Fertilization and uniparental chromosome elimination during crosses with maize haploid inducers

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.

Doubled haploid technology and synthetic apomixis: Recent advances and applications in future crop breeding

Doubled haploid (DH) technology and synthetic apomixis approaches can considerably shorten breeding cycles and enhance breeding efficiency. Compared with traditional breeding methods, DH technology offers the advantage of rapidly generating inbred lines, while synthetic apomixis can effectively fix hybrid vigor. In this review, we focus on (i) recent advances in identifying and characterizing genes responsible for haploid induction (HI), (ii) the molecular mechanisms of HI, (iii) spontaneous haploid genome doubling, and (iv) crop synthetic apomixis. We also discuss the challenges and potential solutions for future crop breeding programs utilizing DH technology and synthetic apomixis. Finally, we provide our perspectives about how to integrate DH and synthetic apomixis for precision breeding and de novo domestication.

Haploid identification in maize

Doubled haploid (DH) line production through in vivo maternal haploid induction is widely adopted in maize breeding programs. The established protocol for DH production includes four steps namely in vivo maternal haploid induction, haploid identification, genome doubling of haploid, and self-fertilization of doubled haploids. Since modern haploid inducers still produce relatively small portion of haploids among undesirable hybrid kernels, haploid identification is typically laborious, costly, and time-consuming, making this step the second foremost in the DH technique. This manuscript reviews numerous methods for haploid identification from different approaches including the innate differences in haploids and diploids, biomarkers integrated in haploid inducers, and automated seed sorting. The phenotypic differentiation, genetic basis, advantages, and limitations of each biomarker system are highlighted. Several approaches of automated seed sorting from different research groups are also discussed regarding the platform or instrument used, sorting time, accuracy, advantages, limitations, and challenges before they go through commercialization. The past haploid selection was focusing on finding the distinguishable marker systems with the key to effectiveness. The current haploid selection is adopting multiple reliable biomarker systems with the key to efficiency while seeking the possibility for automation. Fully automated high-throughput haploid sorting would be promising in near future with the key to robustness with retaining the feasible level of accuracy. The system that can meet between three major constraints (time, workforce, and budget) and the sorting scale would be the best option.

Accelerating haploid induction rate and haploid validation through marker-assisted selection for qhir1 and qhir8 in maize

Doubled haploid (DH) technology becomes more routinely applied in maize hybrid breeding. However, some issues in haploid induction and identification persist, requiring resolution to optimize DH production. Our objective was to implement simultaneous marker-assisted selection (MAS) for qhir1 (MTL/ZmPLA1/NLD) and qhir8 (ZmDMP) using TaqMan assay in F2 generation of four BHI306-derived tropical × temperate inducer families. We also aimed to assess their haploid induction rate (HIR) in the F3 generation as a phenotypic response to MAS. We highlighted remarkable increases in HIR of each inducer family. Genotypes carrying qhir1 and qhir8 exhibited 1 - 3-fold higher haploid frequency than those carrying only qhir1. Additionally, the qhir1 marker was employed for verifying putative haploid seedlings at 7 days after planting. Flow cytometric analysis served as the gold standard test to assess the accuracy of the R1-nj and the qhir1 marker. The qhir1 marker showed high accuracy and may be integrated in multiple haploid identifications at early seedling stage succeeding pre-haploid sorting via R1-nj marker.

Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.

Paternal chromosome elimination of inducer triggers induction of double haploids in Brassica napus

A synthetic octoploid rapeseed, Y3380, induces maternal doubled haploids when used as a pollen donor to pollinate plant. However, the mechanism underlying doubled haploid formation remains elusive. We speculated that double haploid induction occurs as the inducer line's chromosomes pass to the maternal egg cell, and the zygote is formed through fertilization. In the process of zygotic mitosis, the paternal chromosome is specifically eliminated. Part of the paternal gene might have infiltrated the maternal genome through homologous exchange during the elimination process. Then, the zygote haploid genome doubles (early haploid doubling, EH phenomenon), and the doubled zygote continues to develop into a complete embryo, finally forming doubled haploid offspring. To test our hypothesis, in the current study, the octoploid Y3380 line was back bred with the 4122-cp4-EPSPS exogenous gene used as a marker into hexaploid Y3380-cp4-EPSPS as paternal material to pollinate three different maternal materials. The fertilization process of crossing between the inducer line and the maternal parent was observed 48 h after pollination, and the fertilization rate reached 97.92% and 98.72%. After 12 d of pollination, the presence of cp4-EPSPS in the embryo was detected by in situ PCR, and at 13-23 d after pollination, the probability of F1 embryos containing cp4-EPSPS gene was up to 97.27%, but then declined gradually to 0% at 23-33 d. At the same time, the expression of cp4-EPSPS was observed by immunofluorescence in the 3rd to 29th day embryo. As the embryos developed, cp4-EPSPS marker genes were constantly lost, accompanied by embryonic death. After 30 d, the presence of cp4-EPSPS was not detected in surviving embryos. Meanwhile, SNP detection of induced offspring confirmed the existence of double haploids, further indicating that the induction process was caused by the loss of specificity of the paternal chromosome. The tetraploid-induced offspring showed infiltration of the induced line gene loci, with heterozygosity and homozygosity. Results indicated that the induced line chromosomes were eliminated during embryonic development, and the maternal haploid chromosomes were synchronously doubled in the embryo. These findings support our hypothesis and lay a theoretical foundation for further localization or cloning of functional genes involved in double haploid induction in rapeseed.

Haploid Induction in Indica Rice: Exploring New Opportunities

Haploid plants are of significant interest to crop breeders due to their ability to expedite the development of inbred lines. Chromosome-doubling of haploids, produced by either in vitro or in vivo methods, results in fully homozygous doubled haploids. For nearly five decades, in vitro methods of anther and microspore culture have been attempted in many crops. In rice, in vitro methods are used with some success in japonica cultivars, although indica types have remained recalcitrant to a large extent. This review aims to explore the reasons for the lack of success of in vitro methods in indica rice and discuss new advancements in in vivo haploid induction protocols in other cereals and their relevance to rice. In particular, the current level of understanding of in vivo haploid inducer systems that utilize MTL and CENH3 mutants is analyzed in detail. One notable advantage of in vivo haploid induction systems is that they do not require tissue culture competence. This makes these methods more accessible and potentially transformative for research, offering a pragmatic approach to improving indica rice cultivars. By embracing these in vivo methods and harnessing the power of gene editing technologies like CRISPR/Cas9 systems, breeders can reshape their approach to indica rice improvement.

