One-step creation of CMS lines using a BoCENH3-based haploid induction system in Brassica crop

Advances in gene editing-led route for hybrid breeding in crops

With the global demand for sustainable agriculture on the rise, RNA-guided nuclease technology offers transformative applications in crop breeding. Traditional hybrid breeding methods, like three-line and two-line systems, are often labor-intensive, transgenic, and economically burdensome. While chemical mutagens facilitate these systems, they not only generate weak alleles but also produce strong alleles that induce permanent sterility through random mutagenesis. In contrast, RNA-guided nuclease system, such as clustered regularly interspaced short palindromic repeats (CRISPR)- associated protein (Cas) system, facilitates more efficient hybrid production by inducing male sterility through targeted genome modifications in male sterility genes, such as MS8, MS10, MS26, and MS45 which allows precise manipulation of pollen development or pollen abortion in various crops. Moreover, this approach allows haploid induction for the rapid generation of recombinant and homozygous lines from hybrid parents by editing essential genes, like CENH3, MTL/NLD/PLA, and DMP, resulting in high-yield, transgene-free hybrids. Additionally, this system supports synthetic apomixis induction by employing the MiMe (Mitosis instead of Meiosis) strategy, coupled with parthenogenesis in hybrid plants, to create heterozygous lines and retain hybrid vigor in subsequent generations. RNA-guided nuclease-induced synthetic apomixis also enables genome stacking for autopolyploid progressive heterosis via clonal gamete production for trait maintenance to enhance crop adaptability without compromising yield. Additionally, CRISPR-Cas-mediated de novo domestication of wild relatives, along with recent advances to circumvent tissue culture- recalcitrance and -dependency through heterologous expression of morphogenic regulators, holds great promise for incorporating diversity-enriched germplasm into the breeding programs. These approaches aim to generate elite hybrids adapted to dynamic environments and address the anticipated challenges of food insecurity.

Advances in Genome Editing Through Haploid Induction Systems

Groundbreaking advances in gene editing technologies are transforming modern plant breeding by enabling precise genetic modifications that dramatically accelerate crop improvement. Haploid and diploid induction systems have emerged as particularly powerful tools in this landscape, offering both efficient gene editing capabilities and rapid production of homozygous lines while seamlessly integrating with the advanced genome-editing platforms such as CRISPR-Cas systems. This review synthesizes the current state of knowledge regarding the mechanisms, applications, and recent progress in haploid and diploid induction systems for gene editing. We examine their transformative potential for enhancing genetic gains and compressing breeding timelines, with significant implications for global food security. Additionally, we provide a critical analysis of emerging challenges of genome editing in crops and outline promising future directions for research and development.

Past innovations and future possibilities in plant chromosome engineering

Plant chromosome engineering has emerged as a pivotal tool in modern plant breeding, facilitating the transfer of desirable traits through the incorporation of alien chromosome fragments into plants. Here, we provide a comprehensive overview of the past achievements, current methodologies and future prospects of plant chromosome engineering. We begin by examining the successful integration of specific examples such as the incorporation of rye chromosome segments (e.g. the 1BL/1RS translocation), Dasypyrum villosum segments (e.g. the 6VS segment for powdery mildew resistance), Thinopyrum intermedium segments (e.g. rust resistance genes) and Thinopyrum elongatum segments (e.g. Fusarium head blight resistance genes). In addition to trait transfer, advancements in plant centromere engineering have opened new possibilities for chromosomal manipulation. This includes the development of plant minichromosomes via centromere-mediated techniques, the generation of haploids through CENH3 gene editing, and the induction of aneuploidy using KaryoCreate. The advent of CRISPR/Cas technology has further revolutionized chromosome engineering, enabling large-scale chromosomal rearrangements, such as inversions and translocations, as well as enabling targeted insertion of large DNA fragments and increasing genetic recombination frequency. These advancements have significantly expanded the toolkit for genetic improvement in plants, opening new horizons for the future of plant breeding.

The haploid induction ability analysis of various mutation of OsMATL and OsDMPs in rice

BACKGROUND

The high-frequency induction rate of haploid is crucial for double haploid (DH) breeding. The combination of multiple haploid-induced genes, such as ZmPLA1/MATL/NLD and ZmDMP, can synergistically enhance the haploid induction rate (HIR) in maize. However, the potential synergistic effects between OsMATL and OsDMP genes in rice remain unclear.

