Controlling diurnal flower-opening time by manipulating the jasmonate pathway accelerates development of indica-japonica hybrid rice breeding

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.

The OsMYC2-JA feedback loop regulates diurnal flower-opening time via cell wall loosening in rice

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.

Conversion of superior bread wheat genotype HD3209 carrying Lr19/Sr25 into CMS line for development of rust-resistant wheat hybrids

Hybrid development is one of the most promising strategies for boosting crop yields. Parental lines used to create hybrids must have good per se performance and disease resistance for developing superior hybrids. Indian wheat line HD3209 was developed by introducing the rust resistance genes Lr19/Sr25 into the background of popular wheat variety HD2932. The wheat line HD3209 carrying Lr19/Sr25 has been successfully and rapidly converted to the CMS line A-HD3209, with 96.01% background genome recovery, based on selection for agro-morphological traits, rust resistance, pollen sterility, and foreground and background analyses utilizing SSR markers. The converted CMS line A-HD3209 was completely sterile and nearly identical to the recurrent parent HD3209. Based on high per se performance and rust resistance, the study concludes that the derived CMS line A-HD3209 is promising and can be employed successfully in hybrid development.

Revisiting growth-defence trade-offs and breeding strategies in crops

Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.

Strong culm: a crucial trait for developing next-generation climate-resilient rice lines

Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.

Perception of strigolactones and the coordinated phytohormonal regulation on rice (Oryza sativa) tillering is affected by endogenous ascorbic acid

Phytohormones play a key role in regulating tiller number. Ascorbic acid (Asc)-phytohormone interaction plays a pivotal role in the regulation of senescence. We analysed the relationship between Asc and the enzyme concentrations and gene transcript abundances related to the signal perception of strigolactones (SLs), the contents of four phytohormones (abscisic acid, ABA; jasmonic acid, JA; indole acetic acid, IAA; cytokinin, CTK), the enzyme concentrations and gene transcript abundances related to the synthesis or transportation of these four phytohormones. Our results showed that Asc deficiency leads to the upregulation of enzyme concentrations, gene transcript abundances related to the SL signal perception, ABA synthesis and IAA transport. The altered level of Asc also leads to a change in the contents of ABA, JA, IAA and CTK. These findings support the conclusion that Asc or Asc/DHA play an important role in the signal perception and transduction of SLs, and Asc may affect the coordinated regulation of SL, IAA and CTK on rice (Oryza sativa ) tillering.

Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice (Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method

Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.

10k-level integrated rice database shows power for exploiting rare variants

This Highlight features a recent study by Shang Lianguang and Qian Qian's groups, who re-analyzed published resequencing data covering 10,548 accessions of Asian cultivated rice Oryza sativa and wild rice Oryza rufipogon from 98 countries worldwide to generate a super-large rice genomic variation dataset.

NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning

BACKGROUND

Single-cell RNA sequencing (scRNA-seq) measurements of gene expression show great promise for studying the cellular heterogeneity of rice roots. How precisely annotating cell identity is a major unresolved problem in plant scRNA-seq analysis due to the inherent high dimensionality and sparsity.

RESULTS

To address this challenge, we present NRTPredictor, an ensemble-learning system, to predict rice root cell stage and mine biomarkers through complete model interpretability. The performance of NRTPredictor was evaluated using a test dataset, with 98.01% accuracy and 95.45% recall. With the power of interpretability provided by NRTPredictor, our model recognizes 110 marker genes partially involved in phenylpropanoid biosynthesis. Expression patterns of rice root could be mapped by the above-mentioned candidate genes, showing the superiority of NRTPredictor. Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses.

CONCLUSION

Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a valuable resource for deciphering the rice root cellular heterogeneity and the molecular mechanisms of flooding, Pi, and salt stresses. Based on the proposed model, a free webserver has been established, which is available at https://www.cgris.net/nrtp .

Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population

Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.

Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis

Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica-indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica-japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.

Combining Ability Analysis of Yield-Related Traits of Two Elite Rice Restorer Lines in Chinese Hybrid Rice

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.

High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement

Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.

Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice

NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1A, which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

Advances on the Study of Diurnal Flower-Opening Times of Rice

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.

Loss of function of SSIIIa and SSIIIb coordinately confers high RS content in cooked rice

The sedentary lifestyle and refined food consumption significantly lead to obesity, type 2 diabetes, and related complications, which have become one of the major threats to global health. This incidence could be potentially reduced by daily foods rich in resistant starch (RS). However, it remains a challenge to breed high-RS rice varieties. Here, we reported a high-RS mutant rs4 with an RS content of ~10.8% in cooked rice. The genetic study revealed that the loss-of-function SSIIIb and SSIIIa together with a strong Wx allele in the background collaboratively contributed to the high-RS phenotype of the rs4 mutant. The increased RS contents in ssIIIa and ssIIIa ssIIIb mutants were associated with the increased amylose and lipid contents. SSIIIb and SSIIIa proteins were functionally redundant, whereas SSIIIb mainly functioned in leaves and SSIIIa largely in endosperm owing to their divergent tissue-specific expression patterns. Furthermore, we found that SSIII experienced duplication in different cereals, of which one SSIII paralog was mainly expressed in leaves and another in the endosperm. SSII but not SSIV showed a similar evolutionary pattern to SSIII. The copies of endosperm-expressed SSIII and SSII were associated with high total starch contents and low RS levels in the seeds of tested cereals, compared with low starch contents and high RS levels in tested dicots. These results provided critical genetic resources for breeding high-RS rice cultivars, and the evolutionary features of these genes may facilitate to generate high-RS varieties in different cereals.

Mixed cropping with duck co-culture: an agroecological system to improve grain quality and farm profitability

BACKGROUND

Previous studies found that mixed cropping combined with duck co-culture (MCDC) system could improve the efficiency of grain production and positively affect soil nutrient contents. However, the effects on grain quality, and profitable income have not been evaluated yet. In this study, a field experiment with four combinations of different rice varieties and ducks was conducted during both the early and late rice growing seasons.

RESULTS

The field survey demonstrated that MCDC system significantly decreased the grain appearance of chalky rice rate and the chalkiness degree with an average of 56.82%, and 54.28%, respectively. Leaf SPAD value, photosynthetic rate, and aboveground dry weight were all improved in the MCDC and mixed-cropping systems, relative to the mono-cropping system. The net income obtained from the mono-cropping, mixed cropping (no ducks), and MCDC (with ducks) systems (from grain and ducks' meat) was 581.2 USD ha^-1 yr^-1 , 1001.8 USD ha^-1 yr^-1 , and 5242.1 USD ha^-1 yr^-1 in both growing seasons, respectively.

CONCLUSION

Planting genetically diverse rice varieties and co-culture with ducks increased rice growth rates, productivity and grain quality. The MCDC system would provide more ecological and economic benefits compared with the conventional mono-cropping system. © 2022 Society of Chemical Industry.

The legacies of the "Father of Hybrid Rice" and the seven representative achievements of Chinese rice research: A pioneering perspective towards sustainable development

The "Father of Hybrid Rice", Yuan Longping, created high-yield hybrid rice that can feed tens of millions of people annually. The research achievements of Yuan and his team on low cadmium-accumulating rice and sea rice, in addition to hybrid rice, as well as those of a large number of Chinese scientists engaged in rice research in other six areas, including the rice genome, purple endosperm rice, de novo domestication of tetraploid rice, perennial rice, rice blast disease, and key genes for high nitrogen use efficiency, play an important role in promoting the realization of the United Nations Sustainable Development Goals 2 and 12. The purpose of this review is not to elaborate on the details of each research, but to innovatively summarize the significance and inspiration of these achievements to ensure global food security and achieve sustainable agriculture. In the future, cultivating new rice varieties through modern biotechnology, such as genome editing, will not only reduce hunger, but potentially reduce human-land conflicts, improve the environment, and mitigate climate change.

Understanding the regulation of cereal grain filling: The way forward

During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.

Grain shape is a factor affecting the stigma exsertion rate in rice

Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R²) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R² values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.

