A natural gene drive system confers reproductive isolation in rice

Identification and Genetic Analysis of Collinearity Loci for Interspecific Hybrid Sterility in Genus Oryza

BACKGROUND

Hybrid sterility is a common phenomenon in hybrids between the Asian cultivated rice (Oryza sativa L.) and its relatives with AA genome, which limits the utilization of interspecific heterosis and favorable gene introgression. Numerous loci for hybrid sterility have been identified between O. sativa and its relatives. However, it remains elusive whether hybrid sterility between different species is controlled by a set of conserved loci, and whether there are variations in the genetic mode of these loci.

RESULTS

In this study, six novel hybrid sterility loci for pollen sterility were identified from different cross combinations between O. sativa and its three wild relatives. S59 caused hybrid pollen sterility in hybrids between O. sativa and O. rufipogon. S60 and S61 controlled the hybrid pollen sterility between O. sativa and O. glumaepatula. S62, S63 and S64 governed the hybrid pollen sterility between O. sativa and O. barthii. Genetic and linkage analysis showed that S59, S60, and S62 were located in near the same region on the short arm of chromosome 5. S61 and S63 were mapped near RM27460 on the short arm of chromosome 12. S64 was restricted into the 60.27 kb region between RM4853 and RM3372 on the short arm of chromosome 3. The genetic behavior of six novel hybrid sterility loci follows one-locus allelic interaction model, the male gametes carrying the alleles of O. sativa in the heterozygotes were selectively aborted except for S62.

CONCLUSIONS

The findings from this research would provide a better understanding for the genetic nature of interspecific hybrid sterility in rice.

From De Novo Conceived Small Molecules to Multifunctional Supramolecular Nanoparticles: Dual Biofilm and T3SS Intervention, Enhanced Foliar Affinity, and Effective Rice Disease Control

Conventional antimicrobials typically exhibit suboptimal deposition on rice leaves, resulting in poor efficacy, further impaired by biofilms and Type III Secretion Systems (T3SS). Herein, this study presents a supramolecular strategy to fabricate BtP27@β-CD, a sunflower-like material engineered through host-guest recognition between de novo designed molecule BtP27 and β-cyclodextrin. BtP27@β-CD manifests enhanced foliar affinity and in vivo efficiency, demonstrating superior protective (62.67%) and curative (51.16%) activities against bacterial leaf blight at a low-dose of 200 µg mL-1 compared to commercial thiodiazole-copper (37.78%/38.13%) without compromising safety. This multifunctional material, structurally derived from dufulin, inherit progenitor's systemic and conductive properties, alongside the capacity to activate salicylic acid-mediated plant defense pathways. Moreover, it is endowed with the anticipated abilities to disorganize biofilm barriers, annihilate encased pathogens, and inhibit T3SS. This constitutes the inaugural report of a supramolecular-based biofilm/T3SS dual inhibitor. An expanded investigation into substrate and indication screening identified additional molecules that self-assemble with β-cyclodextrin to form supramolecular materials, exhibiting superior potency against other rice diseases, with protective potency ranging from 63.53% to 73.30% and curative efficacy spanning 42.18% to 60.41% at 200 µg mL-1. In brief, this work establishes a paradigm for designing guest molecules from scratch to construct supramolecular materials with tailored characteristics.

Non-Additive Gene Expression in Carbon and Nitrogen Metabolism Drives Growth Heterosis in Populus deltoides

Growth heterosis is crucial for Populus deltoides breeding, a key industrial-timber and ecological-construction tree species in temperate regions. However, the molecular mechanisms underlying carbon (C)-nitrogen (N) metabolism coordination in regulating growth heterosis remain unclear. Herein high-hybrids of P. deltoides exhibited high-parent heterosis and mid-parent heterosis in growth traits and key enzymes of C-N metabolism. In hybrids, gene expression patterns were mainly biased toward female parent. Parental contribution to growth heterosis in P. deltoides is differentiation, rather than absolute maternal or paternal dominance contributions. Parental genes were predominantly and dynamically inherited in a non-additive manner, mainly with dominant expression patterns. A total of 44 non-additive genes associated with photosynthetic C fixation, starch and sucrose metabolism, sucrose transport, photorespiration, and nitrogen metabolism coregulated growth heterosis by coordinating C-N metabolism. Growth-regulating factors 4 interacted with DELLA genes to promote growth by enhancing this coordination. Additionally, five critical genes were identified. Briefly, the above genes in high-hybrids improved photosynthesis and N utilisation by regulating carbohydrate accumulation and enzyme activity, while reducing respiratory energy consumption, thereby providing more energy for growth and promoting growth heterosis. Our findings offer new insights and theoretical basis for deep understanding genetic and molecular regulation mechanisms of tree heterosis and its application in precision hybrid breeding.

