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Background: Isolated microspore culture is a useful biotechnological technique applied in modern plant breeding programs as it can produce doubled haploid (DH) plants and accelerate the development of new varieties. Furthermore, as a single-cell culture technique, the isolated microspore culture provides an excellent platform for studying microspore embryogenesis. However, the reports on isolated microspore culture are rather limited in rice due to the low callus induction rate, poor regeneration capability, and high genotypic dependency. The present study developed an effective isolated microspore culture protocol for high-frequency androgenesis in four japonica rice genotypes. Several factors affecting the isolated microspore culture were studied to evaluate their effects on callus induction and plantlet regeneration. Results: Low-temperature pre-treatment at 4 ℃ for 10–15 days could effectively promote microspore embryogenesis in japonica rice. A simple and efficient method was proposed for identifying the microspore developmental stage. The anthers in yellow-green florets located on the second type of primary branch on the rice panicle were found to be the optimal stage for isolated microspore culture. The most effective induction media for callus induction were IM2 and IM3, depending on the genotype. The optimal concentration of 2, 4-D in the medium for callus induction was 1 mg/L. Callus induction was negatively affected by a high concentration of KT over 1.5 mg/L. The differentiation medium suitable for japonica rice microspore callus comprised 1/2 MS, 2 mg/L 6-BA, 0.5 mg/L NAA, 30 g/L sucrose, and 6 g/L agar. The regeneration frequency of the four genotypes ranged from 61–211 green plantlets per 100 mg calli, with Chongxiangjing showing the highest regeneration frequency. Conclusions: This study presented an efficient protocol for improved callus induction and green plantlet regeneration in japonica rice via isolated microspore culture, which could provide valuable support for rice breeding and genetic research. [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]

Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies. [ABSTRACT FROM AUTHOR]

Drought condition is one of the major problems in producing rice in Indonesia. In plant breeding, selection is the main step to create superior varieties. An indicator of drought stress-tolerant rice varieties is the root distribution pattern because it describes the behavior of the roots in searching for water for photosynthesis and metabolism processes. One of the morphological traits related to drought tolerance in rice is root growth and development. This study aimed to determine the morphological and anatomical characteristics of drought-tolerant rice roots and identify drought-tolerant genotypes. The experiments were arranged in a factorial randomized block design with four replications. The first factor was genotype, consisting of ten genotypes. The second factor was drought stress, consisting of two environments without drought and with drought stress. Drought was given only in the vegetative phase, i.e., 1-14 days after planting. WINDEX analysis was performed to determine rice drought tolerance and identify drought-tolerant genotypes. The results showed that three out of the ten tested genotypes had higher WINDEX values, namely BP30411f (7.62), B13983-KA-6-3 (7.99), and BP29790d-PWK-2-SKI-1-3 (9.25). Based on the root distribution pattern, plants with longer primary root lengths, more seminal roots, longer seminal root lengths, and high root angles were predicted to be drought tolerant characteristics. Selection of these characters could be used in future rice breeding programs to obtain plants with superior genotypes. [ABSTRACT FROM AUTHOR]

Improving plant performance in salinity-prone conditions is a significant challenge in breeding programs. Genomic selection is currently integrated into many plant breeding programs as a tool for increasing selection intensity and precision for complex traits and for reducing breeding cycle length. A rice reference panel (RP) of 241 Oryza sativa L. japonica accessions genotyped with 20,255 SNPs grown in control and mild salinity stress conditions was evaluated at the vegetative stage for eight morphological traits and ion mass fractions (Na and K). Weak to strong genotype-by-condition interactions were found for the traits considered. Cross-validation showed that the predictive ability of genomic prediction methods ranged from 0.25 to 0.64 for multi-environment models with morphological traits and from 0.05 to 0.40 for indices of stress response and ion mass fractions. The performances of a breeding population (BP) comprising 393 japonica accessions were predicted with models trained on the RP. For validation of the predictive performances of the models, a subset of 41 accessions was selected from the BP and phenotyped under the same experimental conditions as the RP. The predictive abilities estimated on this subset ranged from 0.00 to 0.66 for the multi-environment models, depending on the traits, and were strongly correlated with the predictive abilities on cross-validation in the RP in salt condition (r = 0.69). We show here that genomic selection is efficient for predicting the salt stress tolerance of breeding lines. Genomic selection could improve the efficiency of rice breeding strategies for salinity-prone environments. [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]

Genotype by environment interaction (GEI) is one of the main challenges in plant breeding. A complete characterization of it is necessary to decide on proper breeding strategies. Random regression models (RRMs) allow a genotype‐specific response to each regressor factor. RRMs that include selected environmental variables represent a promising approach to deal with GEI in genomic prediction. They enable to predict for both tested and untested environments, but their utility in a plant breeding scenario remains to be shown. We used phenotypic, climatic, pedigree, and genomic data from two public subtropical rice (Oryza sativa L.) breeding programs; one manages the indica population and the other manages the japonica population. First, we characterized GEI for grain yield (GY) with a set of tools: variance component estimation, mega‐environment (ME) definition, and correlation between locations, sowing periods, and MEs. Then, we identified the most influential climatic variables related to GY and its GEI and used them in RRMs for single‐step genomic prediction. Finally, we evaluated the predictive ability of these models for GY prediction in tested and untested years and environments using the complete dataset and within each ME. Our results suggest large GEI in both populations while larger in indica than in japonica. In indica, early sowing periods showed crossover (i.e., rank‐change) GEI with other sowing periods. Climatic variables related to temperature, radiation, wind, and precipitation affecting GY were identified and differed in each population. RRMs with selected climatic covariates improved the predictive ability in both tested and untested years and environments. Prediction using the complete dataset performed better than predicting within each ME. Core Ideas: Random regression models improved the predictive ability for grain yield in a realistic plant breeding scenario.Prediction using the complete dataset performed better than predicting within mega‐environments.Large amounts of genotype by environment interaction affect grain yield in both indica and japonica populations.Indica genotype ranking drastically changed in early sowing compared with intermediate and late sowing.Climatic variables affecting grain yield are different between our indica and japonica rice breeding populations. [ABSTRACT FROM AUTHOR]