RESULTS

Knocking out OsMATL in both HuaHang No.48 (HH48) and Nipponbare (NIP) cultivars resulted in reduced seed setting rate (SSR) and haploid induction (HI). Notably, in this study, the HI capacity of OsMATL knockout mutants in indica rice surpassed that of japonica rice knockout mutants, with the proton active site in the third exon exhibiting a higher HIR compared to the first and fourth exons. Furthermore, when OsDMP1 or OsDMP3 was combined with OsMATL, they increased HIR, and an antagonistic relationship was observed between HIR and SSR in HH48 matl4dmp1 and HH48 matl4dmp3.

CONCLUSIONS

In rice, the proton active site in the third exon of OsMATL exhibited higher induction efficiency, and OsDMP1 or OsDMP3 exerted a synergistic effect with OsMATL. These findings provide a foundation for further research on DH breeding in rice.

Past and future of cytoplasmic male sterility and heterosis breeding in crop plants

Plant breeding needs to embrace genetic innovations to ensure stability in crop yields under fluctuating climatic conditions. Development of commercial hybrid varieties has proven to be a sustainable and economical alternative to deliver superior yield, quality and resistance with uniformity in a number of food crops. Cytoplasmic male sterility (CMS), a maternally inherited inability to produce functional pollen, facilitates a three-line system for efficient hybrid seed production strategies in crops. The CMS system has illustrated its potential as a robust pollination control mechanism to support the billion-dollar seed industry. In plants, CMS arises due to a genomic conflict between mitochondrial open reading frames (orfs) and nuclear-encoding restoration-of-fertility (Rf) genes, leading to floral abnormalities and pollen sterility. Research on pollen sterility and fertility restoration provides deeper insights into cytoplasmic-nuclear interplay in plants and elucidates key molecular targets for hybrid breeding in crops. More recently, programmable gene editing (e.g., TALEN, CRISPR-Cas) has emerged as a promising tool to functionally validate CMS and Rf genes and obviate the need for pollen donors or Rf-genes for hybrid breeding. Modern genomic prediction models have allowed establishment of high-performing heterotic groups and patterns for sustaining long-term gain in hybrid breeding. This article reviews latest discoveries elucidating the molecular mechanisms behind CMS and fertility restoration in plants. We then present our perspective on how evolving genetic technologies are contributing to advance fundamental knowledge of the CMS-Rf genetic system for producing crop hybrids with high heterosis.

Species-wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity using Arabidopsis thaliana as a model species. A reanalysis of whole-genome resequencing data of 1,541 representative accessions shows that the genetic diversity among the mitochondrial genomes is eight times lower than among the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60 A. thaliana accessions with the nuclear genomes (nucleotypes) of four A. thaliana accessions to create a panel of 232 cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a method to reveal plasmotypic effects. Within A. thaliana, several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species.

Application of genome editing in plant reproductive biology: recent advances and challenges

KEY MESSAGE

This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.

Plant kinetochore complex: composition, function, and regulation

The kinetochore complex, an important protein assembly situated on the centromere, plays a pivotal role in chromosome segregation during cell division. Like in animals and fungi, the plant kinetochore complex is important for maintaining chromosome stability, regulating microtubule attachment, executing error correction mechanisms, and participating in signaling pathways to ensure accurate chromosome segregation. This review summarizes the composition, function, and regulation of the plant kinetochore complex, emphasizing the interactions of kinetochore proteins with centromeric DNAs (cenDNAs) and RNAs (cenRNAs). Additionally, the applications of the centromeric histone H3 variant (the core kinetochore protein CENH3, first identified as CENP-A in mammals) in the generation of ploidy-variable plants and synthesis of plant artificial chromosomes (PACs) are discussed. The review serves as a comprehensive roadmap for researchers delving into plant kinetochore exploration, highlighting the potential of kinetochore proteins in driving technological innovations in synthetic genomics and plant biotechnology.

Haploid induction: an overview of parental factor manipulation during seed formation

In plants, in vivo haploid induction has gained increasing attention for its significant potential applications in crop breeding and genetic research. This strategy reduces the chromosome number in progeny after fertilization, enabling the rapid production of homozygous plants through double haploidization, contrasting with traditional inbreeding over successive generations. Haploidy typically initiates at the onset of seed development, with several key genes identified as paternal or maternal factors that play critical roles during meiosis, fertilization, gamete communication, and chromosome integrity maintenance. The insights gained have led to the development of efficient haploid inducer lines. However, the molecular and genetic mechanisms underlying these factors vary considerably, making it challenging to create broadly applicable haploidy induction systems for plants. In this minireview, we summarize recent discoveries and advances in paternal and maternal haploid induction factors, examining their current understanding and functionalities to further develop efficient haploid inducer systems through the application of parental factor manipulation.