Autophagy in Plant Health and Disease

Autophagy has emerged as an essential quality control pathway in plants that selectively and rapidly removes damaged or unwanted cellular components to maintain cellular homeostasis. It can recycle a broad range of cargoes, including entire organelles, protein aggregates, and even invading microbes. It involves the de novo biogenesis of a new cellular compartment, making it intimately linked to endomembrane trafficking pathways. Autophagy is induced by a wide range of biotic and abiotic stress factors, and autophagy mutant plants are highly sensitive to stress, making it an attractive target for improving plant stress resilience. Here, we critically discuss recent discoveries related to plant autophagy and highlight open questions and future research areas.

Molecular mapping of a novel locus S68 for intrasubspecific hybrid sterility in indica-indica hybrid

Oryza. sativa subsp. indica, a subspecies of Asian cultivated rice, plays a crucial role in global rice production, particularly in the utilization of hybrid vigor. However, the genetic basis of hybrid sterility among indica-indica intrasubspecific hybrids remains elusive, hindering the effective exploitation of heterosis in rice breeding programs. In this study, a near isogenic line (NIL) was developed using the indica variety Swarna as the donor parent and the indica variety IR64 as the recurrent parent. A novel locus, designated S68, responsible for intrasubspecific hybrid sterility was mapped to the region between RM14247 and RM3413 on the short arm of chromosome 3, spanning approximately 190 kb. S68 followed one-locus allelic interaction model. In IR64/NIL-S68 hybrids, the gametes from IR64 exhibit a transmission advantage, while those from Swarna are aborted in the heterozygote. This is the first hybrid sterile locus identified in indica-indica intrasubspecific hybrids, which enhances our understanding of the genetic mechanisms underlying intrasubspecific hybrid sterility and the genetic divergence within indica rice, thereby providing guidance for hybrid breeding programs within the indica subspecies.

Applications and status of gene drive in plants

Gene drive can modify or suppress plant populations, offering solutions to challenges associated with globalization and climate change. However, common features of plant biology complicate its application. Self-limiting methods provide a controlled, reversible path forward.

Effect analysis of S5-interacting genes on rice hybrid sterility using nontransgenic gamete killer

While hybrids between japonica and indica rice exhibit strong heterosis, they often suffer from hybrid sterility (HS). Hybrid fertility of the embryo sac is predominantly regulated by a three-gene system (comprising closely linked ORF3, ORF4 and ORF5) at rice S5 locus. The cooperation of ORF5+ and ORF4+ can result in endoplasmic reticulum (ER) stress and sporophytically kill all embryo sacs, while ORF3+ can gametophytically protect the residing embryo sac. We previously identified four S5-interacting genes (SIGs) using a transgenic line BLORF5+ (Balilla carrying transgenic ORF5+) and a wide compatibility variety Dular (DL or D). Homozygote and hemizygote of ORF5+ transgene had significantly different spikelet fertility (SF), which disturbed the phenotypic effects of SIGs. However, HS effects of SIGs under the endogenous (nontransgenic) gamete killer remained unknown. We formerly constructed a semisterile near isogenic line (NIL) S5-BL/NJ by introgressing S5 fragment of indica rice Nanjing11 (NJ or N, carrying ORF3+ORF4-ORF5+ haplotypes) into the genome of japonica rice Balilla (BL or B, carrying ORF3-ORF4+ORF5- haplotypes). The gamete-protecting effect of ORF3+ in NJ may confuse SF effect of the SIGs, so we knocked out ORF3+ of S5-NJ/NJ and crossed it with BL to get gamete-killing S5-BL/NJΔORF3+, which can kill all (KA) gametes (abbreviated as enS5KA). Compared with the exS5KA line (a NIL carrying ORF5+ transgenic, wihch can kill all gamete), the enS5KA line conferred SIGs a more pronounced SF effect. The enS5KA,SIG-DDDD (four SIGs carry homozygous DL alleles) genotype caused a SF of about 78 %, while SF of exS5KA,SIG-DDDD was only about 62 %. Moreover, all SIGs acted in a sporophytic manner without segregation distortion of genotype. Although enS5KA,SIG-DDDD plants had high SF, the ER stress still existed. The ovule section revealed that enS5KA,SIG-BBBB genotype (four SIGs carry homozygous BL allele, with ER stress and SF < 5 %) caused abnormal degradation of nucellar cells and functional megaspores. In contrast, enS5KA,SIG-DDDD genotype preserved most nucellar cells and functional megaspores. These results lay the foundation for further research on HS mechanism of S5 and SIGs and cloning of candidate genes.

Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated rice Oryza sativa L

Anagenesis accumulates favorable mutations that enable crops to adapt to continually improving artificial production environments, while cladogenesis results in the deposition of beneficial variations across diverse ecotypes. Integrating advantageous genetic variations from diverse evolutionary sources establishes the foundation for the continued genetic improvement of crops. For a long time, rice breeding practices have been guided by the established belief that the Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and subsp. japonica. Integrating elite genetic variants from both subspecies has been a major strategy for genetic improvement. This approach has proven successful through the achievements of temperate japonica breeding programs in China, Japan, and Korea over the past decades. The genetic differentiation within the Asian cultivated rice has been successfully harnessed for heterosis breeding, thereby enhancing rice yield productivity. Genomic investigations have revealed more genetic divergences in the Asian cultivated rice, prompting the proposal of six subgroups within it. This indicates that there is greater potential for uncovering additional genetic divergences and diversity in future breeding practices. Genetic introgression and gene flow among subgroups have led to improvements in agronomic traits within the indica, temperate japonica, and tropical japonica subgroups during the modern rice breeding process. The introgression process has widened the genetic diversity within subgroups and reduced the genetic distance between them, resulting in the creation of new genetic blocks and subpopulations. Artificial introgression has accelerated the evolution process in rice breeding history. Advancements in the study of genetic divergence and diversity in rice offer valuable insights to guide breeding practices. The mini subgroups aus, basmatic, and rayada possess untapped genetic potential but have been poorly studied worldwide; more samples should be further investigated. This information will be invaluable for harnessing these advantageous variations through introgression breeding. Further studying the nature of reproductive barriers among subgroups will enhance our understanding of genetic differentiation, allow us to overcome these barriers and facilitate effective genetic exchange, and even enable us to harness heterosis among subgroups.

Functional constraints of wtf killer meiotic drivers

Killer meiotic drivers are selfish DNA loci that sabotage the gametes that do not inherit them from a driver+/driver- heterozygote. These drivers often employ toxic proteins that target essential cellular functions to cause the destruction of driver- gametes. Identifying the mechanisms of drivers can expand our understanding of infertility and reveal novel insights about the cellular functions targeted by drivers. In this work, we explore the molecular mechanisms underlying the wtf family of killer meiotic drivers found in fission yeasts. Each wtf killer acts using a toxic Wtfpoison protein that can be neutralized by a corresponding Wtfantidote protein. The wtf genes are rapidly evolving and extremely diverse. Here we found that self-assembly of Wtfpoison proteins is broadly conserved and associated with toxicity across the gene family, despite minimal amino acid conservation. In addition, we found the toxicity of Wtfpoison assemblies can be modulated by protein tags designed to increase or decrease the extent of the Wtfpoison assembly, implicating assembly size in toxicity. We also identified a conserved, critical role for the specific co-assembly of the Wtfpoison and Wtfantidote proteins in promoting effective neutralization of Wtfpoison toxicity. Finally, we engineered wtf alleles that encode toxic Wtfpoison proteins that are not effectively neutralized by their corresponding Wtfantidote proteins. The possibility of such self-destructive alleles reveals functional constraints on wtf evolution and suggests similar alleles could be cryptic contributors to infertility in fission yeast populations. As rapidly evolving killer meiotic drivers are widespread in eukaryotes, analogous self-killing drive alleles could contribute to sporadic infertility in many lineages.