SUMMARY: Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ‐aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature‐sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild‐type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold‐inducible in WYG but cold‐irresponsive in HHZ. Further studies showed that indica varieties carry both WYG‐type and HHZ‐type OsOAT, whereas japonica varieties mostly carry WYG‐type OsOAT. Cultivars carrying HHZ‐type OsOAT are mainly distributed in low‐latitude regions, whereas varieties carrying WYG‐type OsOAT are distributed in both low‐ and high‐latitude regions. Moreover, indica varieties carrying WYG‐type OsOAT generally have higher seed‐setting rates than those carrying HHZ‐type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG‐type OsOAT during domestication and breeding to cope with low temperatures. Significance Statement: The identification of genes important for cold tolerance can promote the molecular breeding of cold‐tolerant rice varieties. This study discovered two major natural alleles of OsOAT that conferred different levels of cold tolerance, thereby providing a good candidate gene for breeding of rice plants with enhanced cold tolerance. [ABSTRACT FROM AUTHOR]

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design (BbD), but remains not well established. Here, we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China (NEC). We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study (GWAS)-detected quantitative trait loci (QTLs), or introgressions from indica sub-species with chronological changes in allele frequencies. Then we summarized a rice breeding trend/principle in NEC, and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in practice. Our study provides a paradigm for decoding the breeding history of a specific crop to guide BbD, which may have implications in different crop breeding. The genomic decoding of rice breeding history in Northeast China, along with the successful example in breeding of Zhongkefa5, shows guiding value for rice breeding-by-design (BbD) and may have implications in different crop breeding. [ABSTRACT FROM AUTHOR]

Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, however it is not acceptable for hybrid rice due to the high seed cost. Improving direct seeding by breeding is seen as the ultimate solution to these problems. For hybrid breeding, identifying superior hybrids among a massive number of hybrids from crossings between male and female parental populations by phenotypic evaluation is tedious and costly. Contrastingly, genomic selection/prediction (GS/GP) could efficiently detect the superior hybrids capitalizing on genomic data, which holds a great potential in plant hybrids breeding. In this study, we utilized 402 rice inbred varieties and 401 hybrids to investigate the effectiveness of GS on rice mesocotyl length, a representative indicative trait of direct seeding suitability. Several GP methods and training set designs were studied to seek the optimal scenario of hybrid prediction. It was shown that using half-sib hybrids as training set with the phenotypes of all parental lines being fitted as a covariate could optimally predict mesocotyl length. Partitioning the molecular markers into trait-associated and -unassociated groups based on genome-wide association study using all parental lines and hybrids could further improve the prediction accuracy. This study indicates that GS could be an effective and efficient method for hybrid breeding for rice direct seeding. [ABSTRACT FROM AUTHOR]

Summary: Plant architecture and stress tolerance play important roles in rice breeding. Specific leaf morphologies and ideal plant architecture can effectively improve both abiotic stress resistance and rice grain yield. However, the mechanism by which plants simultaneously regulate leaf morphogenesis and stress resistance remains elusive. Here, we report that SRL10, which encodes a double‐stranded RNA‐binding protein, regulates leaf morphology and thermotolerance in rice through alteration of microRNA biogenesis. The srl10 mutant had a semi‐rolled leaf phenotype and elevated sensitivity to high temperature. SRL10 directly interacted with catalase isozyme B (CATB), and the two proteins mutually increased one other's stability to enhance hydrogen peroxide (H2O2) scavenging, thereby contributing to thermotolerance. The natural Hap3 (AGC) type of SRL10 allele was found to be present in the majority of aus rice accessions, and was identified as a thermotolerant allele under high temperature stress in both the field and the growth chamber. Moreover, the seed‐setting rate was 3.19 times higher and grain yield per plant was 1.68 times higher in near‐isogenic line (NIL) carrying Hap3 allele compared to plants carrying Hap1 allele under heat stress. Collectively, these results reveal a new locus of interest and define a novel SRL10–CATB based regulatory mechanism for developing cultivars with high temperature tolerance and stable yield. Furthermore, our findings provide a theoretical basis for simultaneous breeding for plant architecture and stress resistance. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rice is an important food crop plant in the world and is also a model plant for genetics and breeding research. The germination rate is an important indicator that measures the performance of rice seeds. Currently, solutions involving image processing techniques have substantial challenges in the identification of seed germination. The detection of rice seed germination without human intervention involves challenges because the rice seeds are small and densely distributed. RESULTS: In this article, we develop a convolutional neural network (YOLO‐r) that can detect the germination status of rice seeds and automatically evaluate the total number of germinations. Image partition, the Transformer encoder, a small target detection layer, and CDIoU loss are exploited in YOLO‐r to improve the detection accuracy. A total of 21 429 seeds were collected, which have different phenotypic characteristics in length, shape, and color. The results show that the mean average precision of YOLO‐r is 0.9539, which is higher than the compared models. Moreover, the average detection time per image of YOLO‐r was 0.011 s, which meets the real‐time requirements. The experimental results demonstrate that YOLO‐r is robust to complex situations such as water stains, impurities, awns, adhesion, and so on. The results also show that the mean absolute error of the predicted germination rate mainly exists within 0.1. CONCLUSIONS: Numerous experimental studies have demonstrated that YOLO‐r can predict rice germination rate in a fast, easy, and accurate manner. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding. [ABSTRACT FROM AUTHOR]

