Analysis of effectiveness of R1-nj anthocyanin marker for in vivo haploid identification in maize and molecular markers for predicting the inhibition of R1-nj expression

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.

Fine mapping and candidate gene analysis of qSRC3 controlling the silk color in maize (Zea mays L.)

KEY MESSAGE

Fine mapping of the maize QTL qSRC3, responsible for red silk, uncovered the candidate gene ZmMYB20, which encodes an R2R3-MYB transcription factor, has light-sensitive expression, and putatively regulates genes expression associated with anthocyanin biosynthesis. Colorless silk is a key characteristic contributing to the visual quality of fresh corn intended for market distribution. Nonetheless, the identification of Mendelian trait loci and associated genes that control silk color has been scarce. In this study, a F2 population arising from the hybridization of the single-segment substitution line qSRC3MT1 with red silk, carrying an introgressed allele from teosinte (Zea mays ssp. mexicana), and the recurrent maize inbred line Mo17, characterized by light green silk, was utilized for fine mapping. We found that the red silk trait is controlled by a semi-dominant genetic locus known as qSRC3, and its expression is susceptible to light-mediated inhibition. Moreover, qSRC3 explained 68.78% of the phenotypic variance and was delimited to a 133.2 kb region, which includes three genes. Subsequent expression analyses revealed that ZmMYB20 (Zm00001d039700), which encodes an R2R3-MYB transcription factor, was the key candidate gene within qSRC3. Yeast one-hybrid and dual-luciferase reporter assays provided evidence that ZmMYB20 suppresses the expression of two crucial anthocyanin biosynthesis genes, namely ZmF3H and ZmUFGT, by directly binding to their respective promoter regions. Our findings underscore the significance of light-inhibited ZmMYB20 in orchestrating the spatial and temporal regulation of anthocyanin biosynthesis. These results advance the production of colorless silk in fresh corn, responding to the misconception that fresh corn with withered colored silk is not fresh and providing valuable genetic resources for the improvement of sweet and waxy maize.

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.

Effectiveness of R1-nj Anthocyanin Marker in the Identification of In Vivo Induced Maize Haploid Embryos

Doubled haploid (DH) technology has become integral to maize breeding programs to expedite inbred line development and increase the efficiency of breeding operations. Unlike many other plant species that use in vitro methods, DH production in maize uses a relatively simple and efficient in vivo haploid induction method. However, it takes two complete crop cycles for DH line generation, one for haploid induction and the other one for chromosome doubling and seed production. Rescuing in vivo induced haploid embryos has the potential to reduce the time for DH line development and improve the efficiency of DH line production. However, the identification of a few haploid embryos (~10%) resulting from an induction cross from the rest of the diploid embryos is a challenge. In this study, we demonstrated that an anthocyanin marker, namely R1-nj, which is integrated into most haploid inducers, can aid in distinguishing haploid and diploid embryos. Further, we tested conditions that enhance R1-nj anthocyanin marker expression in embryos and found that light and sucrose enhance anthocyanin expression, while phosphorous deprivation in the media had no affect. Validating the use of the R1-nj marker for haploid and diploid embryo identification using a gold standard classification based on visual differences among haploids and diploids for characteristics such as seedling vigor, erectness of leaves, tassel fertility, etc., indicated that the R1-nj marker could lead to significantly high false positives, necessitating the use of additional markers for increased accuracy and reliability of haploid embryo identification.

Popcorn (Zea mays L. var. Everta) haploids identified by Navajo phenotype and ploidy level

For popcorn, obtaining and identifying haploids are still challenging steps. We aimed to induce and screen haploids in popcorn using the Navajo phenotype, seedling vigor, and ploidy level. We used the Krasnodar Haploid Inducer (KHI) in crosses with 20 popcorn source germplasms and five maize controls. The field trial design was completely randomized, with three replications. We assessed the efficacy of induction and identification of haploids based on the haploidy induction rate (HIR) and false positive and negative rates (FPR and FNR). Additionally, we also measured the penetrance of the Navajo marker gene (R1-nj). All putative haploids classified by the R1-nj were germinated together with a diploid sample and evaluated for false positives and negatives based on vigor. Seedlings from 14 females were submitted to flow cytometry to determine the ploidy level. The HIR and penetrance were analyzed by fitting a generalized linear model with a logit link function. The HIR of the KHI, adjusted by cytometry, ranged from 0.0 to 1.2%, with a mean of 0.34%. The average FPR from screening based on the Navajo phenotype was 26.2% and 76.4% for vigor and ploidy, respectively. The FNR was zero. The penetrance of R1-nj ranged from 30.8 to 98.6%. The average number of seeds per ear in temperate germplasm (76) was lower than that obtained in tropical germplasm (98). There is an induction of haploids in germplasm of tropical and temperate origin. We recommend the selection of haploids associated with the Navajo phenotype with a direct method of confirming the ploidy level, such as flow cytometry. We also show that haploid screening based on Navajo phenotype and seedling vigor reduces misclassification. The origin and genetic background of the source germplasm influence the R1-nj penetrance. Because the known inducers are maize, developing doubled haploid technology for popcorn hybrid breeding requires overcoming unilateral cross-incompatibility.