Functional constraints of wtf killer meiotic drivers

Killer meiotic drivers are selfish DNA loci that sabotage the gametes that do not inherit them from a driver+/driver- heterozygote. These drivers often employ toxic proteins that target essential cellular functions to cause the destruction of driver- gametes. Identifying the mechanisms of drivers can expand our understanding of infertility and reveal novel insights about the cellular functions targeted by drivers. In this work, we explore the molecular mechanisms underlying the wtf family of killer meiotic drivers found in fission yeasts. Each wtf killer acts using a toxic Wtfpoison protein that can be neutralized by a corresponding Wtfantidote protein. The wtf genes are rapidly evolving and extremely diverse. Here we found that self-assembly of Wtfpoison proteins is broadly conserved and associated with toxicity across the gene family, despite minimal amino acid conservation. In addition, we found the toxicity of Wtfpoison assemblies can be modulated by protein tags designed to increase or decrease the extent of the Wtfpoison assembly, implicating assembly size in toxicity. We also identified a conserved, critical role for the specific co-assembly of the Wtfpoison and Wtfantidote proteins in promoting effective neutralization of Wtfpoison toxicity. Finally, we engineered wtf alleles that encode toxic Wtfpoison proteins that are not effectively neutralized by their corresponding Wtfantidote proteins. The possibility of such self-destructive alleles reveals functional constraints on wtf evolution and suggests similar alleles could be cryptic contributors to infertility in fission yeast populations. As rapidly evolving killer meiotic drivers are widespread in eukaryotes, analogous self-killing drive alleles could contribute to sporadic infertility in many lineages.

Engineering rice genomes towards green super rice

Rice, cultivated for millennia across diverse geographical regions, has witnessed tremendous advancements in recent decades, epitomized by the emergence of Green Super Rice. These efforts aim to address challenges such as climate change, pest and disease threats, and sustainable agriculture. Driven by the advent of multiomics big data, breakthroughs in genomic tools and resources, hybrid rice breeding techniques, and the extensive utilization of green genes, rice genomes are undergoing delicate modifications to produce varieties with high yield, superior quality, enhanced nutrient efficiency, and resilience to pests and environmental stresses, leading to the development of green agriculture in China. Additionally, the utilization of wild relatives and the promotion of genomic breeding approaches have further enriched our understanding of rice improvement. In the future, international efforts to develop next-generation green rice varieties remain both challenging and imperative for the whole community.

Identification of a novel hybrid sterility locus S67 between temperate japonica subgroup and basmati subgroup in Oryza sativa L

Asian cultivated rice (Oryza sativa L.) is the most important cultivated species in the AA genome species of the genus Oryza. basmati is a special and famous subgroup in Asian cultivated rice, and temperate japonica is one of the most important cultivated subgroup, too. However, hybrid sterility hinders the introgression of favorable traits and the utilization of hybrid vigour between the two subgroups. The genetic basis of intraspecific hybrid sterility between temperate japonica and basmati remained elusive. In this study, a novel hybrid sterility locus S67 was identified, which caused hybrid male sterility in hybrids between the temperate japonica rice variety Dianjingyou 1 (DJY1) and the basmati rice variety Dom-sufid. Initial mapping with BC1F1, BC4F1, BC4F2 populations and DNA markers located S67 between RM5362 and K1-40.6 on the long arm of chromosome 1. Genetic analysis confirmed that S67 caused a transmission advantage for the temperate japonica rice S67-te allele in the hybrid offsprings. This result not only fills the gap in the research on hybrid sterility between basmati and temperate japonica, but also lays a good foundation for the systematic study of the genetic nature of hybrid sterility between basmati and other subgroups, as well as the full exploration and utilization of this subgroup through the creation of wide or specific compatibility lines to overcome hybrid sterility. In addition, this result can also help us broaden our understanding of genetic differentiation within Asian cultivated rice and hybrid sterility between inter-subgroups.