The aim of the research was to create stable breeding material of rice (Oryza sativa L.) resistant to rice blast (Pyricularia oryzae) using the biotechnological method of anther culture in vitro. Anthers from 20 perspective F2 and F3 hybrids of carriers of different genes of resistance to rice blast were used. The phytopathological assessment of the rice doubled haploid lines resistance to Pyricularia oryzae was performed in field experiments. Correlation of resistance level to quantitative signs of productivity of the received rice lines was assessed using the statistical analysis. A high sensitivity of all 20 rice genotypes to in vitro conditions was found. The level of callus formation ranged between 3.4% and 82.5% with the average of 23.7%. The level of green plants regeneration from obtained callus varied between 0.16% and 13.3% with the average of 3.3%. The level of albino plants regeneration was 0.6%. On average, approximately 35% of regenerated plants obtained in the culture were able to produce seeds indicating that doubled haploid lines were obtained. Most of them were characterised by a high plant productivity: 21.80-60.42 g compared to 10.31 g for the productivity of standard cultivar 'Vikont'. A higher productivity was explained by a higher rate of productive bushiness. Eight lines showed a high level of resistance to rice blast (9 points), and 18 lines had an intermediate level of resistance. As a result of the research, perspective lines with a high level of resistance to P. oryzae and increased productivity were obtained. These lines will be used in a further selection programme aimed at obtaining a rice cultivar resistant to P. oryzae. [ABSTRACT FROM AUTHOR]

Transcription activator-like effectors (TALEs) are proteins produced by plant pathogenic Xanthomonas spp. TALEs exhibit a conserved structure and have the ability to directly bind to the promoter region of host target genes where they activate transcription. TALEs in Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) in rice, play important roles in triggering resistance (ETI) and susceptibility (ETS) for rice immunity. This review briefly describes rice resistance breeding in China, TALE properties and their roles, BB resistance (R) and susceptibility (S) genes in rice, the arms-race between TALEs and TALE-targets, and strategies for breeding disease-resistant crops. A systematic overview of the complex roles of TALEs are presented along with ongoing efforts to breed crops with durable and broad-spectrum resistance to the pathogenic bacterium. [ABSTRACT FROM AUTHOR]

Rice is one of the most important staple foods of dietary energy supply worldwide. Its breeding programs based on phenotype selection, yield, and quality have succeeded in developing elite varieties desirable for adaptability to local regions. This study summarized the genomic research on the process of rice breeding programs in a local region, Hokkaido. This review would provide a strategy to develop new rice varieties under the imminent threats of increasing world population, global climate change, and sustainability for agriculture. Genomic shifts in genetic population structure and genes under rice breeding programs in Hokkaido were characterized. These genetic rice features could be suitable for a model of crop breeding programs in any crop species. Rice breeding programs were categorized into three phases depending on the shifts in plant architecture type for yield. After shaping adaptability into the local region, integrating genetic engineering into conventional rice breeding programs would facilitate the development of new rice varieties. [ABSTRACT FROM AUTHOR]

The delta-1-pyrroline-5-carboxylate synthetase (P5CS) gene exercises a protective function in stressed plants. However, the relationship between proline accumulation caused by P5CS and abiotic stress tolerance in plants is not always clear, as P5CS overexpression has been reported to repress plant growth under normal conditions in several reports. We re-evaluated the role of P5CS in drought-tolerant rice breeding by expressing the AtP5CS1 and feedback-inhibition-removed AtP5CS1 (AtP5CS1F128A) genes under the regulation of an ABA-inducible promoter to avoid the potential side effects of P5CS overexpression under normal conditions. ABA-inducible AtP5CS1 and AtP5CS1F128A increased seedling growth in a nutrient solution (under osmotic stress) and grain yield in pot plants. However, the evidently deleterious effects of AtP5CS1 on grain quality, tiller number, and grain yield in the field indicated the unsuitability of P5CS for drought-tolerance breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: Excessive nitrogen fertilizer application is harmful to the environment and reduces the quality of cereal crops. Maintaining crop yields under low nitrogen (LN) conditions and improving quality are important goals for cereal crop breeding. Although the effects of nitrogen assimilation on crop nitrogen‐use efficiency (NUE) have been intensively studied, natural variations of the key assimilation genes underlying grain development and quality are largely unclear. Here, we identified an NUE‐associated gene, OsGS1;1, encoding glutamine synthase, through genome‐wide association analysis, followed by validation experiments and functional analysis. Fifteen single‐nucleotide polymorphisms in the OsGS1;1 region led to alternative splicing that generated two functional transcripts: OsGS1;1a and OsGS1;1b. The elite haplotype of OsGS1;1 showed high OsGS1;1b activity, which improved NUE, affected grain development, and reduced amylose content. The results show that OsGS1;1, which is induced under LN conditions, affects grain formation by regulating sugar metabolism and may provide a new avenue for the breeding of high‐yield and high‐quality rice (Oryza sativa). Significance Statement: OsGS1;1 affects grain formation by regulating sugar metabolism and may provide a new avenue for the breeding of high‐yield and high‐quality rice. [ABSTRACT FROM AUTHOR]