Heat stress promotes haploid formation during CENH3-mediated genome elimination in Arabidopsis

Impaired activity of centromeric histone CENH3 causes inaccurate chromosome segregation and in crosses between the Arabidopsis recombinant CENH3 mutant GFP-tailswap and CENH3G83E with wild-type pollen it results in chromosome loss with the formation of haploids. This genome elimination in the zygote and embryo is not absolute as also aneuploid and diploid progeny is formed. Here, we report that a temporal and moderate heat stress during fertilization and early embryogenesis shifts the ratio in favour of haploid progeny in CENH3 mutant lines. Micronuclei formation, a proxy for genome elimination, was similar in control and heat-treated flowers, indicating that heat-induced seed abortion occurred at a late stage during the development of the seed. In the seeds derived from heat-treated crosses, the endosperm did not cellularize and many seeds aborted. Haploid seeds were formed, however, resulting in increased frequencies of haploids in CENH3-mediated genome elimination crosses performed under heat stress. Therefore, heat stress application is a selective force during genome elimination that promotes haploid formation and may be used to improve the development and efficacy of in vivo haploid induction systems.

Brassica napus Haploid and Double Haploid Production and Its Latest Applications

Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.

The Roads to Haploid Embryogenesis

Although zygotic embryogenesis is usually studied in the field of seed biology, great attention has been paid to the methods used to generate haploid embryos due to their applications in crop breeding. These mainly include two methods for haploid embryogenesis: in vitro microspore embryogenesis and in vivo haploid embryogenesis. Although microspore culture systems and maize haploid induction systems were discovered in the 1960s, little is known about the molecular mechanisms underlying haploid formation. In recent years, major breakthroughs have been made in in vivo haploid induction systems, and several key factors, such as the matrilineal (MTL), baby boom (BBM), domain of unknown function 679 membrane protein (DMP), and egg cell-specific (ECS) that trigger in vivo haploid embryo production in both the crops and Arabidopsis models have been identified. The discovery of these haploid inducers indicates that haploid embryogenesis is highly related to gamete development, fertilization, and genome stability in ealry embryos. Here, based on recent efforts to identify key players in haploid embryogenesis and to understand its molecular mechanisms, we summarize the different paths to haploid embryogenesis, and we discuss the mechanisms of haploid generation and its potential applications in crop breeding. Although these haploid-inducing factors could assist egg cells in bypassing fertilization to initiate embryogenesis or trigger genome elimination in zygotes after fertilization to form haploid embryos, the fertilization of central cells to form endosperms is a prerequisite step for haploid formation. Deciphering the molecular and cellular mechanisms for haploid embryogenesis, increasing the haploid induction efficiency, and establishing haploid induction systems in other crops are critical for promoting the application of haploid technology in crop breeding, and these should be addressed in further studies.

Co-expression of transcription factors ZmC1 and ZmR2 establishes an efficient and accurate haploid embryo identification system in maize

Because of their high efficiency during chromosome doubling, immature haploid maize (Zea mays L.) embryos are useful for doubled haploid production. The R1-nj marker is commonly used in doubled haploid breeding and has improved the efficiency of haploid identification. However, its effectiveness is limited by genetic background and environmental factors. We addressed this technical challenge by developing an efficient and accurate haploid embryo identification marker through co-expression of two transcription factor genes (ZmC1 and ZmR2) driven by the embryo-aleurone-specific bidirectional promoter P_ZmBD1 ; these factors can activate anthocyanin biosynthesis in the embryo and aleurone layer during early seed development. We developed a new haploid inducer, Maize Anthocyanin Gene InduCer 1 (MAGIC1), by introducing the transgenes into the haploid inducer line CAU6. MAGIC1 could identify haploids at 12 days after pollination, which is nine days earlier than CAU6. Importantly, MAGIC1 increased haploid identification accuracy to 99.1%, compared with 88.3% for CAU6. In addition, MAGIC1 could effectively overcome the inhibition of anthocyanin synthesis in some germplasms. Furthermore, an upgraded anthocyanin marker was developed from ZmC1 and ZmR2 to generate MAGIC2, which could identify haploids from diploids due to differential anthocyanin accumulation in immature embryos, coleoptiles, sheaths, roots, leaves, and dry seeds. This haploid identification system is more efficient and accurate than the conventional R1-nj-based method, and it simplifies the haploid identification process. Therefore, this system provides technical support for large-scale doubled haploid line production.

Rapid and Synchronous Breeding of Cytoplasmic Male Sterile and Maintainer Line Through Mitochondrial DNA Rearrangement Using Doubled Haploid Inducer in Brassica napus

When homozygously fertile plants were induced using doubled haploid (DH) induction lines Y3380 and Y3560, the morphology of the induced F1 generation was basically consistent with the female parent, but the fertility was separated, showing characteristics similar to cytoplasmic male sterile (CMS) and maintainer lines. In this study, the morphology, fertility, ploidy, and cytoplasm genotype of the induced progeny were identified, and the results showed that the sterile progeny was polima cytoplasm sterile (pol CMS) and the fertile progeny was nap cytoplasm. The molecular marker and test-cross experimental results showed that the fertile progeny did not carry the restorer gene of pol CMS and the genetic distance between the female parent and the offspring was 0.002. This suggested that those inductions which produced sterile and fertile progeny were coordinated to CMS and maintainer lines. Through the co-linearity analysis of the mitochondrial DNA (mtDNA), it was found that the rearrangement of mtDNA by DH induction was the key factor that caused the transformation of fertility (nap) into sterility (pol). Also, when heterozygous females were induced with DH induction lines, the induction F2 generation also showed the segregation of fertile and sterile lines, and the genetic distance between sterile and fertile lines was approximately 0.075. Therefore, the induction line can induce different types of female parents, and the breeding of the sterile line and the maintainer line can be achieved through the rapid synchronization of sister crosses and self-crosses. The induction of DH inducer in B. napus can provide a new model for the innovation of germplasm resources and open up a new way for its application.

