20 genotypes. Both IR 103309-B-B RGA-B RGA-194 (0.321) and IR 107982-B-41-1-2-1 (0.291) could benefit as parents for further breeding programs having higher EBVs and higher genetic diversity. [ABSTRACT FROM AUTHOR]

The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica rice accessions. In total, 69 SNPs/Indels in seven genes were detected to be associated with grain length (GL), grain width (GW), ratio of grain length–width (L/W) and thousand-grain weight (TGW) using candidate gene-based association analysis, including BG1 and GS3 for GL, GW5 for GW, BG1 and GW5 for L/W, and AET1, SNAC1, qTGW3, DHD1 and GW5 for TGW. Furthermore, two haplotypes were identified for each of the seven genes according to these associated SNPs/Indels, and the amount of genetic variation explained by different haplotypes ranged from 3.24% to 27.66%. Additionally, three, three and eight haplotype combinations for GL, L/W and TGW explained 25.38%, 5.5% and 22.49% of the total genetic variation for each trait, respectively. Further analysis showed that Minghui63 had the superior haplotype combination Haplotype Combination 4 (HC4) for TGW. The most interesting finding was that some widely used restorer lines derived from Minghui63 also have the superior haplotype combination HC4, and our breeding varieties and lines using the haplotype-specific marker panel also confirmed that the TGW of the lines was much higher than that of their sister lines without HC4, suggesting that TGW-HC4 is the superior haplotype combination for TGW and can be utilized in rice breeding. [ABSTRACT FROM AUTHOR]

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability. [ABSTRACT FROM AUTHOR]

Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development. [ABSTRACT FROM AUTHOR]

Flood resistance in rice is very important in weed control, as weeds cannot overcome deep water. At present, there are no released varieties in Russia that would meet these requirements. The creation of such varieties will reduce production costs and pesticide load on the ecosystem. The object of the study was second-generation rice hybrids obtained by crossing the best varieties for economically valuable traits with samples carrying genes for resistance to prolonged flooding with water. To create double rice haploids resistant to prolonged flooding, the anther culture method was used, followed by molecular genetic evaluation of dihaploids for the presence of genes for resistance to prolonged flooding. An estimate of the growth energy under deep flooding was carried out according to our own method. As a result of the cultivation of anthers, 130 androgenic regenerated plants were obtained in 14 hybrid combinations. In terms of responsiveness to neoplasms, 60% of the panicles showed a positive result, while the rest 40% did not demonstrate callus formation. In total, 30 green regenerative lines were obtained from four rice hybrids, differing in visual morphological assessment. Large genotypic differences between the samples were revealed. These lines carry long-term flood resistance genes and can be used in rice breeding programs using dihaploids. As a result of the assessment of the growth energy in a number of obtained samples, the potential for rapid elongation of the first leaves, overcoming a large layer of water and accumulation of vegetative mass, was revealed. [ABSTRACT FROM AUTHOR]

The improvement of grain yield, quality, and resistance can be achieved through the utilization of heterosis. The combination of cytoplasmic male sterility (CMS) and fertility restoration (Rf) gene(s) greatly facilitates the commercial development of three-line hybrid rice based on heterosis. The basis for investigating the relationship between CMS and Rf genes lies in the rapid localization of wild rice fertility restoration genes. A set of the BC4F5 population derived from interspecific crosses between Xieqingzao B (XB) and the BC1F9 XB//Dongxiang wild rice (DWR)/XB line L5339 was used to detect quantitative trait loci (QTL) for fertility restoration. The population was then crossed with two male sterile lines, Zhong9A (Z9A) and DongB11A (DB11A), in order to generate a testcrossing population for investigating spikelet fertility. Based on the linkage mapping, seven QTLs were detected on chromosomes 1, 3, 5, 6, 8, and 10, explaining 2.76 to 12.46% of the phenotypic variation. Of them, two novel fertility restoration QTLs, qRf3 and qRf6, can restore fertility of the CMS-DWR line DB11A by 16.56% and 15.12%, respectively. By employing joint QTL-seq and GradedPool-Seq methods, two novel Rf QTLs for DB11A, qRf3 and qRf6, were identified at the physical locations of 10,900,001–11,700,000 bp and 28,016,785–31,247,556 bp, respectively. These findings are useful for exploring the natural variations of Rf genes in rice. Therefore, rice's new genetic resources for the selection and breeding of rice restorer lines provide promising candidates for QTL fine localization and clarification. [ABSTRACT FROM AUTHOR]