SUMMARY: Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH‐related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis‐related loci of PH in rice, we developed a high‐generation (>F15) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high‐density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH‐related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment‐specific PH QTLs were stably detected in Hainan (qPH‐3.1) or Hubei (qPH‐5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine‐mapped, and the candidate genes qPH‐3.1 and qPH‐5.1 for PH were further validated using CRISPR–Cas9 gene editing. Specifically, qPH‐3.1 was characterized as a pleiotropic gene, and the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis‐related QTLs were identified in the testcross populations, and a better‐parent heterosis locus (qBPH‐5.2) completely covered qPH‐5.1. Furthermore, the cross results of fixed‐genotype RILs verified the dominant effects of qPH‐3.1 and qPH‐5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future. Significance Statement: In the present study we constructed a high‐density genetic map containing 4758 bin markers of a high‐generation recombinant inbred line population from a cross of two elite rice (Oryza sativa L.) varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng). Two major environment‐specific QTLs of plant height were discovered and experimentally validated. [ABSTRACT FROM AUTHOR]

The phenotypic trait of panicle is the key parameter to characterize the growth status, yield, and quality of rice. Accurate phenotyping of panicle is of great significance for field precision management and rice breeding. Unmanned Aerial Vehicle (UAV) image data have been widely used to monitor rice growth status. However, most of studies focused on the vegetative growth stages of rice, and only limited work explored rice panicle phenotyping at the heading and mature stages. Therefore, this study used UAV-based multi-source image data to phenotype rice panicle, analyze the effects of different nitrogen (N) fertilizer levels, growth stages and cultivars on rice panicle phenotyping, and develop the models for monitoring rice panicle coverage, biomass, and lodging. Three field experiments were conducted in Zhuji and Shenyang, China from 2017 to 2018, and a multi-rotor UAV platform equipped with RGB (Red-Green-Blue) and multispectral images was applied to collect rice canopy images. Meanwhile, the ground true values of panicle coverage and lodging were obtained from the RGB images by marking manually object regions, and panicle biomass was measured based on the destructive sampling. The results showed that the panicle phenotyping of rice at different growth stages and N fertilizer treatments was significantly different, and panicle coverage was highly correlated with image features, such as normalized green-red difference index and normalized difference vegetation index. The Support Vector Machine (SVM) combined with the Particle Swarm Optimization (PSO-SVM) accurately identified the panicles from RGB images, and the calculated panicle coverage was highly correlated to the actual marked value with the coefficient of determination (R²) of 0.87. Such a classification model for rice panicles could be applicable to different experimental datasets with the good generalization. Further combination with multispectral reflectance improved the estimation of panicle coverage with the R2 and relatively Root Mean Square Error (rRMSE) of 0.93 and 9.47%, respectively, using the Random Forest (RF) regression model. Fusion of color and texture from RGB images and spectral reflectance from multispectral images improved the estimation of panicle biomass (R² = 0.84, rRMSE = 8.68%), which outperformed the single RGB or multispectral image data. Further, when the model established from UAV-based multi-source image data in 2017 was used to estimate panicle biomass in 2018, a good estimation result was obtained with the R² and rRMSE of 0.61 and 15.98%, respectively. Further, the model updating by adding 10% new samples from 2018 to 2017 greatly improved the transferable estimation of panicle biomass, and the R² and rRMSE were 0.69 and 13.59%, respectively. This indicates that the proposed model for assessing panicle biomass has a high robustness across different planting years. Based on the PSO-SVM classification model, combining color and texture features from RGB images and spectral reflectance from multispectral images accurately identified the panicle lodging with the accuracy of 99.87%. It indicates that UAV-based image features could identify panicle lodging of difference rice cultivars with a close classification accuracy and threshold. The results confirm the feasibility of UAV remote sensing for rice panicle phenotyping, which can provide the decision support for precise crop management and breeding. [ABSTRACT FROM AUTHOR]

The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection. [ABSTRACT FROM AUTHOR]

The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly valued. In this study, a hybrid combination with the super hybrid rice WFYT025 was used to perform a transcriptomic dynamic analysis in grains at the beginning and middle grain-filling stages. A total of 1556 and 1507 transcripts that were differentially expressed between WFYT025 and its parents (DGHP) were identified at 1-day post-anthesis (DPA) and at 10 DPA, respectively. The analysis of the genetic effects of heterosis showed that the over-dominant effect (66.90% and 55.87%) was the main mode of action during grain development. The KEGG pathway and GO analysis of the DGHP indicated that the gibberellin biosynthetic, starch metabolic, and diterpenoid biosynthetic signaling pathways may be associated with heterosis during grain development. To further explore the candidate genes for grain development heterosis, a recombinant inbred line (RILs) population with a high-density genetic map of 2578 bin markers was constructed by crossing the parents of WFYT025, and nine stable QTLs for grain weight-related traits were identified. By comparing the DGHP with 20 QTLs, LOC_Os02g28820, LOC_Os02g32580, LOC_Os04g25440, and LOC_Os12g04980 were identified as grain development heterosis-related candidate genes. These findings provide resources for the study of heterosis during the grain development of super hybrid rice and provide valuable theoretical references for the cloning and functional analysis of heterosis-related genes. [ABSTRACT FROM AUTHOR]