Overexpression of Modified CENH3 in Maize Stock6-Derived Inducer Lines Can Effectively Improve Maternal Haploid Induction Rates

Maize (Zea mays) doubled haploid (DH) breeding is a technology that can efficiently generate inbred lines with homozygous genetic backgrounds. Haploids are usually produced through in vivo induction by haploid inducer lines in maize. Currently, two approaches are usually used to develop maize haploid inducer lines. One is through the conventional breeding improvement based on the Stock6 germplasm, and this strategy is extensively used to induce maternal haploids in commercial maize DH breeding. Another strategy, newly developed but less utilized so far, is by genetic manipulation of the Centromeric Histone3 (CENH3) in regular lines. However, whether both approaches can be combined to develop the haploid inducer line with higher maternal haploid induction rate (HIR) has not been reported. In this study, we manipulated the Stock6-derived inducer lines by overexpressing maize CENH3 fused with different fluorescent protein tags and found that the engineered Stock6-derived lines showed an obvious increase in the maternal HIR. Intriguingly, this above strategy could be further improved by substituting a tail-altered CENH3 for the full-length CENH3 in the tagged expression cassette, resulting in a maternal HIR up to 16.3% that was increased by ~6.1% than Stock6-derived lines control. These results suggested that integration of two in vivo haploid induction methods could rapidly and effectively improve the maternal HIRs of maize Stock6-derived inducer lines, and provided a potentially feasible solution for further optimizing the process of commercial maize DH breeding.

Options for Engineering Apomixis in Plants

In plants, embryogenesis and reproduction are not strictly dependent on fertilization. Several species can produce embryos in seeds asexually, a process known as apomixis. Apomixis is defined as clonal asexual reproduction through seeds, whereby the progeny is identical to the maternal genotype, and provides valuable opportunities for developing superior cultivars, as its induction in agricultural crops can facilitate the development and maintenance of elite hybrid genotypes. In this review, we summarize the current understanding of apomixis and highlight the successful introduction of apomixis methods into sexual crops. In addition, we discuss several genes whose overexpression can induce somatic embryogenesis as candidate genes to induce parthenogenesis, a unique reproductive method of gametophytic apomixis. We also summarize three schemes to achieve engineered apomixis, which will offer more opportunities for the realization of apomictic reproduction.

Loss-of-function alleles of ZmPLD3 cause haploid induction in maize

Doubled haploid technology has been widely applied to multiple plant species and is recognized as one of the most important technologies for improving crop breeding efficiency. Although mutations in MATRILINEAL/Zea mays PHOSPHOLIPASE A1/NOT LIKE DAD (MTL/ZmPLA1/NLD) and Zea mays DOMAIN OF UNKNOWN FUNCTION 679 MEMBRANE PROTEIN (ZmDMP) have been shown to generate haploids in maize, knowledge of the genetic basis of haploid induction (HI) remains incomplete. Therefore, cloning of new genes underlying HI is important for further elucidating its genetic architecture. Here, we found that loss-of-function mutations of Zea mays PHOSPHOLIPASE D3 (ZmPLD3), one of the members from the phospholipase D subfamily, could trigger maternal HI in maize. ZmPLD3 was identified through a reverse genetic strategy based on analysis of pollen-specifically expressed phospholipases, followed by validation through the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR-Cas9) system. Mutations of ZmPLD3 resulted in a haploid induction rate (HIR) similar to that of mtl/zmpla1/nld and showed synergistic effects rather than functional redundancy on tripling the HIR (from 1.19% to 4.13%) in the presence of mtl/zmpla1/nld. RNA-seq profiling of mature pollen indicated that a large number of pollen-specific differentially expressed genes were enriched in processes related to gametogenesis development, such as pollen tube development and cell communication, during the double-fertilization process. In addition, ZmPLD3 is highly conserved among cereals, highlighting the potential application of these in vivo haploid-inducer lines for other important crop plant species. Collectively, our discovery identifies a novel gene underlying in vivo maternal HI and provides possibility of breeding haploid inducers with further improved HIR.

Genetic characteristics and ploidy trigger the high inducibility of double haploid (DH) inducer in Brassica napus

BACKGROUND

Our recently reported doubled haploid (DH) induction lines e.g., Y3380 and Y3560 are allo-octoploid (AAAACCCC, 2n = 8× ≈ 76), which can induce the maternal parent to produce DH individuals. Whether this induction process is related to the production of aneuploid gametes form male parent and genetic characteristics of the male parent has not been reported yet.

RESULTS

Somatic chromosome counts of DH inducer parents, female wax-less parent (W1A) and their F₁ hybrid individuals revealed the reliability of flow cytometry analysis. Y3560 has normal chromosome behavior in metaphase I and anaphase I, but chromosome division was not synchronized in the tetrad period. Individual phenotypic identification and flow cytometric fluorescence measurement of F₁ individual and parents revealed that DH individuals can be distinguished on the basis of waxiness trait. The results of phenotypic identification and flow cytometry can identify the homozygotes or heterozygotes of F₁ generation individuals. The data of SNP genotyping coupled with phenotypic waxiness trait revealed that the genetic distance between W1A and F₁ homozygotes were smaller as compared to their heterozygotes. It was found that compared with allo-octoploids, aneuploidy from allo-octoploid segregation did not significantly increase the DH induction rate, but reduced male infiltration rate and heterozygous site rate of induced F₁ generation. The ploidy, SNP genotyping and flow cytometry results cumulatively shows that DH induction is attributed to the key genes regulation from the parents of Y3560 and Y3380, which significantly increase the induction efficiency as compared to ploidy.

CONCLUSION

Based on our findings, we hypothesize that genetic characteristics and aneuploidy play an important role in the induction of DH individuals in Brassca napus, and the induction process has been explored. It provides an important insight for us to locate and clone the genes that regulate the inducibility in the later stage.