The RUBY reporter enables efficient haploid identification in maize and tomato

In vivo haploid induction has been extended from maize to monocotyledonous plants like rice, wheat, millet and dicotyledonous plants such as tomato, rapeseed, tobacco and cabbage. Accurate identification of haploids is a crucial step of doubled haploid technology, where a useful identification marker is very pivotal. R1-nj is an extensively used visual marker for haploid identification in maize. RFP and eGFP have been shown to be feasible in identifying haploid. However, these methods are either limited to specific species, or require specific equipment. It still lacks an efficient visual marker that is practical across different crop species. In this study, we introduced the RUBY reporter, a betalain biosynthesis system, into maize and tomato haploid inducers as a new marker for haploid identification. Results showed that expression of RUBY could result in deep betalain pigmentation in maize embryos as early as 10 days after pollination, and enabled 100% accuracy of immature haploid embryo identification. Further investigation in tomato revealed that the new marker led to deep red pigmentation in radicles and haploids can be identified easily and accurately. The results demonstrated that the RUBY reporter is a background-independent and efficient marker for haploid identification and would be promising in doubled haploid breeding across different crop species.

Protocol optimization and assessment of genotypic response for inbred line development through doubled haploid production in maize

BACKGROUND

Doubled haploid technology offers the fastest route of inbred line development by rapidly fixing the desirable combinations in a single year. However, the differential response of haploid induction to genetic background of maternal lines accompanied with low induction rate and high mortality rate due to artificial chromosomal doubling of haploid seedlings creates hindrance in doubled haploid production on a commercial scale under tropical conditions. To speed up the hybrid breeding programme in sub-tropical maize, efforts are reported here to optimize the protocol for efficient production of fixed lines using haploid inducers. The second-generation haploid inducers i.e. CIM2GTAILs obtained from CIMMYT, Mexico were used for haploid induction in 13 F₁s of diverse backgrounds. For standardization of chromosomal doubling protocol, various concentrations of colchicine and two seedling growth stages were used to determine the extent of chromosomal doubling and survival rate of doubled haploid plants.

RESULTS

A high mean haploid induction rate is obtained from CIM2GTAIL P2 (10%) as compared to CIM2GTAIL P1 (7.46%). Out of four treatments, CIMMYT reported protocol of chromosome doubling in tropical maize comprising combination of 0.07% colchicine and 0.1% DMSO at V₂ stage is highly effective for acquiring doubled haploid plants in sub-tropical adapted maize with high survival rate of 52.7%. However, increasing the colchicine concentration from 0.07 to 0.1% led to high mortality rate.

CONCLUSION

According to the findings, the haploid induction rate, survival rate and overall success rate varied depending upon the genotype of the inducer and the source population along with the concentrations of chemical used. The optimized protocol developed using CIMMYT haploid inducer CIM2GTAIL P2 for efficient doubled haploid production will not only fasten the breeding programme but will also reduce the production cost of doubled haploid with great efficiency in sub-tropical maize.

Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize

Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of Helitrons transposition in plants. Here, by constructing several artificial defective Helitron (dHel) reporter systems, we aim to identify the autonomous Helitrons (aHel) in maize genetically and to demonstrate the transposition and repair mechanisms of Helitrons upon the dHel-GFP excision in maize. When crossing with various inbred lines, several transgenic lines produced progeny of segregated, purple-blotched kernels, resulting from a leaky expression of the C1 gene driven by the dHel-interrupted promoter. Transcription analysis indicated that the insertion of different dHels into the C1 promoter or exon would lead to multiple distinct mRNA transcripts corresponding to transgenes in the host genome. Simple excision products and circular intermediates of dHel-GFP transposition have been detected from the leaf tissue of the seedlings in F1 hybrids of transgenic lines with corresponding c1 tester, although they failed to be detected in all primary transgenic lines. These results revealed the transposition and repair mechanism of Helitrons in maize. It is strongly suggested that this reporter system can detect the genetic activity of autonomic Helitron at the molecular level. Sequence features of dHel itself, together with the flanking regions, impact the excision activity of dHel and the regulation of the dHel on the transcription level of the host gene.