Cyanobacteria Application Ameliorates Floral Traits and Outcrossing Rate in Diverse Rice Cytoplasmic Male Sterile Lines

In rice, cytoplasmic male sterility (CMS) represents an irreplaceable strategy for producing high-yielding hybrid rice based on the commercial exploitation of heterosis. Thereupon, enhancing floral traits and outcrossing rates in CMS lines increase hybrid seed production and ensure global food security. The exogenous application of cyanobacteria could enhance outcrossing rates in CMS lines and, accordingly, hybrid rice seed production. In the present study, we aimed at exploring the impact of cyanobacteria implementation such as Anabaena oryzae, Nostoc muscorum, and their mixture to promote the floral traits, outcrossing rates, and seed production in hybrid rice. The impact of cyanobacteria (Anabaena Oryza (T2), Nostoc muscorum (T3), and their combination (T4) versus the untreated control (T1) was investigated for two years on the growth, floral, and yield traits of five diverse CMS lines, namely IR69625A (L1), IR58025A (L2), IR70368A (L3), G46A (L4), and K17A(L5). The evaluated CMS lines exhibited significant differences in all measured floral traits (days to heading (DTH), total stigma length (TSL), stigma width (SW), duration of spikelet opening (DSO), spikelet opening angle (SOA)). Additionally, L4 displayed the uppermost total stigma length and stigma width, whereas L1 and L5 recorded the best duration of spikelet opening and spikelet opening angle. Notably, these mentioned CMS lines exhibited the highest plant growth and yield traits, particularly under T4 treatment. Strong positive relationships were distinguished between the duration of the spikelet opening, panicle exertion, panicle weight, seed set, grain yield, total stigma length, spikelet opening angle, stigma width, and number of fertile panicles per hill. Cyanobacteria is a potential promising tool to increase floral traits and seed production in hybrid rice.

A Review of Vector-Borne Rice Viruses

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

Design and test of smashing and scattering device of double-channel feeding ratoon rice harvester

Since it is requested that the smashed straw should not be scattered onto the stubble in the first season harvest, a smashing and scattering device matched with the first season harvester of ratoon rice was designed in this paper to smash and scatter the straw into the rolling area. The main structural parameters affecting the straw scattering performance were determined by theoretical analysis of the deflecting performance of the straw deflector. EDEM software was used to simulate and analyze the straw scattering situation under the action of the deflector. Taking the qualified rate of straw scattering as the performance index, the optimal parameter combination of the straw deflector was determined by L27 (313) orthogonal test, and the operating performance of the device was verified by bench test and field comparison test. The test results show that: The optimal parameter combination was 45° between the straw deflector and the vertical direction, 200 mm height difference between straw deflector and outlet, 0° inclination angle of inner deflector and 35° inclination angle of outer deflector. The qualified rate of straw scattering was 72.2% in the corresponding simulation test, 93.6% in the bench test and 95.2% in the field test, which could meet the demand of first season harvest of ratoon rice.

OsSIDP301, a Member of the DUF1644 Family, Negatively Regulates Salt Stress and Grain Size in Rice

As a major environmental factor, salt stress substantially retards growth and reduces the productivity of rice (Oryza sativa). Members of the DUF1644 family, "the domains of unknown function 1644 motif" are predicted to play an essential regulatory role in response to abiotic stress. However, the specific molecular mechanisms of most members of this family remain elusive. Here, we report that the OsSIDP301 (stress-induced DUF1644 protein) was induced by salt stress and abscisic acid (ABA). We found that overexpression of OsSIDP301 (OE) in plants conferred salt hypersensitivity and reduced grain size, whereas plants with OsSIDP301 RNA interference (RNAi) exhibited salt tolerance and increased grain size in rice. OsSIDP301 determines salt stress tolerance by modulating genes involved in the salt-response and ABA signaling pathways. Further studies suggest that OsSIDP301 regulates grain size by influencing cell expansion in spikelet hulls. Moreover, OsSIDP301 interacts with OsBUL1 COMPLEX1 (OsBC1), which positively regulates grain size in rice. Our findings reveal that OsSIDP301 functions as a negative regulator of salt stress and grain size, and repressing its expression represents a promising strategy for improving salt stress tolerance and yield in rice.

Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.

Gaseous emissions and grain-heavy metal contents in rice paddies: A three-year partial organic substitution experiment

To reduce the utilization of chemical fertilisers, which cause substantial nitrogen loss and widespread nonpoint source pollution, the application of organic manure has become an increasingly popular alternative in rice agriculture. It plays key roles in improving soil quality and maintaining rice yields, but its integrated impacts on trace gas emissions and heavy metal contents in rice grains remain poorly documented. We conducted a three-year field experiment with two application ratios (25% and 50%) of sewage sludge compost (S) and pig manure compost (P) during the rice season in eastern China. The emissions of methane (CH₄), nitrous oxide (N₂O), ammonia (NH₃), and the grain contents of nickel (Ni), copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) were measured. Compared with urea, partial organic application, particularly 50%S and 50%P, led to a considerable increase in CH₄ emission (52%-71%), global warming potential (GWP, 50%-69%), and greenhouse gas intensity (46%-68%). However, it substantially decreased N₂O emission and NH₃ volatilisation, thus lowering the cumulative nitrogen loss by 32%-62%. Moreover, the average concentrations of Ni, Cu, Zn, Cd, and Pb in rice grains were 100-151 μg kg^-1, 2.31-2.78 mg kg^-1, 20.3-24.3 mg kg^-1, 44.3-123 μg kg^-1, and 8.69-15.2 μg kg^-1, respectively, which were significantly lower than food standard limits for rice in China. Both 25%S and 50%S achieved the highest grain yields while significantly decreasing grain Ni and Cd contents. Health risk assessment showed that the target hazard quotient of all the metals was <1 (0.006-0.73), and the hazard index that represents additive effects of pollutants was higher than the threshold, except for 25%S and 50%S. The results suggested 25%S as a potential fertilisation practice in rice fields that not only maintains low GWP and high yields but also seldom poses grain pollution or health risks.

Methylesterification of cell-wall pectin controls the diurnal flower-opening times in rice

Flowers are the core reproductive organ of plants, and flowering is essential for cross-pollination. Diurnal flower-opening time is thus a key trait influencing reproductive isolation, hybrid breeding, and thermostability in plants. However, the molecular mechanisms controlling this trait remain unknown. Here, we report that rice Diurnal Flower Opening Time 1 (DFOT1) modulates pectin methylesterase (PME) activity to regulate pectin methylesterification levels of the lodicule cell walls, which affect lodicule swelling to control diurnal flower-opening time. DFOT1 is specifically expressed in the lodicules, and its expression gradually increases with the approach to flowering but decreases with flowering. Importantly, a knockout of DFOT1 showed earlier diurnal flower opening. We demonstrate that DFOT1 interacts directly with multiple PMEs to promote their activity. Knockout of PME40 also resulted in early diurnal flower opening, whereas overexpression of PME42 delayed diurnal flower opening. Lower PME activity was observed to be associated with higher levels of pectin methylesterification and the softening of cell walls in lodicules, which contribute to the absorption of water by lodicules and cause them to swell, thus promoting early diurnal flower opening. Higher PME activity had the opposite effect. Collectively, our work uncovers a molecular mechanism underlying the regulation of diurnal flower-opening time in rice, which would help reduce the costs of hybrid breeding and improve the heat tolerance of flowering plants by avoiding higher temperatures at anthesis.

Partially functional NARROW LEAF1 balances leaf photosynthesis and plant architecture for greater rice yield