Advances in Gene Editing of Haploid Tissues in Crops

Emerging threats of climate change require the rapid development of improved varieties with a higher tolerance to abiotic and biotic factors. Despite the success of traditional agricultural practices, novel techniques for precise manipulation of the crop's genome are needed. Doubled haploid (DH) methods have been used for decades in major crops to fix desired alleles in elite backgrounds in a short time. DH plants are also widely used for mapping of the quantitative trait loci (QTLs), marker-assisted selection (MAS), genomic selection (GS), and hybrid production. Recent discoveries of genes responsible for haploid induction (HI) allowed engineering this trait through gene editing (GE) in non-inducer varieties of different crops. Direct editing of gametes or haploid embryos increases GE efficiency by generating null homozygous plants following chromosome doubling. Increased understanding of the underlying genetic mechanisms responsible for spontaneous chromosome doubling in haploid plants may allow transferring this trait to different elite varieties. Overall, further improvement in the efficiency of the DH technology combined with the optimized GE could accelerate breeding efforts of the major crops.

Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.

Maize In Planta Haploid Inducer Lines: A Cornerstone for Doubled Haploid Technology

Doubled haploid (DH) technology produces strictly homozygous fertile plant thanks to doubling the chromosomes of a haploid embryo/seedling. Haploid embryos are derived from either male or female germ line cells and hold only half the number of chromosomes found in somatic plant tissues, albeit in a recombinant form due to meiotic genetic shuffling. DH production allows to rapidly fix these recombinant haploid genomes in the form of perfectly homozygous plants (inbred lines), which are produced in two rather than six or more generations. Thus, DH breeding enables fast evaluation of phenotypic traits on homogenous progeny. While for most crops haploid embryos are produced by costly and often genotype-dependent in vitro methods, for maize, two unique in planta systems are available to induce haploid embryos directly in the seed. Two "haploid inducer lines", identified from spontaneous maize mutants, are able to induce embryos of paternal or maternal origin. Although effortless crosses with lines of interest are sufficient to trigger haploid embryos, substantial improvements were necessary to bring DH technology to large scale production. They include the development of modern haploid inducer lines with high induction rates (8-12%), and methods to sort kernels with haploid embryos from the normal ones. Chromosome doubling represents also a crucial step in the DH process. Recent identification of genomic loci involved in spontaneous doubling opens up perspectives for a fully in planta DH pipeline in maize. Although discovered more than 60 years ago, maize haploid inducer lines still make headlines thanks to novel applications and findings. Indeed, maternal haploid induction was elegantly diverted to deliver genome editing machinery in germplasm recalcitrant to transformation techniques. The recent discovery of two molecular players controlling haploid induction allowed to revisit the mechanistic basis of maize maternal haploid induction and to successfully translate haploid induction ability to other crops.

Understanding and exploiting uniparental genome elimination in plants: insights from Arabidopsis thaliana

Uniparental genome elimination (UGE) refers to the preferential exclusion of one set of the parental chromosome complement during embryogenesis following successful fertilization, giving rise to uniparental haploid progeny. This artificially induced phenomenon was documented as one of the consequences of distant (wide) hybridization in plants. Ten decades since its discovery, attempts to unravel the molecular mechanism behind this process remained elusive due to a lack of genetic tools and genomic resources in the species exhibiting UGE. Hence, its successful adoption in agronomic crops for in planta (in vivo) haploid production remains implausible. Recently, Arabidopsis thaliana has emerged as a model system to unravel the molecular basis of UGE. It is now possible to simulate the genetic consequences of distant crosses in an A. thaliana intraspecific cross by a simple modification of centromeres, via the manipulation of the centromere-specific histone H3 variant gene, CENH3. Thus, the experimental advantages conferred by A. thaliana have been used to elucidate and exploit the benefits of UGE in crop breeding. In this review, we discuss developments and prospects of CENH3 gene-mediated UGE and other in planta haploid induction strategies to illustrate its potential in expediting plant breeding and genetics in A. thaliana and other model plants.

Maize transformation: history, progress, and perspectives

Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.

Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

BACKGROUND

Artificial synthesis of octoploid rapeseed double haploid (DH) induction lines Y3380 and Y3560 was made possible by interspecific hybridization and genome doubling techniques. Production of pure lines by DH induction provides a new way to achieve homozygosity earlier in B.napus. Previously, the mechanism of induction, and whether the induction has obvious maternal genotypic differences or not, are not known so far.

RESULTS

In this study, different karyogene and cytoplasmic genotype of B.napus were pollinated with the previously reported DH inducers e.g. Y3380 and Y3560. Our study presents a fine comparison of different cytoplasmic genotypes hybridization to unravel the mechanism of DH induction. Ploidy identification, fertility and SSR marker analysis of induced F₁ generation, revealed that ploidy and phenotype of the induced F₁ plants were consistent with that type of maternal, rather than paternal parent. The SNP chip analysis revealed that induction efficiency of DH inducers were affected by the karyogene when the maternal cytoplasmic genotypes were the same. However, DH induction efficiency was also affected by cytoplasmic genotype when the karyogenes were same, and the offspring of the ogura cytoplasm showed high frequency inducer gene hybridization or low-frequency infiltration.

CONCLUSION

The induction effect is influenced by the interaction between maternal karyogene and cytoplasmic genotype, and the results from the partial hybridization of progeny chromosomes indicate that the induction process may be attributed to the selective elimination of paternal chromosome. This study provides a basis for exploring the mechanism of DH inducer in B.napus, and provides new insights for utilization of inducers in molecular breeding.

Haploid induction and its application in maize breeding

Maize is a heterosis-utilizing crop species, and the application of maize hybrids has significantly improved total maize yields worldwide. Breeding pure lines is the most important part of heterosis utilization. The double haploid (DH) breeding technology is the approach rising recently in breeding pure lines; compared to the conventional recurrent-selfing method, it can significantly accelerate the crop breeding process. Similar to molecular breeding and transgenic techniques, maize DH breeding has been playing an increasingly important role in commercial breeding and is becoming the core technique in modern maize breeding. In this review, we summarize recent progress in maize DH breeding and put forth our opinions on the future development of double haploid techniques in modern maize breeding.

Improving the sorting efficiency of maize haploid kernels using an NMR-based method with oil content double thresholds

BACKGROUND

Maize haploid breeding technology can be used to rapidly develop homozygous lines, significantly shorten the breeding cycle and improve breeding efficiency. Rapid and accurate sorting haploid kernels is a prerequisite for the large-scale application of this technology. At present, the automatic haploid sorting based on nuclear magnetic resonance (NMR) using a single threshold method has been realized. However, embryo-aborted (EmA) kernels are usually produced during in vivo haploid induction, and both haploids and EmA kernels have lower oil content and are separated together using a single threshold method based on NMR. This leads to a higher haploid false discrimination rate (FDR) and requires secondary manual sorting to select the haploid kernels from the mixtures, which increases the sorting cost and decreases the haploid sorting efficiency. In order to improve the correct discrimination rate (CDR) in sorting haploids, a method to distinguish EmA kernels is required.