Background: Allopolyploid breeding is an efficient technique for improving the low seed setting rate of autotetraploids in plant breeding and one of the most promising breeding methods. However, there have been few comprehensive studies of the posttranscriptional mechanism in allopolyploids. Results: By crossing cultivated rice (Oryza sativa, genome AA) with wild rice (Oryza punctata, genome BB), we created hybrid rice lines with different ploidy and genome compositions [diploid hybrid F01 (AB), allotetraploid hybrid F02 (AABB) and F03 (AAAB)]. The genetic differences of the hybrids and the mechanism of allopolyploid breeding dominance were revealed through morphological and cytological observations and single molecule real-time sequencing techniques. The tissues and organs of allotetraploid hybrid F02 exhibited "gigantism" and the highest levels of fertility. The numbers of non-redundant transcripts, gene loci and new isoforms in the polyploid rice lines were higher and the isoform lengths greater than those of the diploid line. Moreover, alternative splicing (AS) events occurred twice as often in the polyploid rice lines than the diploid line. During these events, intron retention dominated. Furthermore, a large number of new genes and isoforms specific to the lines of different ploidy were discovered. Conclusions: The results indicated that alternative polyadenylation (APA) and AS events contributed to the complexity and superiority of polyploids in the activity of translation regulators, nucleic acid binding transcription factor activities and the regulation of molecular function. Therefore, these APA and AS events in allopolyploid rice were found to play a role in regulation. Our study provides new germplasm for polyploid rice breeding and reveals complex regulatory mechanisms that may be related to heterosis and fertility. [ABSTRACT FROM AUTHOR]

Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional–structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L‐type and S‐type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct‐seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct‐seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding. Summary Statement: Multiscale mechanistic modelling identified several integrated root phenotypes in rice with superior yield under low N availability. Synergism among root phenes was an important component of phenotypic performance. [ABSTRACT FROM AUTHOR]

Adoption of new plant varieties has played a significant role in eradicating global hunger. Previous research has mainly focused on farmer adoption and impact of new crop varieties, although upstream adoption of technologies in plant breeding can generate substantial multiplier effects on downstream impacts. This study moves upstream in the innovation system to generate policy advice on adoption and transfer of accelerated rice breeding technologies. More specifically, we assess the determinants of global adoption of rapid generation advance (RGA) through a sample of 158 rice breeders operating in various research institutes worldwide. Moving upstream in the innovation system has important theoretical and empirical implications due to the smaller number of decision‐making units in the adoption process and the increasing role of institutional and managerial factors that may overrule individual adoption motivations. We revisit multi‐stage models and devise the most robust estimation method that can be used in this situation. To generate insights on the impact of individual versus institutional adopter characteristics on upstream technology adoption, we juxtapose the response curves of the determinants of RGA adoption in rice breeding among alternative adoption stages, levels of conditionality and model specifications. Our findings confirm the importance of institutional and managerial factors and suggest that adoption and transfer of breeding technologies require breeding institutes to provide an enabling environment in which breeders are encouraged to take risks and are given sufficient freedom to experiment with and implement new technologies. [ABSTRACT FROM AUTHOR]

Understanding heritability has historically been critical to the incorporation of traits of interest into plant breeding programmes for improvement. In our previous study, we assessed the heritability of several photosynthetic traits in indica rice, including biochemical limitations of photosynthesis. Here, we discuss that even without directly evaluating sink limitation, there is still great value in this study for understanding how photosynthetic traits in rice could be incorporated into a breeding programme and which traits could be given priority. Additionally, we assert that limitation by Jmax will likely be more relevant than TPU limitation in the immediate future and could be a valuable factor for selection. However, we agree with Fabre and Dingkuhn (2022, https://doi.org/10.1111/pbr.13000) that sink limitation should be further examined within the context of plant improvement in the future. [ABSTRACT FROM AUTHOR]

Key message: Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding. [ABSTRACT FROM AUTHOR]

Flag leaf angle impacts the photosynthetic capacity of densely grown plants and is thus an important agronomic breeding trait for crop architecture and yield. The hormone auxin plays a key role in regulating this trait, yet the underlying molecular and cellular mechanisms remain unclear. Here, we report that two rice (Oryza sativa) auxin response factors (ARFs), OsARF6 and OsARF17, which are highly expressed in lamina joint tissues, control flag leaf angle in response to auxin. Loss-of-function double osarf6 osarf17 mutants displayed reduced secondary cell wall levels of lamina joint sclerenchymatous cells (Scs), resulting in an exaggerated flag leaf angle and decreased grain yield under dense planting conditions. Mechanical measurements indicated that the mutant lamina joint tissues were too weak to support the weight of the flag leaf blade, resembling the phenotype of the rice increased leaf angle1 (ila1) mutant. We demonstrate that OsARF6 and OsARF17 directly bind to the ILA1 promoter independently and synergistically to activate its expression. In addition, auxin-induced ILA1 expression was dependent on OsARF6 and OsARF17. Collectively, our study reveals a mechanism that integrates auxin signaling with the secondary cell wall composition to determine flag leaf angle, providing breeding targets in rice, and potentially other cereals, for this key trait. [ABSTRACT FROM AUTHOR]