NARROW LEAF1 (NAL1) is an elite gene in rice (Oryza sativa), given its close connection to leaf photosynthesis, hybrid vigor, and yield-related agronomic traits; however, the underlying mechanism by which this gene affects these traits remains elusive. In this study, we systematically measured leaf photosynthetic parameters, leaf anatomical parameters, architectural parameters, and agronomic traits in indica cultivar 9311, in 9311 with the native NAL1 replaced by the Nipponbare NAL1 (9311-NIL), and in 9311 with the NAL1 fully mutated (9311-nal1). Leaf length, width, and spikelet number gradually increased from lowest to highest in 9311-nal1, 9311, and 9311-NIL. In contrast, the leaf photosynthetic rate on a leaf area basis, leaf thickness, and panicle number gradually decreased from highest to lowest in 9311-nal1, 9311, and 9311-NIL. RNA-seq analysis showed that NAL1 negatively regulates the expression of photosynthesis-related genes; NAL1 also influenced expression of many genes related to phytohormone signaling, as also shown by different leaf contents of 3-Indoleacetic acid, jasmonic acid, Gibberellin A3, and isopentenyladenine among these genotypes. Furthermore, field experiments with different planting densities showed that 9311 had a larger biomass and yield advantage under low planting density compared to either 9311-NIL or 9311-nall. This study shows both direct and indirect effects of NAL1 on leaf photosynthesis; furthermore, we show that a partially functional NAL1 allele helps maintain a balanced leaf photosynthesis and plant architecture for increased biomass and grain yield in the field.

Verifying the Breeding Value of A Rare Haplotype of Chalk7, GS3, and Chalk5 to Improve Grain Appearance Quality in Rice

Grain quality is a key determinant of commercial value in rice. Efficiently improving grain quality, without compromising grain yield, is a challenge in rice breeding programs. Here we report on the identification and application of a grain quality gene, Chalk7, which causes a slender shape and decreases grain chalkiness in rice. Three allele-specific markers for Chalk7, and two other grain genes (GS3 and Chalk5) were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of near-isogenic lines, each containing one to three favorable alleles in a common background of an elite variety. We found that the favorable allele combination of the three loci, which rarely occurs in natural rice germplasm, greatly reduces chalky grains without negatively impacting on grain yield. The data for newly developed allele-specific markers and pre-breeding lines will facilitate the improvement of grain appearance quality in rice.

Rapid and Directional Improvement of Elite Rice Variety via Combination of Genomics and Multiplex Genome Editing

High yield and superior quality are the main goals pursued by breeders for crop improvement. However, both of them are complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombination is time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysis based multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Application of this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, the rare excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created by multiplex genome editing and successfully improved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a method for rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.

Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice

Recently food shortage has become the major flagging scenario around the globe. To resolve this challenge, there is dire need to significantly increase crop productivity per unit area. In the present study, 24 genotypes of rice were grown in pots to assess their tillering number, number of primary and secondary branches per panicle, number of grains per panicle, number of grains per plant, and grain yield, respectively. In addition, the potential function of miR156 was analyzed, regulating seed sequence in rice. Furthermore, OsSPL14 gene for miR156 was sequenced to identify additional mutations within studied region. The results demonstrated Bas-370 and L-77 showed highest and lowest tillers, respectively. Bas-370, Rachna basmati, Bas-2000, and Kashmir Basmati showed high panicle branches whereas, L-77, L-46, Dilrosh, L-48, and L-20 displayed lowest panicle branches. Bas-370 and four other studied accessions contained C allele whereas, L-77 and 18 other investigated accessions had heterozygous (C and T) alleles in their promoter region. C-T allelic mutation was found in 3^rd exon of the OsSPL14 gene. The sequence analysis of 12 accessions revealed a novel mutation (C-T) present ~2bp upstream and substitution of C-A allele. However, no significant correlation for novel mutation was found for tillering and panicle branches in studied rice accessions. Taken together present results suggested novel insight into the binding of miR156 to detected mutation found in 3^rd exon of the OsSPL14 gene. Nevertheless, L-77, L-46, Dilrosh, L-48, and L-20 could be used as potential breeding resource for improving panicle architecture contributing yield improvement of rice crop.

Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design

Breeding rice (Oryza sativa L.) with high yield, superior quality, desired grain shape and high resistance is the goal of breeding to meet the needs of current consumers. It is usually hard to combine multiple complex traits based on traditional breeding methods because they are frequently antagonistic to each other. However, molecular design breeding, as a novel breeding method, is an optional alternative to this challenge. To demonstrate molecular design breeding, 15 favorable genes from five parent lines were pyramided together to develop elite rice with high-yield, superior-quality, desired grain shape and high resistance to brown planthopper (BPH). The parental lines were 9311, the recurrent parent, carrying APO1, Ghd7, Ghd8 and Gn1a for high yield, GS3 and qSW5 for grain shape, and Wx and ALK for eating and cooking quality; 1880 with Gn8.1 for large panicles; Luo-Yu-Xiang carrying GW7 for grain shape and SBE3, SSIV2 and SSIII for eating and cooking quality; Luoyang6 with Bph6 and Luoyang9 with Bph9 for BPH resistance. After careful screening for the 15 targeted genes, desired phenotype and maximum genetic background from 9311, three molecular design lines with desired phenotypes, named as MD1 (Molecular design 1), MD2 and MD3 were developed. MD3 carried all 15 targeted genes, and MD1 and MD2 had 14 of the 15 targeted genes. Only SBE3 was not introgressed into MD1 and MD2 but this had minimal impact on the gel consistency and alkali spreading value. These newly bred lines exhibited higher yield potential, better grain quality with slender grains, low amylose content, high gel consistency and alkali spreading value, and higher BPH resistance compared to the parent 9311. In this study, we successfully created three novel rice lines with high yield, superior quality and improved BPH resistance by rational molecular design. Our results demonstrate molecular design is a powerful strategy to improve multiple complex traits and will provide a reference for the future commercial rice improvement.

Combined Role of Fe Nanoparticles (Fe NPs) and Staphylococcus aureus L. in the Alleviation of Chromium Stress in Rice Plants

Chromium (Cr) is a toxic heavy metal whose high concentration in soil badly affects plant growth, photosynthesis, and overall yield. Metal-derived nano-particles and metal-resistant bacteria can strengthen the plant defense system against different abiotic stresses; however, little is known about the use of nanoparticles in conjunction with bacteria. This study examined the combined effect of Fe nanoparticles (Fe NPs) and a chromium-resistant bacterium Staphylococcus aureus, on rice plants grown on chromium saturated medium. Chromium stress reduced rice growth, biomass, and chlorophyll contents by causing oxidative damage leading to overproduction of electrolyte leakage, hydrogen peroxide, and malondialdehyde. Fe NPs significantly improved plant growth, biomass, yield, and photosynthetic activity by enhancing the chlorophyll contents and alleviating oxidative damage. Application of Fe NPs also reduced the uptake and accumulation of Cr in the plants by increasing the bioavailability of micronutrients to the plant. The Fe NPs decreased oxidative damage and enhanced the enzymatic and non-enzymatic activity in the plant to withstand Cr stress compared to the plants without Fe NPs treatments. The inoculation of rice plants with the chromium-resistant bacteria S. aureus further enhanced the positive impact of Fe NPs by transforming the toxic form of chromium (Cr⁶⁺) into a less toxic form of chromium (Cr³⁺). The bacterial inoculation reduced Cr uptake by plants through adsorption of Cr ions, resulting in decreased chromium ion bioavailability. At chromium level 100 mg/kg, the foliar application of Fe NPs from 0 to 20 mg/L increased the total chlorophyll contents from 2.8 to 3.9. The application of S. aureus further enhanced the chlorophyll contents from 4.4 to 5.4, respectively. The current study suggested that combining Fe NPs and S. aureus could be a viable strategy for reducing Cr toxicity and accumulation in rice plants and most likely other plants.