RESULTS

Single kernel weight and oil content were measured for the diploid, haploid, and EmA kernels derived from three maize hybrids and nine inbred lines by in vivo induction. The results showed that the distribution of oil content showed defined boundaries between the three types of kernels, while the single kernel weight didn't. According to the distribution of oil content in the three types of kernels, a double-threshold method was proposed to distinguish the embryo-aborted kernels, haploid and diploid kernels based on NMR and their oil content. The double thresholds were set based on the minimum oil content of diploid kernels and the maximum content of EmA kernels as the upper and lower boundary values, respectively. The CDR of EmA kernels in different maize materials was > 97.8%, and the average FDR was reduced by 27.9 percent.

CONCLUSIONS

The oil content is an appropriate indicator to discriminate diploid, haploid and EmA kernels. An oil content double-threshold method based on NMR was first developed in this study to identify the three types of kernels. This methodology could reduce the FDR of haploids and improve the sorting efficiency of automated sorting system. Thus, this technique represents a potentially efficient method for haploid sorting and provides a reference for the process of automated sorting of haploid kernels with high efficiency using NMR.

Puzzling out plant reproduction by haploid induction for innovations in plant breeding

Mixing maternal and paternal genomes in embryos is not only responsible for the evolutionary success of sexual reproduction, but is also a cornerstone of plant breeding. However, once an interesting gene combination is obtained, further genetic mixing is problematic. To rapidly fix genetic information, doubled haploid plants can be produced: haploid embryos having solely the genetic information from one parent are allowed to develop, and chromosome doubling generates fully homozygous plants. A powerful path to the production of doubled haploids is based on haploid inducer lines. A simple cross between a haploid inducer line and the line with gene combinations to be fixed will trigger haploid embryo development. However, the exact mechanism behind in planta haploid induction remains an enduring mystery. The recent discoveries of molecular actors triggering haploid induction in the maize crop and the model Arabidopsis thaliana pinpoint an essential role of processes related to gamete development, gamete interactions and genome stability. These findings enabled translation of haploid induction capacity to other crops as well as the use of haploid inducer lines to deliver genome editing machinery into various crop varieties. These recent advances not only hold promise for the next generations of plant breeding strategies, but they also provide a deeper insight into the fundamental bases of sexual reproduction in plants.

Breeding Maize Maternal Haploid Inducers

Maize doubled haploid (DH) lines are usually created in vivo, through crosses with maternal haploid inducers. These inducers have the inherent ability of generating seeds with haploid embryos when used to pollinate other genotypes. The resulting haploid plants are treated with a doubling agent and self-pollinated, producing completely homozygous seeds. This rapid method of inbred line production reduces the length of breeding cycles and, consequently, increases genetic gain. Such advantages explain the wide adoption of this technique by large, well-established maize breeding programs. However, a slower rate of adoption was observed in medium to small-scale breeding programs. The high price and/or lack of environmental adaptation of inducers available for licensing, or the poor performance of those free of cost, might explain why smaller operations did not take full advantage of this technique. The lack of adapted inducers is especially felt in tropical countries, where inducer breeding efforts are more recent. Therefore, defining optimal breeding approaches for inducer development could benefit many breeding programs which are in the process of adopting the DH technique. In this manuscript, we review traits important to maize maternal haploid inducers, explain their genetic basis, listing known genes and quantitative trait loci (QTL), and discuss different breeding approaches for inducer development. The performance of haploid inducers has an important impact on the cost of DH line production.

A DMP-triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis

Doubled haploid technology using inducer lines carrying mutations in ZmPLA1/MTL/NLD and ZmDMP^1-4 has revolutionized traditional maize breeding. ZmPLA1/MTL/NLD is conserved in monocots and has been used to extend the system from maize to other monocots^5-7, but no functional orthologue has been identified in dicots, while ZmDMP-like genes exist in both monocots and dicots^4,8,9. Here, we report that loss-of-function mutations in the Arabidopsis thaliana ZmDMP-like genes AtDMP8 and AtDMP9 induce maternal haploids, with an average haploid induction rate of 2.1 ± 1.1%. In addition, to facilitate haploid seed identification in dicots, we established an efficient FAST-Red fluorescent marker-based haploid identification system that enables the identification of haploid seeds with >90% accuracy. These results show that mutations in DMP genes also trigger haploid induction in dicots. The conserved expression patterns and amino acid sequences of ZmDMP-like genes in dicots suggest that DMP mutations could be used to develop in vivo haploid induction systems in dicots.

Genomic prediction of maternal haploid induction rate in maize

Genomic prediction (GP) might be an efficient way to improve haploid induction rate (HIR) and to reduce the laborious and time-consuming task of phenotypic selection for HIR in maize (Zea mays L.). In this study, we evaluated GP accuracies for HIR and other agronomic traits of importance to inducers by independent and cross-validation. We propose the use of GP for cross prediction and parental selection in the development of new inducer breeding populations. A panel of 159 inducers from Iowa State University (ISU set) was genotyped and phenotyped for HIR and several agronomic traits. The data of an independent set of 53 inducers evaluated by the University of Hohenheim (UOH set) was used for independent validation. The HIR ranged from 0.61 to 20.74% and exhibited high heritability (0.90). High cross-validation prediction accuracy was observed for HIR (r = 0.82), whereas for other traits it ranged from 0.36 (self-induction rate) to 0.74 (days to anthesis). Prediction accuracies across different sets were higher when the larger panel (ISU set) was used as a training population (r = 0.54). The average HIR of the 12,561 superior predicted progenies (μ_SP ) ranged from 1.00-18.36% and was closely related to the corresponding midparent genomic estimated breeding value (GEBV). A predicted genetic variance (V_G ) of reduced magnitude was observed in the twenty crosses with highest midparent GEBV or μ_SP for HIR. Our results indicate that although GP is a useful tool for parental selection, decisions about which cross combinations should be pursued need to be based on optimal trade-offs between maximizing both μ_SP and V_G .