Structural duality enables a single protein to act as a toxin-antidote pair for meiotic drive

In sexual reproduction, selfish genetic elements known as killer meiotic drivers (KMDs) bias inheritance by eliminating gametes that do not carry them. The selective killing behavior of most KMDs can be explained by a toxin-antidote model, where a toxin harms all gametes while an antidote provides resistance to the toxin in carriers. This study investigates whether and how the KMD element tdk1 in the fission yeast Schizosaccharomyces pombe deploys this strategy. Intriguingly, tdk1 relies on a single protein product, Tdk1, for both killing and resistance. We show that Tdk1 exists in a nontoxic tetrameric form during vegetative growth and meiosis but transforms into a distinct toxic form in spores. This toxic form acquires the ability to interact with the histone reader Bdf1 and assembles into supramolecular foci that disrupt mitosis in noncarriers after spore germination. In contrast, Tdk1 synthesized during germination of carrier spores is nontoxic and acts as an antidote, dismantling the preformed toxic Tdk1 assemblies. Replacement of the N-terminal region of Tdk1 with a tetramer-forming peptide reveals its dual roles in imposing an autoinhibited tetrameric conformation and facilitating the assembly of supramolecular foci when autoinhibition is released. Moreover, we successfully reconstituted a functional KMD element by combining a construct that exclusively expresses Tdk1 during meiosis ("toxin-only") with another construct that expresses Tdk1 specifically during germination ("antidote-only"). This work uncovers a remarkable example of a single protein employing structural duality to form a toxin-antidote pair, expanding our understanding of the mechanisms underlying toxin-antidote systems.

Applications of CRISPR Technologies in Forestry and Molecular Wood Biotechnology

Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests. This review provides a comprehensive overview of CRISPR applications in forestry, exploring its potential for enhancing disease resistance, improving abiotic stress tolerance, modifying wood properties, and accelerating growth. We discuss the mechanisms and applications of various CRISPR systems, including base editing, prime editing, and multiplexing strategies. Additionally, we highlight recent advances in overcoming key challenges such as reagent delivery and plant regeneration, which are crucial for successful implementation of CRISPR in trees. We also delve into the potential and ethical considerations of using CRISPR gene drive for population-level genetic alterations, as well as the importance of genetic containment strategies for mitigating risks. This review emphasizes the need for continued research, technological advancements, extensive long-term field trials, public engagement, and responsible innovation to fully harness the power of CRISPR for shaping a sustainable future for forests.

Enhanced antimicrobial activity against oral bacteria Actinomyces viscous by cinnamaldehyde emulsion microencapsulated with cyclodextrin glycosyltransferase-catalyzed products

Actinomyces viscous (A. viscous) is well documented as a major cariogenic bacterium in the oral cavity and needs to be inhibited and removed timely. Essential oils (EOs) are recognized as secure antibacterial agents for treating oral diseases, but their volatility and insolubility limit their application. In this study, cinnamaldehyde was screened as the optimum EO for inhibiting the A. viscous growth by a micro-agar dilution method and microencapsulated by cyclodextrin glycosyltransferase (CGTase)-catalyzed products. The antibacterial effects against A. viscous were investigated and compared with the free cinnamaldehyde. Antibacterial diameter, antibacterial efficiency and stability, and time-kill curve results revealed that the cinnamaldehyde emulsion had better antibacterial properties. 1 MIC of the cinnamaldehyde emulsion had an inhibitory zone of 9.92 nm, a 100 % inhibition rate when acting for 2 min or 5 min, and still maintained the same inhibitory effect for 2 years. The extracellular environment showed more pH decrease, conductivity increase, and protein leakage, suggesting damage to the cell membrane. Microstructure and flow cytometric analysis further revealed that the CGTase-catalyzed products induced more changes in the A. viscous membrane integrity. Based on the results, CGTase-catalyzed products can be used as a potential substance for encapsulating EOs for treating oral bacteria.

Evolutionary Modes of wtf Meiotic Driver Genes in Schizosaccharomyces pombe

Killer meiotic drivers are a class of selfish genetic elements that bias inheritance in their favor by destroying meiotic progeny that do not carry them. How killer meiotic drivers evolve is not well understood. In the fission yeast, Schizosaccharomyces pombe, the largest gene family, known as the wtf genes, is a killer meiotic driver family that causes intraspecific hybrid sterility. Here, we investigate how wtf genes evolve using long-read-based genome assemblies of 31 distinct S. pombe natural isolates, which encompass the known genetic diversity of S. pombe. Our analysis, involving nearly 1,000 wtf genes in these isolates, yields a comprehensive portrayal of the intraspecific diversity of wtf genes. Leveraging single-nucleotide polymorphisms in adjacent unique sequences, we pinpoint wtf gene-containing loci that have recently undergone gene conversion events and infer their ancestral state. These events include the revival of wtf pseudogenes, lending support to the notion that gene conversion plays a role in preserving this gene family from extinction. Moreover, our investigation reveals that solo long terminal repeats of retrotransposons, frequently found near wtf genes, can act as recombination arms, influencing the upstream regulatory sequences of wtf genes. Additionally, our exploration of the outer boundaries of wtf genes uncovers a previously unrecognized type of directly oriented repeats flanking wtf genes. These repeats may have facilitated the early expansion of the wtf gene family in S. pombe. Our findings enhance the understanding of the mechanisms influencing the evolution of this killer meiotic driver gene family.