Embrapa has led breeding programs for irrigated and upland rice (Oryza sativa L.) since 1977, generating a large amount of pedigree and phenotypic data. However, there were no systematic standards for data recording nor long‐term data preservation and reuse strategies. With the new aim of making data reuse practical, we recovered all data available and structured it into the Embrapa Rice Breeding Dataset (ERBD). In its current version, the ERBD includes 20,504 crosses involving 9,974 parents, the pedigrees of most of the 4,532 inbred lines that took part in advanced field trials, and phenotypic data from 2,711 field trials (1,118 irrigated, 1,593 upland trials), representing 226,458 field plots. Those trials were conducted over 38 years (1982–2019), in 247 locations, in latitudes ranging from 3°N to 33°S. Phenotypic traits included grain yield, days to flowering, plant height, canopy lodging, and five important fungal diseases: leaf blast, panicle blast, brown spot, leaf scald, and grain discoloration. The total number of data points surpasses 1.27 million. Descriptive statistics were computed over the dataset, split by cropping systems (irrigated or upland). The mean heritability of grain yield was high for both systems, at around.7, whereas the mean coefficient of variation was 13.9% for irrigated trials and 18.7% for upland trials. The ERBD offers the possibility of conducting studies on different aspects of rice breeding and genetics, including genetic gain, G×E analysis, genome‐wide association studies and genomic prediction. Core Ideas: Historical datasets are useful for genetic research and development of breeding tools.Phenotypic data from crop breeding programs connect elite genotypes with target environments.Converting available records in analyzable format is a worthwhile investment. [ABSTRACT FROM AUTHOR]

Rice, the number one staple food crop of Nepal, contributes nearly 20% to the agricultural gross domestic product, almost 7% to gross domestic product, and supplies with 40% of the food calorie consumption of Nepalese people. Despite of increasing production, the national demand of rice cannot be fulfilled, and billions of rupees are spent yearly for importing rice from India. This article reviews history, recent scenario, prospects, and importance of rice breeding research in Nepal for self-sufficiency. Though plant breeding inception point in Nepal was 1951, the systematic research in rice was started from 1972 after the establishment of the National Rice Research Program. Introduction and evaluation of high yielding exotic germplasm of rice was the initial rice breeding activities. After analysing several foreign materials, CH-45 variety of rice was first recommended in 1959. Nepal Agriculture Research Council (NARC), the leading organisation for rice varietal improvement to date, has been doing rice research activities such as germplasm conservation, exchange, varietal development, verification of technologies, and knowledge updates in collaboration with various organizations. International Rice Research Institute (IRRI), since 1966, has been playing an important role in Nepal's rice research. Major plant breeding achievements are introduction of exotic materials and their evaluation, local landraces identification, collection and analysis, crossing of local landraces with exotic genetic materials, heterosis breeding, tissue culture technology, genetic marker technology, and National Genebank. RAPD and SSR, DNA-based markers, are mostly used for diversity appraisal and selecting desirable genotypes. Integration of advanced tools such as genetic engineering, bioinformatics, protoplast fusion, and SNP markers could not be still applied in rice research and development. Hence, emphasis should be given to improve the capacity and abilities of the rice scientists and should release more short duration, drought, and submergence-tolerant rice varieties by optimum utilisation of local landraces combining modern and conventional breeding. [ABSTRACT FROM AUTHOR]

Traditional breeding for high-yielding crops has mainly relied on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties, as dwarfism increases lodging resistance and allows for high nitrogen use, resulting in high grain yield. Although the adoption of semi-dwarf varieties in rice and wheat breeding brought big success to the 'Green Revolution' in the 20th century, it consequently increased the demand for nitrogen-based fertilizer, which causes severe threat to ecosystems and sustainable agriculture. To make the 'Green Revolution' truly green, it is necessary to develop new varieties with high nitrogen use efficiency (NUE). Under this demand, research on NUE, mainly for rice, has made great strides in the last decade. This mini-review focuses on three aspects of recent epoch-making findings on rice breeding for high NUE. The first one on 'NUE genes related to GA signaling' shows how promising it is to improve NUE in semi-dwarf Green Revolution varieties. The second aspect centers around the nitrate transporter1.1B, NRT1.1B; studies have revealed a nutrient signaling pathway through the discovery of the nitrate-NRT1.1B-SPX4-NLP3 cascade. The last one is based on the recent finding that the teosinte branched1, cycloidea, proliferating cell factor (TCP)-domain protein 19 underlies the genomic basis of geographical adaptation to soil nitrogen; OsTCP19 regulates the expression of a key transacting factor, DLT/SMOS2, which participates in the signaling of four different phytohormones, GA, auxin, brassinosteroid and strigolactone. Collectively, these breakthrough findings represent a significant step toward breeding high-NUE rice in the future. [ABSTRACT FROM AUTHOR]

The dynamic changes in agricultural practices have negatively impacted rice cultivation resulting in serious weedy rice (Oryza sativa L.) infestations. In this study, field surveys were conducted at six granaries to evaluate the abundance, spatial‐distribution patterns, and morphological characteristics of weedy rice in Peninsular Malaysia. An average of 5.28 plants/m2 weedy rice density was recorded, with coverage area that ranged from 29% to 66% and occurrence at >67% frequency. Seed morphological characteristics identified the existence of at least 18 biotypes. A total of 134 weedy rice samples were characterized morphologically, and Principle Component Analysis results showed that these samples are highly diverse and are dispersed across Peninsular Malaysia. These genetically diverse reservoir of weedy rice characteristics present opportunities of exploitation in the future, especially through rice breeding and crop improvement. Weedy rice from Kelantan and Selangor displayed unique clusters in the PCA plot which suggest higher tendencies for environmental adaptation although the influencing factors have yet to be determined. Dispersion studies based on Lloyd patchiness index revealed that more than 50% of surveyed field blocks in five states displayed uniform distribution as opposed to cluster distribution observed in the remaining field blocks. These variations in dispersion suggested that farmers in Peninsular Malaysia employed inconsistent weedy rice management practices in every granary and farm block. Observation of weedy rice infestation pattern via spatial distribution suggested that weed management requires proper coordination of control efforts among farmers to ensure the degree of infestation is maintained under a controlled level. [ABSTRACT FROM AUTHOR]