Variation in anthocyanin pigmentation by R1-navajo gene, development and validation of breeder-friendly markers specific to C1-Inhibitor locus for in-vivo haploid production in maize

BACKGROUND

In-vivo maternal haploids serve as the basis of doubled haploid (DH) breeding in maize. R1-navajo (R1-nj) gene governing anthocyanin colouration in the endosperm and embryo is widely used to identify haploid seeds. However, the expression of R1-nj depends on genetic-background of source-germplasm used for deriving DH-lines. Further, presence of C1-Inhibitor (C1-I) gene suppresses the expression of R1-nj, thus makes the selection of haploids difficult.

METHODS

In the present study, 178 subtropically-adapted maize inbreds were crossed with two R1-nj donors 'that do not have haploid induction genes'. Of these, 76.4% inbreds developed purple colour in endosperm, while 23.6% did not show any colouration. In case of scutellum, 62.9% inbreds possessed colour and 37.1% were colourless. The anthocyanin intensity varied greatly, with 19.66% and 42.98% inbreds displayed the least intensity, while 16.85% and 0.84% inbreds showed the highest intensity in endosperm and scutellum, respectively. Two C1-I specific breeder-friendly markers (MGU-CI-InDel8 and MGU-C1-SNP1) covering (i) 8 bp InDel and (ii) A to G SNP, respectively, were developed. MGU-CI-InDel8 and MGU-C1-SNP1 markers predicted presence of C1-I allele with 92.9% and 84.7% effectiveness, respectively. However, when both markers were considered together, they provided 100% effectiveness.

CONCLUSIONS

These markers of C1-I gene would help in saving valuable resources and time during haploid induction in maize. The information generated here assume great significance in DH breeding of maize.

Influential factors and transcriptome analyses of immature diploid embryo anthocyanin accumulation in maize

BACKGROUND

Anthocyanins are widely applied as a marker for haploid identification after haploid induction in maize. However, the factors affecting anthocyanin biosynthesis in immature embryos and the genes regulating this process remain unclear.

RESULTS

In this study, we analyzed the influence of genetic background of the male and female parents, embryo age and light exposure on anthocyanin accumulation in embryos. The results showed that light exposure was the most crucial factor enhancing the pigmentation of immature embryos. The identification accuracy of haploid embryos reached 96.4% after light exposure, but was only 11.0% following dark treatment. The total anthocyanin content was 7-fold higher in immature embryos cultured for 24 h under light conditions compared to embryos cultured in the dark. Transcriptome analysis revealed that the differentially expressed genes between immature embryos cultured for 24 h in dark and light chambers were significantly enriched in the pathways of flavonoid, flavone, flavonol and anthocyanin biosynthesis. Among the genes involved in anthocyanin biosynthesis, five up-regulated genes were identified: F3H, DFR, ANS, F3'H and the MYB transcription factor-encoding gene C1. The expression patterns of 14 selected genes were confirmed using quantitative reverse transcription-polymerase chain reaction.

CONCLUSION

Light is the most important factor facilitating anthocyanin accumulation in immature embryos. After 24 h of exposure to light, the expression levels of the structural genes F3H, DFR, ANS, F3'H and transcription factor gene C1 were significantly up-regulated. This study provides new insight into the factors and key genes regulating anthocyanin biosynthesis in immature embryos, and supports improved efficiency of immature haploid embryo selection during doubled haploid breeding of maize.