A cryptic inhibitor of cytokinin phosphorelay controls rice grain size

Plant hormone cytokinin signals through histidine-aspartic acid (H-D) phosphorelay to regulate plant growth and development. While it is well known that the phosphorelay involves histidine kinases, histidine phosphotransfer proteins (HPs), and response regulators (RRs), how this process is regulated by external components remains unknown. Here we demonstrate that protein phosphatase with kelch-like domains (PPKL1), known as a signaling component of steroid hormone brassinosteroid, is actually a cryptic inhibitor of cytokinin phosphorelay in rice (Oryza sativa). Mutation at a specific amino acid D364 of PPKL1 activates cytokinin response and thus enlarges grain size in a semi-dominant mutant named s48. Overexpression of PPKL1 containing D364, either with the deletion of the phosphatase domain or not, rescues the s48 mutant phenotype. PPKL1 interacts with OsAHP2, one of authentic HPs, and D364 resides in a region resembling the receiver domain of RRs. Accordingly, PPKL1 can utilize D364 to suppress OsAHP2-to-RR phosphorelay, whereas mutation of D364 abolishes the effect. This function of PPKL1 is independent of the phosphatase domain that is required for brassinosteroid signaling. Importantly, editing of the D364-residential region produces a diversity of semi-dominant mutations associated with variously increased grain sizes. Further screening of the edited plants enables the identification of two genotypes that confer significantly improved grain yield. Collectively, our study uncovers a noncanonical cytokinin signaling suppressor and provides a robust tool for seed rational design.

The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean

A whole-genome resequencing-derived SNP dataset used for genome-wide association analysis revealed 12 loci significantly associated with drought stress based on survival rate after drought stress at seedling stage. We further confirmed the drought-related function of an aquaporin gene (PvXIP1;2) located at Locus_10. A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3,832,340 SNPs. The coefficient of variation ranged from 40.90 to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice (Oryza sativa L.)

Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F₂ individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F₂ population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11032-022-01275-y.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Cytoplasmic and nuclear genome variations of rice hybrids and their parents inform the trajectory and strategy of hybrid rice breeding

The male sterility (MS) line is a prerequisite for efficient production of hybrid seeds in rice, a self-pollinating species. MS line breeding is pivotal for hybrid rice improvement. Understanding the historical breeding trajectory will help to improve hybrid rice breeding strategies. Maternally inherited cytoplasm is an appropriate tool for phylogenetic reconstruction and pedigree tracing in rice hybrids. In this study, we analyzed the cytoplasmic genomes of 1495 elite hybrid rice varieties and identified five major types of cytoplasm, which correspond to different hybrid production systems. As the cytoplasm donors for hybrids, 461 MS lines were also divided into five major types based on cytoplasmic and nuclear genomic architecture. Specific core accessions cooperating with different fertility-associated genes drove the sequence divergence of MS lines. Dozens to hundreds of convergent and divergent selective sweeps spanning several agronomic trait-associated genes were identified among different types of MS lines. We further analyzed the cross patterns between different types of MS lines and their corresponding restorers. This study systematically analyzed the cytoplasmic genomes of rice hybrids revealed their relationships with nuclear genomes of MS lines, and illustrated the trajectory of hybrid rice breeding and the strategies for breeding different types of MS lines providing new insights for future improvement of hybrid rice.

Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice

Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F₂ population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.

Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice

BACKGROUND

Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established.

RESULTS

In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism.

CONCLUSIONS

Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

Mapping causal genes and genetic interactions for agronomic traits using a large F2 population in rice

Dissecting the genetic mechanisms underlying agronomic traits is of great importance for crop breeding. Agronomic traits are usually controlled by multiple quantitative trait loci (QTLs) and genetic interactions, and mapping the underlying causal genes is still labor-intensive and time-consuming. Here, we present a genetic tool for directly targeting the specific causal genes by using a single-gene resolution linkage map that was constructed from 3756 F2 rice plants via targeted sequencing technology and Tukey-Kramer multiple comparisons test. Three large- and moderate-effect QTLs, qHD6-2, qGL3-1, and qGW5-2, were successfully mapped to their specific causal genes, Hd1, GS3, and GW5, respectively. A complex genetic interaction network containing 30 QTL-QTL interactions was constructed, revealing that the alternative allele of hub QTL, qHD6-2, can hide or release the genetic contributions of the alleles at interacting loci. Moreover, arranging genetic interactions in the models lead to more accurate phenotypic predictions. These results provide a community resource and new feasible strategy for deciphering the genetic mechanisms of complex agronomic traits and accelerating crop breeding.

Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice

BACKGROUND

Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production.

RESULTS

Here, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance.

CONCLUSIONS

This is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.