Mapping of QTL for kernel abortion caused by in vivo haploid induction in maize (Zea mays L.)

Kernel abortion is common phenomenon in vivo haploid induction and closely linked with haploid induction rate, but little information of kernel abortion is available and its genetic basis still unclear. We used two mapping populations including 186 and 263 F2.3 family lines to analyze the different degree of kernel abortion and identify quantitative trait loci (QTL) responsible for kernel abortion during haploid induction. In total 62 putative QTL, accounting for 3.27-14.70% of the phenotypic variation in kernel abortion traits, were detected across all 10 chromosomes. Ten QTL with over 10% contribution to phenotypic variation were affecting the fifth level of endosperm abortion (EnA5th), endosperm abortion (EnA) and total abortion (TA). Co-localization among kernel abortion traits QTL was observed in both populations and among different kernel abortion types. Five overlaps were indentified in the QTL for kernel abortion traits and HIR traits. Maize chromosome bins 3.01-3.02, 3.04-3.06, 4.05-4.06, 5.03-5.04, 8.06 were QTL hotspots for three or four traits related to the kernel abortion during haploid induction. Total kernel abortion rate (TAR) and HIR showed highly significant positive correlation. These findings may help to reveal haploid induction mechanisms and improve haploid production efficiency.

Genomic Outcomes of Haploid Induction Crosses in Potato (Solanum tuberosum L.)

The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.

Engineered minichromosomes in plants

Artificial chromosome platforms are described in plants. Because the function of centromeres is largely epigenetic, attempts to produce artificial chromosomes with plant centromere DNA have failed. The removal of the centromeric sequences from the cell strips off the centromeric histone that is the apparent biochemical marker of centromere activity. Thus, engineered minichromosomes have been produced by telomere mediated chromosomal truncation. The introduction of telomere repeats will cleave the chromosome at the site of insertion and attach the accompanying transgenes in the process. Such truncation events have been documented in maize, Arabidopsis, barley, rice, Brassica and wheat. Truncation of the nonvital supernumerary B chromosome of maize is a favorite target but engineered minichromosomes derived from the normal A chromosomes have also been recovered. Transmission through mitosis of small chromosomes is apparently normal but there is loss during meiosis. Potential solutions to address this issue are discussed. With procedures now well established to produce the foundation for artificial chromosomes in plants, current efforts are directed at building them up to specification using gene stacking methods and editing techniques.

Clonal Reproduction through Seeds in Sight for Crops

Apomixis or asexual reproduction through seeds, enables the preservation of hybrid vigor. Hybrids are heterozygous and segregate for genotype and phenotype upon sexual reproduction. While apomixis, that is, clonal reproduction, is intuitively antithetical to diversity, it is rarely obligate and actually provides a mechanism to recover and maintain superior hybrid gene combinations for which sexual reproduction would reveal deleterious alleles in less fit genotypes. Apomixis, widespread across flowering plant orders, does not occur in major crop species, yet its introduction could add a valuable tool to the breeder's toolbox. In the past decade, discovery of genetic mechanisms regulating meiosis, embryo and endosperm development have facilitated proof-of-concept for the synthesis of apomixis, bringing apomictic crops closer to reality.

Doubled haploid technology for line development in maize: technical advances and prospects

KEY MESSAGE

Increased efficiencies achieved in different steps of DH line production offer greater benefits to maize breeding programs. Doubled haploid (DH) technology has become an integral part of many commercial maize breeding programs as DH lines offer several economic, logistic and genetic benefits over conventional inbred lines. Further, new advances in DH technology continue to improve the efficiency of DH line development and fuel its increased adoption in breeding programs worldwide. The established method for maize DH production covered in this review involves in vivo induction of maternal haploids by a male haploid inducer genotype, identification of haploids from diploids at the seed or seedling stage, chromosome doubling of haploid (D0) seedlings and finally, selfing of fertile D0 plants. Development of haploid inducers with high haploid induction rates and adaptation to different target environments have facilitated increased adoption of DH technology in the tropics. New marker systems for haploid identification, such as the red root marker and high oil marker, are being increasingly integrated into new haploid inducers and have the potential to make DH technology accessible in germplasm such as some Flint, landrace, or tropical material, where the standard R1-nj marker is inhibited. Automation holds great promise to further reduce the cost and time in haploid identification. Increasing success rates in chromosome doubling protocols and/or reducing environmental and human toxicity of chromosome doubling protocols, including research on genetic improvement in spontaneous chromosome doubling, have the potential to greatly reduce the production costs per DH line.

Composition and random elimination of paternal chromosomes in a large population of wheat × barley (Triticum aestivum L. × Hordeum vulgare L.) hybrids

Statistical analysis of the chromosomal composition in a population of 210 primary plants regenerated from two intergeneric wheat-barley cross combinations revealed the random nature of uniparental elimination for barley chromosomes. Uniparental chromosome elimination is a common process in interspecific and intergeneric cereal hybrids. To characterize the frequency of paternal chromosomes, a population of 218 independent green plants was generated from two wheat (♀) × barley (♂) cross combinations via embryo rescue. The chromosomal composition of 210 primary plants was analyzed with chromosome-specific DNA markers representing all seven barley chromosomes. The analysis revealed an equal proportion of haploid and full hybrids (20.5% and 19.5%, respectively), while the rest of the population contained hypoploids (partial hybrids) with no preference for any possible numbers (one to six) of barley chromosome additions. Contrary to the previous reports, there was no statistical bias or preferential elimination for any individual barley chromosome (1H-7H) in this population. The reasons for the apparent contradiction and the implications of the above findings for cereal breeding are discussed.