Seasonal Variation of Tropical Savanna Altered Agronomic Adaptation of Stock-6-Derived Inducer Lines

Tropicalization is one of the major objectives in breeding haploid inducers to address the poor adaptation of temperate haploid inducers in doubled haploid production in tropical maize. Gaining a better understanding of weather profiles in targeted agroecology is important. This study aimed to investigate the seasonal variation of tropical savanna climate and its impact on agronomic traits and haploid induction rate (HIR) of Stock-6-derived haploid inducer lines. A total of 14 haploid inducers were evaluated across two typical growing seasons between 2020 and 2021. Weather data were collected on daily minimum and maximum temperatures, relative humidity, precipitation, and solar radiation whereas phenotypic data were recorded on plant phenology, tassel attributes, plant stature, ear components, inducer seed rate (ISR), and HIR. The effects of season, genotype, and genotype by season were significant for all traits except season factor on ISR. Seasonal variation existed where the dry season was more suitable for haploid induction and inducer maintenance, as haploid inducers revealed better agronomic performance and seed set, delayed flowering dates, and higher HIR. Since the crossover performance of haploid inducers over seasons was detected, further implications on genotype selection in each season are discussed.

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.

Investigating the Effect of the Interaction of Maize Inducer and Donor Backgrounds on Haploid Induction Rates

Doubled haploid technology is a feasible, fast, and cost-efficient way of producing completely homozygous lines in maize. Many factors contribute to the success of this system including the haploid induction rate (HIR) of inducer lines, the inducibility of donor background, and environmental conditions. Sixteen inducer lines were tested on eight different genetic backgrounds of five categories in different environments for the HIR to determine possible interaction specificity. The HIR was assessed using the R1-nj phenotype and corrected using the red root marker or using a gold-standard test that uses plant traits. RWS and Mo-17-derived inducers showed higher average induction rates and the commercial dent hybrid background showed higher inducibility. In contrast, sweet corn and flint backgrounds had a relatively lower inducibility, while non-stiff stalk and stiff stalk backgrounds showed intermediate inducibility. For the poor-performing donors (sweet corn and flint), there was no difference in the HIR among the inducers. Anthocyanin inhibitor genes in such donors were assumed to have increased the misclassification rate in the F₁ fraction and, hence, result in a lower HIR.

Selection Gain of Maize Haploid Inducers for the Tropical Savanna Environments

Lacking elite haploid inducers performing high haploid induction rate (HIR) and agronomic performance is one of fundamental factors hindering the rapid adoption of doubled haploid technology in maize hybrid breeding, especially under tropical savanna climate. Breeding haploid inducers for specific agro-ecology, thus, is indispensable yet challenging. We used temperate inducer Stock6 as genetic source for haploid induction ability and eight tropical maize genotypes as principal donors for agronomic adaptation. Three cycles of modified ear-to-row with 5% intra-family selection were applied in a population set of 78 putative haploid inducer families emphasized on agronomic performance, R1-nj anthocyanin intensity, and inducer seed set. Genetic gains, variance components, and heritability on given traits were estimated. Hierarchical clustering based on five selection criteria was performed to investigate the phenotypic diversity of putative families. Cycle effect was predominant for all observed traits. Realized genetic gain was positive for HIR (0.40% per cycle) and inducer seed set (30.10% or 47.30 seeds per ear per cycle). In this study, we reported the first haploid inducers for regions under tropical savanna climate. Three inducer families, KHI-42, KHI-54, and KHI-64, were promising as they possessed HIR about 7.8% or 14 haploid seeds per tester ear and inducer seed rate about 95.0% or 208 inducer seeds per ear. The breeding method was effective for enhancing the seed set and the expression of R1-nj anthocyanin marker of inducers, yet it showed a low effectiveness to improve haploid induction rate. Introgression of temperate inducer Stock6 into tropical gene pool followed by phenotypic selections through modified ear-to-row selection on inducer seed set and R1-nj marker did not compromise the agronomic traits of tropical inducer families. Implications and further strategies for optimizing genetic gain on HIR are discussed.

Establishment of an efficient seed fluorescence reporter-assisted CRISPR/Cas9 gene editing in maize

Genome editing by clustered regularly interspaced short palindromic sequences (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized functional gene analysis and genetic improvement. While reporter-assisted CRISPR/Cas systems can greatly facilitate the selection of genome-edited plants produced via stable transformation, this approach has not been well established in seed crops. Here, we established the seed fluorescence reporter (SFR)-assisted CRISPR/Cas9 systems in maize (Zea mays L.), using the red fluorescent DsRED protein expressed in the endosperm (En-SFR/Cas9), embryos (Em-SFR/Cas9), or both tissues (Em/En-SFR/Cas9). All three SFRs showed distinct fluorescent patterns in the seed endosperm and embryo that allowed the selection of seeds carrying the transgene of having segregated the transgene out. We describe several case studies of the implementation of En-SFR/Cas9, Em-SFR/Cas9, and Em/En- SFR/Cas9 to identify plants not harboring the genome-editing cassette but carrying the desired mutations at target genes in single genes or in small-scale mutant libraries, and report on the successful generation of single-target mutants and/or mutant libraries with En-SFR/Cas9, Em-SFR/Cas9, and Em/En-SFR/Cas9. SFR-assisted genome editing may have particular value for application scenarios with a low transformation frequency and may be extended to other important monocot seed crops.