The first step in developing high yielding heterotic hybrids is to find restorers that can effectively restore the fertility of CMS lines. Two distinct and dominant nuclear genes for restoring fertility, Rf3 and Rf4, are primarily in charge of the fertility restoration of CMS-WA lines in rice. Identifying fertility restorer lines can be accelerated and made simpler by molecular mapping of Rf3 and Rf4. The present investigation was carried out to validate the presence of two fertility restorer genes Rf3 and Rf4 in the F4 generations of two populations viz., CBSN 25/WRM 21-24 (86 families) and CBSN 25/WRM 93-20 (79 families) using seven SSR molecular markers. The results revealed that 17 plants in the cross CBSN 25/WRM 21-24 and 47 plants in CBSN 25/WRM 93-20 were found to be double positives for both Rf3 and Rf4 genes. Hence, after stabilization these identified plants from both crosses could be used as male parents or restorers in CMS-based hybrid rice breeding programs. [ABSTRACT FROM AUTHOR]

The development of novel rice hybrids is a prospectus area of research for enhancing grain yield to meet the growing population demands. An experiment was conducted in 2016–2017 to develop novel rice hybrids for aerobic ecology with lesser yield penalties than irrigated ecosystems, with the added advantage of reduced methane emissions and water budget as witnessed in irrigated systems. Based on the restorer-maintainer reaction and spikelet fertility (%), ten restorer lines were selected to cross with three CMS (Cytoplasmic male sterile) lines in the Line by Tester fashion in Yasangi (summer) season 2016–2017. They resulted in 30 experimental hybrids besides 13 parental lines (10 restorer lines and 3 B—lines of akin CMS lines) and checks (GK 5022, CR Dhan 201) assessed during the Vankalam (rainy) season 2017 at three different places/locations viz., Rajendranagar, Warangal, and Kampasagar. The outcome of the experiment was that two experimental hybrids viz., APMS-6A × HRSV-7 and IR-79156A × ATR-372, were categorized as stable hybrids with desirable sca (Specific combining ability) effects, heterosis (ranging from 7% to 13%) over best check GK 5022, along with an in-essence performance for yield and other yield attributing characters. [ABSTRACT FROM AUTHOR]

The main goals of rice breeding nowadays include increasing yield, improving grain quality, and promoting complete mechanized production to save labor costs. Rice grain shape, specified by three dimensions, including grain length, width and thickness, has a more precise meaning than grain size, contributing to grain appearance quality as well as grain weight and thus yield. Furthermore, the divergence of grain shape characters could be utilized in mechanical seed sorting in hybrid rice breeding systems, which has been succeeded in utilizing heterosis to achieve substantial increase in rice yield in the past decades. Several signaling pathways that regulate rice grain shape have been elucidated, including G protein signaling, ubiquitination-related pathway, mitogen-activated protein kinase signaling, phytohormone biosynthesis and signaling, microRNA process, and some other transcriptional regulatory pathways and regulators. This review summarized the recent progress on molecular mechanisms underlying rice grain shape determination and the potential of major genes in future breeding applications. [ABSTRACT FROM AUTHOR]

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed. [ABSTRACT FROM AUTHOR]

Summary: In rice breeding, thermosensitive genic male sterility (TGMS) lines based on the tms5 locus have been extensively employed. Here, we reported a novel rice TGMS line ostms15 (Oryza sativa ssp. japonica ZH11) which show male sterility under high temperature and fertility under low temperature. Field evaluation from 2018 to 2021 revealed that its sterility under high temperature is more stable than that of tms5 (ZH11), even with occasional low temperature periods, indicating its considerable value for rice breeding. OsTMS15 encodes an LRR‐RLK protein MULTIPLE SPOROCYTE1 (MSP1) which was reported to interact with its ligand to initiate tapetum development for pollen formation. In ostms15, a point mutation from GTA (Val) to GAA (Glu) in its TIR motif of the LRR region led to the TGMS phenotype. Cellular observation and gene expression analysis showed that the tapetum is still present in ostms15, while its function was substantially impaired under high temperature. However, its tapetum function was restored under low temperature. The interaction between mOsTMS15 and its ligand was reduced while this interaction was partially restored under low temperature. Slow development was reported to be a general mechanism of P/TGMS fertility restoration. We propose that the recovered protein interaction together with slow development under low temperature compensates for the defective tapetum initiation, which further restores ostms15 fertility. We used base editing to create a number of TGMS lines with different base substitutions based on the OsTMS15 locus. This work may also facilitate the mechanistic investigation and breeding of other crops. [ABSTRACT FROM AUTHOR]