Genome-wide Inference of Somatic Translocation Events During Potato Dihaploid Production

Potato ( L.) breeders often use dihaploids, which are 2× progeny derived from 4× autotetraploid parents. Dihaploids can be used in diploid crosses to introduce new genetic material into breeding germplasm that can be integrated into tetraploid breeding through the use of unreduced gametes in 4× by 2× crosses. Dihaploid potatoes are usually produced via pollination by haploid inducer lines known as in vitro pollinators (IVP). In vitro pollinator chromosomes are selectively degraded from initially full hybrid embryos, resulting in 2× seed. During this process, somatic translocation of IVP DNA may occur. In this study, a genome-wide approach was used to identify such events and other chromosome-scale abnormalities in a population of 95 dihaploids derived from a cross between potato cultivar Superior and the haploid inducing line IVP101. Most Superior dihaploids showed translocation rates of <1% at 16,947,718 assayable sites, yet two dihaploids showed translocation rates of 1.86 and 1.60%. Allelic ratios at translocation sites suggested that most translocations occurred in individual cell lineages and were thus not present in all cells of the adult plants. Translocations were enriched in sites associated with high gene expression and H3K4 dimethylation and H4K5 acetylation, suggesting that they tend to occur in regions of open chromatin. The translocations likely result as a consequence of double-stranded break repair in the dihaploid genomes via homologous recombination during which IVP chromosomes are used as templates. Additionally, primary trisomy was observed in eight individuals. As the trisomic chromosomes were derived from Superior, meiotic nondisjunction may be common in potato.

Development of a Haploid-Inducer Mediated Genome Editing System for Accelerating Maize Breeding

Crop breeding aims to generate pure inbred lines with multiple desired traits. Doubled haploid (DH) and genome editing using CRISPR/Cas9 are two powerful game-changing technologies in crop breeding. However, both of them still fall short for rapid generation of pure elite lines with integrated favorable traits. Here, we report the development of a Haploid-Inducer Mediated Genome Editing (IMGE) approach, which utilizes a maize haploid inducer line carrying a CRISPR/Cas9 cassette targeting for a desired agronomic trait to pollinate an elite maize inbred line and to generate genome-edited haploids in the elite maize background. Homozygous pure DH lines with the desired trait improvement could be generated within two generations, thus bypassing the lengthy procedure of repeated crossing and backcrossing used in conventional breeding for integrating a desirable trait into elite commercial backgrounds.

One-step genome editing of elite crop germplasm during haploid induction

Genome editing using CRISPR-Cas9 works efficiently in plant cells¹, but delivery of genome-editing machinery into the vast majority of crop varieties is not possible using established methods². We co-opted the aberrant reproductive process of haploid induction (HI)^3-6 to induce edits in nascent seeds of diverse monocot and dicot species. Our method, named HI-Edit, enables direct genomic modification of commercial crop varieties. HI-Edit was tested in field and sweet corn using a native haploid-inducer line⁴ and extended to dicots using an engineered CENH3 HI system⁷. We also recovered edited wheat embryos using Cas9 delivered by maize pollen. Our data indicate that a transient hybrid state precedes uniparental chromosome elimination in maize HI. Edited haploid plants lack both the haploid-inducer parental DNA and the editing machinery. Therefore, edited plants could be used in trait testing and directly integrated into commercial variety development.

State-of-the-art and novel developments of in vivo haploid technologies

The ability to generate (doubled) haploid plants significantly accelerates the crop breeding process. Haploids have been induced mainly through the generation of plants from cultivated gametophic (haploid) cells and tissues, i.e., in vitro haploid technologies, or through the selective loss of a parental chromosome set upon inter- or intraspecific hybridization. Here, we focus our review on the mechanisms responsible for the in vivo formation of haploids in the context of inter- and intraspecific hybridization. The application of a modified CENH3 for uniparental genome elimination, the IG1 system used for paternal as well as the BBM-like and the patatin-like phospholipase essential for maternal haploidy induction are discussed in detail.

Maize Dek15 Encodes the Cohesin-Loading Complex Subunit SCC4 and Is Essential for Chromosome Segregation and Kernel Development

Cohesin complexes maintain sister chromatid cohesion to ensure proper chromosome segregation during mitosis and meiosis. In plants, the exact components and functions of the cohesin complex remain poorly understood. Here, we positionally cloned the classic maize (Zea mays) mutant defective kernel 15 (dek15), revealing that it encodes a homolog of SISTER CHROMATID COHESION PROTEIN 4 (SCC4), a loader subunit of the cohesin ring. Developing dek15 kernels contained fewer cells than the wild type, but had a highly variable cell size. The dek15 mutation was found to disrupt the mitotic cell cycle and endoreduplication, resulting in a reduced endosperm and embryo lethality. The cells in the dek15 endosperm and embryo exhibited precocious sister chromatid separation and other chromosome segregation errors, including misaligned chromosomes, lagging chromosomes, and micronuclei, resulting in a high percentage of aneuploid cells. The loss of Dek15/Scc4 function upregulated the expression of genes involved in cell cycle progression and stress responses, and downregulated key genes involved in organic synthesis during maize endosperm development. Our yeast two-hybrid screen identified the chromatin remodeling proteins chromatin remodeling factor 4, chromatin remodeling complex subunit B (CHB)102, CHB105, and CHB106 as SCC4-interacting proteins, suggesting a possible mechanism by which the cohesin ring is loaded onto chromatin in plant cells. This study revealed biological functions for DEK15/SCC4 in mitotic chromosome segregation and kernel development in maize.

Centromere histone H3- and phospholipase-mediated haploid induction in plants

Simple and consistent production of haploid is always an appealing pursuit for both crop breeders and researchers. Although diverse strategies have been developed to produce haploids over the past decades, most of them are applicable in only a limited number of plant species. In 2010, Ravi and Chan reported that haploid Arabidopsis thaliana plants can be efficiently induced through the introduction of a single genetic alteration in centromere histone H3 (CENH3). Subsequent studies demonstrated that haploids can be efficiently induced either through genetic engineering of CENH3 N-terminal tail or histone fold domain or by replacing CENH3 with an ortholog. The mutation of a pollen-specific phospholipase gene, MATRILINEAL (MTL) has been revealed to trigger the haploid induction (HI) in maize, which present another promising HI approach by the editing of MTL in plant. Here, we review the progress of the CENH3-medialed HI and propose a revised centromere-size model by suggesting a competitive loading process between wild-type and mutant CENH3 during HI. This model can explain both the findings of HI failure when wild-type and mutant CENH3 genes are coexpressed and the alien centromere loading of CENH3 in stable hybrids. In addition, we review the current understanding of MTL-mediated HI in plant. The conservation of CENH3 and MTL in plants indicates wide potential application for HI. We discuss the utility and potential of these two methods in crops by comparing their mechanisms and applications to date in plants. This review will promote the study and application of both CENH3- and MTL-mediated haploid induction in plants.