Tetraploid interspecific hybrids between Asian and African rice species restore fertility depending on killer-protector loci for hybrid sterility

Interspecific F1 hybrids between Asian (Oryza sativa) and African rice (Oryza glaberrima) exhibit severe sterility caused by the accumulation of hybrid sterility genes/loci at 15 or more loci. The mechanisms underlying the hybrid sterility genes are largely unknown; however, a few genes associated with the killer-protector system, which is the system most frequently associated with hybrid sterility genes, have been identified. We previously produced fertile plants as tetraploids derived from diploid interspecific F1 hybrids through anther culture; therefore, it was suggested that hybrid sterility could be overcome following tetraploidization. We investigated whether tetraploid interspecific plants produced by crossing are fertile and tested the involvement of hybrid sterility genes in the process. Fertile tetraploid interspecific F1 hybrid plants were obtained by crossing 2 tetraploids of O. sativa and O. glaberrima. To elucidate the relationships between pollen fertility and the hybrid sterility loci in the tetraploid F1 microspores, we performed genetic analyses of the tetraploid F2 hybrids and diploid plants obtained from the microspores of tetraploid interspecific hybrids by anther culture. The result suggested that the tetraploid interspecific hybrids overcame pollen and seed infertility based on the proportion of loci with the killer-protector system present in the tetraploids. The heterozygous hybrid sterility loci with the killer-protector system in the tetraploid segregate the homozygous killed allele (16.7-21.4%), with more than three-quarters of the gametes surviving. We theoretically and experimentally demonstrated that fertile rice progenies can be grown from tetraploid interspecific hybrids.

Teosinte Pollen Drive guides maize diversification and domestication by RNAi

Selfish genetic elements contribute to hybrid incompatibility and bias or 'drive' their own transmission1,2. Chromosomal drive typically functions in asymmetric female meiosis, whereas gene drive is normally post-meiotic and typically found in males. Here, using single-molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Z. mays ssp. mexicana) that depends on RNA interference (RNAi). 22-nucleotide small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1 and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas3, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize4. A survey of maize traditional varieties and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least four chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive probably had a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of 'self' small RNAs in the germ lines of plants and animals.

Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date

The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of quantitative trait locus (QTL) mapping, but single nucleotide polymorphism (SNP)-based GWAS does not fully reach its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice. A total of 44 000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24 414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of <55 kb for major effect genes and <123 kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding.

Selfing Promotes Spread and Introgression of Segregation Distorters in Hermaphroditic Plants

Segregation distorters (SDs) are genetic elements that distort the Mendelian segregation ratio to favor their own transmission and are able to spread even when they incur fitness costs on organisms carrying them. Depending on the biology of the host organisms and the genetic architecture of the SDs, the population dynamics of SDs can be highly variable. Inbreeding is considered an effective mechanism for inhibiting the spread of SDs in populations, and can evolve as a defense mechanism against SDs in some systems. However, we show that inbreeding in the form of selfing in fact promotes the spread of SDs acting as pollen killers in a toxin-antidote system in hermaphroditic plants by two mechanisms: (i) By reducing the effective recombination rate between killer and antidote loci in the two-locus system and (ii) by increasing the proportion of SD alleles in individual flowers, rather than in the general gene-pool. We also show that in rice (Oryza sativa L.), a typical hermaphroditic plant, all molecularly characterized SDs associated with pollen killing were involved in population hybridization and have introgressed across different species. Paradoxically, these loci, which are associated with hybrid incompatibility and can be thought of as Bateson-Dobzhansky-Muller incompatibility loci are expected to reduce gene-flow between species, in fact cross species boundaries more frequently than random loci, and may act as important drivers of introgression.

Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

Cleave and Rescue gamete killers create conditions for gene drive in plants

Gene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed.

Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination

Synthetic gene drives, inspired by natural selfish genetic elements and transmitted to progeny at super-Mendelian (>50%) frequencies, present transformative potential for disseminating traits that benefit humans throughout wild populations, even facing potential fitness costs. Here we constructed a gene drive system in plants called CRISPR-Assisted Inheritance utilizing NPG1 (CAIN), which uses a toxin-antidote mechanism in the male germline to override Mendelian inheritance. Specifically, a guide RNA-Cas9 cassette targets the essential No Pollen Germination 1 (NPG1) gene, serving as the toxin to block pollen germination. A recoded, CRISPR-resistant copy of NPG1 serves as the antidote, providing rescue only in pollen cells that carry the drive. To limit potential consequences of inadvertent release, we used self-pollinating Arabidopsis thaliana as a model. The drive demonstrated a robust 88-99% transmission rate over two successive generations, producing minimal resistance alleles that are unlikely to inhibit drive spread. Our study provides a strong basis for rapid genetic modification or suppression of outcrossing plant populations.

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata

The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.

Cleave and Rescue gamete killers create conditions for gene drive in plants

Gene drive elements promote the spread of linked traits, even when their presence confers a fitness cost to carriers, and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs (the Cleaver/Toxin) that disrupts endogenous versions of an essential gene, and a recoded version of the essential gene resistant to cleavage (the Rescue/Antidote). ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. We demonstrate the essential features of ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61, whose expression is required in male and female gametes for their survival. Resistant (uncleavable but functional) alleles, which can slow or prevent drive, were not observed. Modeling shows plant ClvRs are likely to be robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications in plant breeding, weed control, and conservation are discussed.

Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia

High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.

Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier

Postzygotic reproductive isolation, which results in the irreversible divergence of species, is commonly accompanied by hybrid sterility, necrosis/weakness, or lethality in the F1 or other offspring generations. Here we show that the loss of function of HWS1 and HWS2, a couple of duplicated paralogs, together confer complete interspecific incompatibility between Asian and African rice. Both of these non-Mendelian determinants encode the putative Esa1-associated factor 6 (EAF6) protein, which functions as a characteristic subunit of the histone H4 acetyltransferase complex regulating transcriptional activation via genome-wide histone modification. The proliferating tapetum and inappropriate polar nuclei arrangement cause defective pollen and seeds in F2 hybrid offspring due to the recombinant HWS1/2-mediated misregulation of vitamin (biotin and thiamine) metabolism and lipid synthesis. Evolutionary analysis of HWS1/2 suggests that this gene pair has undergone incomplete lineage sorting (ILS) and multiple gene duplication events during speciation. Our findings have not only uncovered a pair of speciation genes that control hybrid breakdown but also illustrate a passive mechanism that could be scaled up and used in the guidance and optimization of hybrid breeding applications for distant hybridization.

Gene drive in plants emerges from infancy

Selfish genetic elements (SGEs) display biased transmission to offspring. However, their breeding potential has remained obscure. Wang et al. recently reported a natural gene-drive system that can be harnessed to prevent hybrid incompatibility and to develop a synthetic gene-drive (SGD) system for crop improvement.

Transformative Approaches for Sustainable Weed Management: The Power of Gene Drive and CRISPR-Cas9

Weeds can negatively impact crop yields and the ecosystem's health. While many weed management strategies have been developed and deployed, there is a greater need for the development of sustainable methods for employing integrated weed management. Gene drive systems can be used as one of the approaches to suppress the aggressive growth and reproductive behavior of weeds, although their efficacy is yet to be tested. Their popularity in insect pest management has increased, however, with the advent of CRISPR-Cas9 technology, which provides specificity and precision in editing the target gene. This review focuses on the different types of gene drive systems, including the use of CRISPR-Cas9-based systems and their success stories in pest management, while also exploring their possible applications in weed species. Factors that govern the success of a gene drive system in weeds, including the mode of reproduction, the availability of weed genome databases, and well-established transformation protocols are also discussed. Importantly, the risks associated with the release of weed populations with gene drive-bearing alleles into wild populations are also examined, along with the importance of addressing ecological consequences and ethical concerns.

CRISPR/Cas Technology Revolutionizes Crop Breeding

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