Hybrid rice breeding is an important strategy for enhancing grain yield. Breeding high-performance parental lines and identifying combining abilities is a top priority for hybrid breeding. Yuenongsimiao (YNSM) and its derivative variety Yuehesimiao (YHSM) are elite restorer lines with a high ability of fertility restoration, from which 67 derived hybrid combinations have been authorized to different degrees in more than 110 instances in China. In this study, we found that YNSM and YHSM contained three candidate restorer-of-fertility (Rf) genes, Rf3, Rf4, and Rf5/Rf1a, that might confer their restoration ability. Subsequently, we investigated heterosis and combining ability of YNSM and YHSM using 50 F1 hybrids from a 5 × 10 incomplete diallelic mating design. Our results indicated that hybrid combinations exhibited significant genetic differences, and the additive effects of the parental genes played a preponderant role in the inheritance of observed traits. The metrics of plant height (PH), 1000-grain weight (TGW), panicle length (PL), and the number of spikelets per panicle (NSP) were mainly affected by genetic inheritance with higher heritability. Notably, the general combining ability (GCA) of YHSM exhibited the largest positive effect on the number of grains per panicle (NGP), NSP, PL, and TGW. Thus, YHSM had the largest GCA effect on yield per plant (YPP). In addition, the GCA of YNSM exhibited a positive impact on YPP, mainly due to the critical contribution of seed setting percentage (SSP). Moreover, YNSM and YHSM exhibited negative GCA effects on PH, implying that YNSM and YHSM could effectively enhance plant lodging resistance by reducing the plant height of the derived hybrids. Remarkably, among the hybrids, Yuanxiang A/YNSM (YXA/YNSM), Shen 08S/Yuemeizhan (S08S/YMZ), and Quan 9311A/YHSM (Q9311A/YHSM) represent promising new combinations with a higher specific combining ability (SCA) effect value on YPP with a value more than 3.50. Our research thus highlights the promising application for the rational utilization of YNSM and YHSM in hybrid rice breeding. [ABSTRACT FROM AUTHOR]

The principal goal of rice (Oryza sativa L.) breeding is to increase the yield. In the past, hybrid rice was mainly indica intra-subspecies hybrids, but its yield has been difficult to improve. The hybridization between the indica and japonica subspecies has stronger heterosis; the utilization of inter-subspecies heterosis is important for long-term improvement of rice yields. However, the different diurnal flower-opening times (DFOTs) between the indica and japonica subspecies seriously reduce the efficiency of cross-pollination and yield and increase the cost of indica–japonica hybrid rice seeds, which has become one of the main constraints for the development of indica–japonica hybrid rice breeding. The DFOT of plants is adapted to their growing environment and is also closely related to species stability and evolution. Herein, we review the structure and physiological basis of rice flower opening, the factors that affect DFOT, and the progress of cloning and characterization of DFOT genes in rice. We also analyze the problems in the study of DFOT and provide corresponding suggestions. [ABSTRACT FROM AUTHOR]

Improving plant nitrogen-use efficiency (NUE) has great significance for various crops, particularly in hybrid breeding. Reducing nitrogen inputs is key to achieving sustainable rice production and mitigating environmental problems. In this study, we analyzed the transcriptomic and physiological changes in two indica restorer lines (Nanhui511 [NH511] and Minghui23 [MH23]) under high nitrogen (HN) and low nitrogen (LN) conditions. Compared to MH23, NH511 was more sensitive to different nitrogen supplies and exhibited higher nitrogen uptake and NUE under HN conditions by increasing lateral root and tiller numbers in the seedling and maturation stages, respectively. NH511 also exhibited a lower survival rate than MH23 when planted in a chlorate-containing hydroponic solution, indicating its HN uptake ability under different nitrogen-supply conditions. Transcriptomic analysis showed that NH511 has 2456 differentially expressed genes, whereas MH23 had only 266. Furthermore, these genes related to nitrogen utilization showed differential expression in NH511 under HN conditions, while the opposite was observed in MH23. Our findings revealed that NH511 could be regarded as elite rice and used for breeding high-NUE restorer lines by regulating and integrating nitrogen-utilization genes, which provides novel insights for the cultivation of high-NUE hybrid rice. [ABSTRACT FROM AUTHOR]