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops. [ABSTRACT FROM AUTHOR]

‘Jungdream’ is an early maturing, high-quality rice cultivar developed in 2017 by the crop breeding team at Crop Research Division, GARES, Hwaseong, Korea. ‘Jungdream’ was first developed in 2008 from crossing a medium-late maturity cultivar ‘Chilbo’ and an early maturity cultivar ‘Ungwang’. The heading date of this cultivar is July 28 th in the Gyeonggido Province. Its culm length is 63 cm, and it has 19 panicles per hill and 82 spikelets per panicle. It is a medium-small grain brown rice cultivar with a 1000-grain weight of 20.6 g. Its cold tolerance is lower than that of ‘Hwaseong’, which is the standard cultivar in the central region, as is its degree of lodging tolerance. ‘Jungdream’ is resistant to rice blast and stripe virus diseases but is susceptible to bacterial leaf blight and other viral diseases and pests. The appearance of milled ‘Jungdream’ rice is clear, and its amylose content is 16.5%, which is lower than that of ‘Hwaseong’. The palatability of cooked ‘Jungdream’ rice is better than that of ‘Chucheong’, which is the main cultivated crop in Gyeonggido. Its milling ratio is 75.0%, which is lower than that of ‘Hwaseong’. The yield of milled ‘Jungdream’ rice was 5.42 MT/ha in the local adaptability tests during standard cultivation in four regions from 2015 to 2017. ‘Jungdream’ is highly adaptable to the environmental conditions in the Gyeonggido Province (Registration No. 8236). [ABSTRACT FROM AUTHOR]

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido. [ABSTRACT FROM AUTHOR]

Parallel domestication has been widely acknowledged but its genetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate genetic improvement and breeding of rice and crops in general. [ABSTRACT FROM AUTHOR]

Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3 , qRL6 , qRL7 , and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11 , namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement. [ABSTRACT FROM AUTHOR]

Summary: Hybrid breeding has been shown to effectively increase rice productivity. However, identifying desirable hybrids out of numerous potential combinations is a daunting challenge. Genomic selection holds great promise for accelerating hybrid breeding by enabling early selection before phenotypes are measured. With the recent advances in multi‐omic technologies, hybrid prediction based on transcriptomic and metabolomic data has received increasing attention. However, the current omic‐based hybrid prediction has ignored parental phenotypic information, which is of fundamental importance in plant breeding. In this study, we integrated parental phenotypic information into various multi‐omic prediction models applied in hybrid breeding of rice and compared the predictabilities of 15 combinations from four sets of predictors from the parents, that is genome, transcriptome, metabolome and phenome. The predictability for each combination was evaluated using the best linear unbiased prediction and a modified fast HAT method. We found significant interactions between predictors and traits in predictability, but joint prediction with various combinations of the predictors significantly improved predictability relative to prediction of any single source omic data for each trait investigated. Incorporation of parental phenotypic data into various omic predictors increased the predictability, averagely by 13.6%, 54.5%, 19.9% and 8.3%, for grain yield, number of tillers per plant, number of grains per panicle and 1000 grain weight, respectively. Among nine models of incorporating parental traits, the AD‐All model was the most effective one. This novel strategy of incorporating parental phenotypic data into multi‐omic prediction is expected to improve hybrid breeding progress, especially with the development of high‐throughput phenotyping technologies. [ABSTRACT FROM AUTHOR]

This study was carried out to analysis of genetic diversity of rice marketed in Turkey. Sixty rice varieties used as a material. A total of 50 SSR markers distributed to all 12 rice chromosomes were used for the diversity analysis of the genotypes. Out of these, 43 SSRs produced clear, distinct polymorphic bands among the rice varieties, and a total of 227 alleles were obtained. The number of alleles per locus ranged from 9 to 1. The mean number of alleles per locus was 5.25, and 22 markers (51%) had 6 or more alleles. Clustering of 60 varieties based on 43 SSR markers was carried out. While aromatic varieties were placed into an out‐group Rocca and Baldo which are parents of many rice varieties and 47 varieties were placed into the same clusters. This SSR polymorphism analysis revealed genomic relationships in rice marketed in Turkey. Practical applications: Results of this study could be used to diversity analysis of rice and other crops and rice breeding programs. It could be used to study genetic diversity of polished rice at the market and consumer preference by countries. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate diversity, experimental conditions and dynamics of the Irrigated Rice Breeding Program of Minas Gerais - Brazil, by meta-analysis. The target traits were grain yield, plant height and days to flowering. Evaluations were based on estimates of 376 genotypes grown at three locations, in two final comparative trials, in 14 growing seasons. Stability of the overall averages of the traits plant height and days to flowering was observed, indicating an adequate plant height and medium cycle. High average yields (>5,000 kg ha-1), good experimental accuracy and genetic variability were recorded. However, the genetic variability of all traits decreased over time, indicating the need to increase genotypic diversity. The parameter estimates of the morphoagronomic traits studied in time meta-analysis indicated the dynamic nature and good accuracy of the Irrigated Rice Breeding Program of Minas Gerais. [ABSTRACT FROM AUTHOR]