In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

BACKGROUND

In vivo haploid induction (HI) based on Stock6-derived inducer lines has been the most prevalent means of producing haploids. Nevertheless, the biological mechanism of HI is not fully understood, the twin-embryo kernels had been found during haploid induction, which may provide potential evidence for the abnormal double fertilization during HI.

RESULTS

We investigated twin-embryo frequency in progenies of different haploid inducers. Results reveal that increasing the HI potential significantly improved the frequency of twin-embryo kernels. Compared with the average twin-embryo kernel frequency (average frequency = 0.07%) among progenies pollinated by the haploid inducer line CAUHOI, the frequency of twin-embryo was improved to 0.16% in progenies pollinated by the haploid inducer line CAU5. This result was further confirmed by pollinating single hybrid ND5598 with four haploid inducers possessing differentiated HIRs, where twin-embryo frequency was highly correlated with HIR. Among 237 twin-embryo kernels, we identified 30 haploid twin-embryo kernels (12.66%), a frequency which was much greater than the average HI rate for three other inducer lines (frequency range 2-10%). In addition, aneuploids, occurred at high frequency (8 in 41 twin plants). This level of aneuploidy provides new insight into the abnormal double fertilization during HI. Moreover, we observed differences in growth rate between twin plants in the field, as 4.22% of the twin plants grew at a significantly different rate. Both simple sequence repeats markers (SSR) and 3072 SNP-chip genotyping results revealed that > 90% of the twin plants shared the same origin, and the growth difference could be attributed to aneuploidy, competition for nutrients, and possible hormone regulation.

CONCLUSION

These results demonstrate that an enhanced HI ability can increase twin-embryo kernel frequency, and high frequency of both haploid twin-embryo kernels and aneuploidy observed in this research give us new insights to understand the mechanism of both HI and abnormal embryogenesis.

Hetero-fertilization together with failed egg-sperm cell fusion supports single fertilization involved in in vivo haploid induction in maize

In vivo doubled-haploid technology is widely applied in commercial maize breeding programs because of its time-saving and cost-reducing features. The production of maize haploids primarily depends on the use of Stock6-derived haploid inducer lines. Although the gene underlying haploid induction, MTL/ZmPLA1/NLD, was cloned recently, the mechanism of haploid induction is still unknown. Hetero-fertilization can occur via a single fertilization, which provides a means to investigate single-fertilization events by studying the hetero-fertilization phenomenon. In this study, we found that the hetero-fertilization rate increased significantly when female maize lines were first individually crossed with pollen from the inducer CAU5 in dual-pollination experiments 4 h before a second pollination with common lines. We also examined embryogenesis during haploid induction by confocal laser-scanning microscopy and observed single-fertilized ovules, indicating that single fertilization occurred during haploid induction. We therefore postulate that both single fertilization and chromosome elimination contribute to haploid induction in maize. We also propose a scheme for the formation of hetero-fertilized and haploid kernels. Our results provide an efficient approach to identify hetero-fertilized kernels for research on interactions between embryo and endosperm.

Maternal doubled haploid production in interploidy hybridization between Brassica napus and Brassica allooctaploids

We found a new in vivo route to produce maternal doubled haploid of Brassica napus . The pollen donor, an allooctaploid rapeseed, acts as a DH inducer. Inbred line has a powerful advantage in cultivar breeding and genetic analysis. Compared to the traditional breeding methods, doubled haploid production can save years off the breeding process. Though genotype-dependent tissue culture methods are widely used in the Brassica crops, seed-based in vivo doubled haploid developing systems are rare in nature and in the laboratory. As interspecific cross and interploid hybridization play an important role in genome evolution and plant speciation, we created a new Brassica artificial hybrid, a Brassica allooctaploid (AAAACCCC, 2n = 8× = 76), by interspecific crossing and genome doubling. A homozygous line was observed at the third self-generation of a synthesized Brassica allohexaploid (AAAACC, 2n = 6× = 58). Crosses between B. napus as female and Brassica allooctaploid as pollen donor were conducted, which yielded maternal doubled haploid B. napus that were identified based on phenotype, ploidy, and molecular analysis. The Brassica octaploid acted as a maternal doubled haploid inducer and had a relatively high induction rate. Our research provides a new insight for generation of homozygous lines in vivo using a single-step approach, as well as promotes the understanding in breeding programs and genetic studies involving the Brassicas.

Novel technologies in doubled haploid line development

haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome doubling are the two main steps required for DH technology. Haploids have been generated through the culture of immature male and female gametophytes, and through inter- and intraspecific via chromosome elimination. Here, we focus on haploidization via chromosome elimination, especially the recent advances in centromere-mediated haploidization. Once haploids have been induced, genome doubling is needed to produce DH lines. This study has proposed a new strategy to improve haploid genome doubling by combing haploids and minichromosome technology. With the progress in haploid induction and genome doubling methods, DH technology can facilitate reverse breeding, cytoplasmic male sterile (CMS) line production, gene stacking and a variety of other genetic analysis.

Single nucleus sequencing reveals spermatid chromosome fragmentation as a possible cause of maize haploid induction

Production of maternal haploids using a conspecific haploid inducer is routine and highly efficient in maize. However, the underlying mechanism of haploid induction (HI) is unclear. We develop a method to isolate three nuclei from a pollen grain and four microspores from a tetrad for whole-genome sequencing. A high rate of aneuploidy is observed at the three-nucleus stage (6/22 pollens) rather than at the tetrad stage (1/72 microspores) in one HI line CAU5. Frequent aneuploidy is also observed in another two inducer lines, but not in two regular lines, which implies that HI may be associated with pollen aneuploidy. We further sequence the individual embryos and endosperms of 88 maize kernels crossing between regular and inducer lines. Genome-wide elimination of the CAU5-derived chromosome is identified in eight of 81 embryos. Together, these results suggest that continuous chromosome fragmentation occurring post meiosis in the gametophyte may cause haploidy of the embryo.

Plant breeders can produce haploid maize lines using haploid inducer lines as pollen donors. Here, by sequencing the genomes of single pollen nuclei, Li et al. show that haploid inducer spermatids are frequently aneuploid and suggest chromosome fragmentation as a possible cause of haploid induction.

Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines

Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.

Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize

Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.