Rice is sensitive to high-temperature stress during almost all stages of growth and development. High-temperature stress has become one of the main factors restricting high yield and superior quality of rice. In this study, recombinant inbred lines (RILs) derived from an indica rice cross between two restorer lines were planted in two years. One sowing date was applied in 2019, and four sowing dates were set in 2020 according to the period of local high temperatures in recent years. Two traits closely related to high-temperature tolerance, heading date (HD), and spikelet fertility (SF) were measured. In each trial, the HD showed a bimodal distribution, whereas SF had a continuous and left-skewed distribution. QTL analysis was performed using a high-density bin map. For HD, a total of six QTL were detected. All of them correspond in position to the cloned genes, among which qHD8 in the DTH8/Ghd8 region showed the largest genetic effect. For SF, a total of eight QTL were detected. Five of them, qSF1, qSF2, qSF3.1, qSF3.2, and qSF8, showed high-temperature tolerance and had an important potential in rice breeding. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) technology is an efficient strategy for producing completely homozygous lines for breeding programs. Mutations in the MATRILINEAL (MTL) phospholipase trigger intraspecific haploid induction in cereals. Although an in vivo haploid induction system based on OsMTL-edited plants has been established in rice (Oryza sativa), DH technology is still limited by other factors, such as haploid identification, which is one of the essential steps required for DH technology. In the study, we addressed this technical challenge by integrating specific molecular and phenotypic markers into rice haploid inducers. We first generated large fragment insertion or deletion mutations within the OsMTL gene and designed a pair of primers flanking the mutational sites to be used as the specific and universal molecular markers between wild-type and Osmtl plants. Next, we screened for hairy leaf as a single dominant trait and integrated it into specific molecular marker-based haploid inducers using the cross and self-cross method. When crossing cytoplasmic male sterile lines with these haploid inducers, we utilized the specific InDel marker and hairy leaf phenotypic marker to identify putative haploids (or double haploids). These putative haploids were further confirmed through ploidy and phenotypic analysis, demonstrating the high efficiency of haploid identification using these markers. The haploid induction rate (HIR) of the developed specific molecular and phenotypic marker-based haploid inducers ranged from 3.7% to 12.5%. We have achieved successful integration of distinct molecular and phenotypic markers into rice haploid inducers. Our advanced marker-based system has significantly enhanced the accuracy of haploid identification, thereby expediting the adoption of DH technology in rice breeding. [ABSTRACT FROM AUTHOR]

Climate change has caused high salinity in many fields, particularly in the mud flats in coastal regions. The resulting salinity has become one of the most significant abiotic stresses affecting the world's rice crop productivity. Developing elite cultivars with novel salinity-tolerance traits is regarded as the most cost-effective and environmentally friendly approach for utilizing saline-alkali land. To develop a highly efficient green strategy and create novel rice germplasms for salt-tolerant rice breeding, this study aimed to improve rice salinity tolerance by combining targeted CRISPR/Cas9-mediated editing of the OsRR22 gene with heterosis utilization. The novel alleles of the genic male-sterility (GMS) and elite restorer line (733Srr22-T1447-1 and HZrr22-T1349-3) produced 110 and 1 bp deletions at the third exon of OsRR22 and conferred a high level of salinity tolerance. Homozygous transgene-free progeny were identified via segregation in the T2 generation, with osrr22 showing similar agronomic performance to wild-type (733S and HZ). Furthermore, these two osrr22 lines were used to develop a new promising third-generation hybrid rice line with novel salinity tolerance. Overall, the results demonstrate that combining CRISPR/Cas9 targeted gene editing with the "third-generation hybrid rice system" approach allows for the efficient development of novel hybrid rice varieties that exhibit a high level of salinity tolerance, thereby ensuring improved cultivar stability and enhanced rice productivity. [ABSTRACT FROM AUTHOR]