The rice crop is affected by diseases throughout its cycle, impacting negatively on grain yield and quality. The control of the disease impact can be accomplished via crop breeding, using highly multiple resistant genotypes. This study aimed to evaluate the efficiency of multiple‐character and specific selection of multiple resistance to major culture‐associated diseases (neck blast, leaf scald and grain discoloration) in rice lines of the Upland Rice Genetic Breeding Program. The experiments were conducted in 35 sites during 12 agricultural years, where 124 lines were evaluated for the severity of fungal diseases, under natural field conditions. Multiple parameters were calculated based on the diseases´ scores: genetic, phenotypic and environmental variances, heritability, selection gain, renewal rate, and genetic and renewal progress. Genetic variance for the disease resistance was identified in the population, and the selection gain for multiple‐character selection was of 3.16 year−1 throughout the breeding process with a renewal rate of over 35%. The programme has showed efficiency in selecting multiple resistant genotypes to the mentioned diseases, highlighting genotypes with high potential for market release. [ABSTRACT FROM AUTHOR]

Recent advances in high-throughput sequencing technologies have enabled large-scale cost-effective genotypic analyses, and consequently, obtaining reliable phenotypic data has now become a major bottleneck in data-driven plant breeding. In order to construct a phenotype database for commercial rice varieties released by the National Institute of Crop Science, Rural Development Administration, we initiated a systematic phenotype evaluation project, with the aim of investigating the major agronomic traits of Korean rice varieties released during the period between 1979 and 2017. Despite the narrow genetic background, we found that the days to heading (DTH) and culm length (CL) of the 297 Korean rice varieties assessed exhibited wide phenotypic variation under different environments. Under normal planting cultivation in 2018, the DTH ranged from 48 to 104 days in Suwon, 46 to 111 days in Wanju, and 39 to 97 days in Miryang, with CL values ranging from 59 to 134 cm, 55 to 122 cm, and 57 to 106 cm, respectively. During early planting cultivation in 2019, the DTH ranged from 56 to 113 days (Suwon), 58 to 109 days (Wanju), and 58 to 100 days (Miryang), with corresponding CL values ranging from 63 to 119 cm, 55 to 93 cm, and 51 to 115 cm. Despite the difference of one month in planting dates in 2018 and 2019, DTH in the different years and regions showed highly significant positive correlations (r=0.90-0.98), whereas CL showed positive but weaker correlations (r=0.45-0.82). Furthermore, we detected a weak, although significant, correlation between DTH and CL in each environment (r=-0.18-0.35). Analyses of additive main effects and multiplicative interaction (AMMI) were conducted for DTH and CL to identify rice varieties with stable phenotypes under different environments. We anticipate that the findings of this study will provide a useful rice phenotype database to facilitate genotype-phenotype association studies and data-driven rice breeding. [ABSTRACT FROM AUTHOR]

Recently, hybrid rice area in China has increased to over 16 million ha per year, accounting for 57% of total rice areas and approximately 65% of total rice production. With the breeding success in developing the third-generation hybrid rice, particularly since the release of "Sanyou No. 1", hybrid rice has become increasingly popular as late rice in the double-cropping areas. Commercialization of two-line hybrid rice demonstrates the expertise of Chinese hybrid rice experts, led by Professor Yuan, and ensures China standing at the forefront of global hybrid rice development. [Extracted from the article]

SUMMARY: Advancements in ‐omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross‐breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non‐GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non‐GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross‐breeding do not involve detrimental metabolic pathways. The study successfully employed RNA‐sequencing and high‐performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross‐breeding in rice. Significance Statement: We compared the biological variation at mRNA and metabolite levels among four genetically engineered rice lines and nine conventionally bred rice cultivars that represent a range of genetic and phenotypic diversity in rice. The results provide evidence that genetic engineering does not cause unintended effects that go beyond conventional cross‐breeding in rice. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa) is crop that adapts well to diverse soil and climate conditions; breeding programs have generally been committed to identifying and selecting genotypes that are stable and have high productivity in various environments. In this sense, studies of adaptability and stability are of paramount importance to aid in the recommendation of cultivars, since it allows growers to obtain detailed information about the behavior of the genotypes in each region. We evaluatde the adaptability and stability of irrigated rice genotypes grown with continuous flooding, for the selection and recommendation of cultivars for crops or breeding programs. Eighteen genotypes were evaluated for grain yield in four agricultural years at three sites, covering 12 environments. The adaptability and stability were assessed by the methods of Eberhart and Russell, multiple centroids and GGE biplot. Genotypes behaved differently regarding stability and adaptability in the different environments. Both methodologies identified BRA 02691 and MGI 0607-1 as promising to be released as cultivars; however, classification inconsistencies occurred, such as for the line BRA 031001. Multiple centroid and GGE biplot methods demonstrated greater sensitivity than the Eberhart and Russell method. Using the methods simultaneously provides an innovative approach to the interpretation of GxE interactions and is a viable alternative for genotype classification. The genotype MGI 0607-1 showed promising behavior independent of the methodology used. [ABSTRACT FROM AUTHOR]