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.

Diallelic Analysis of Tropical Maize Germplasm Response to Spontaneous Chromosomal Doubling

Chromosome doubling is an important step in the production of maize doubled haploid (DH) lines to induce fertility in the male and female reproductive organs of haploid plants. Chromosomal doubling is routinely accomplished by treating haploid seedlings with mitosis-inhibiting chemicals. However, chromosomal doubling involves several labor-intensive steps and toxic chemicals. Spontaneous chromosomal doubling without any chemical treatments occurs at high frequency in haploids from a few maize genotypes. This study focused on elucidating the genetic components of two traits important for using spontaneous doubling in maize-breeding programs, namely, haploid male fertility (HMF) and haploid fertility (HF). In two different sets of diallel crosses, haploids were derived and assessed for HMF and HF in two environments in replicated trials. The results revealed significant genotypic variations for both traits. The general combining ability (GCA) and specific combining (SCA) were significant for both traits. Significant and positive GCA effects of up to 14% and 9% were found for HMF and HF, respectively. No significant reciprocal effects and genotype-by-environment (G×E) interactions were found for HF in both experiments, but HMF showed significant effects for both in one of the experiments. The GCA effects were more important than the SCA effects for HMF and HF across environments, implying that selection could facilitate their improvement. The high correlations between F1-hybrid performance and mid-parent values, as well as that between F1-hybrid performance and GCA effects, also supports the assumption that these traits are controlled by a few genes. SCA effects also played a role, especially when lines with low spontaneous doubling were used as parents. Overall, spontaneous doubling can be introgressed and improved in elite germplasm with selection, and it has the potential to be employed in DH pipelines.

Development of in Vivo Haploid Inducer Lines for Screening Haploid Immature Embryos in Maize

Doubled haploid technology is widely applied in maize. The haploid inducer lines play critical roles in doubled haploid breeding. We report the development of specialized haploid inducer lines that enhance the purple pigmentation of crossing immature embryos. During the development of haploid inducer lines, two breeding populations derived from the CAU3/S23 and CAU5/S23 were used. Molecular marker-assisted selection for both qhir1 and qhir8 was used from BC₁F₁ to BC₁F₄. Evaluation of the candidate individuals in each generation was carried out by pollinating to the tester of ZD958. Individuals with fast and clear pigmentation of the crossing immature embryos, high number of haploids per ear, and high haploid induction rate were considered as candidates. Finally, three new haploid inducer lines (CS1, CS2, and CS3) were developed. The first two (CS1 and CS2) were from the CAU3/S23, with a haploid induction rate of 8.29%–13.25% and 11.54%–15.54%, respectively. Meanwhile, the CS3 was from the CAU5/S23. Its haploid induction rate was 8.14%–12.28%. In comparison with the donor haploid inducer lines, the 24-h purple embryo rates of the newly developed haploid inducer lines were improved by 10%–20%, with a ~90% accuracy for the identification of haploid immature embryos. These new haploid inducer lines will further improve the efficiency of doubled haploid breeding of maize.

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.

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 .

DNA content equivalence in haploid and diploid maize leaves

The qPCR assay developed to differentiate haploid and diploid maize leaf samples was unsuccessful due to DNA content difference. Haploid cells are packed more closely together with less cellular expansion. Increased ploidy content (> 2 N) directly correlates with increased cell size in plants, but few studies have examined cell morphology in plants with reduced ploidy (i.e., haploids). To pioneer a scalable new ploidy test, we compared DNA content and cellular morphology of haploid and diploid maize leaves. The amount of genomic DNA recovered from standardized leaf-punch samples was equivalent between these two ploidy types, while both epidermal and mesophyll cell types were smaller in haploid plants. Pavement cells had a substantially smaller size than mesophyll cells, and this effect was more pronounced in the abaxial epidermis. Interveinal distance and guard cell size were significantly reduced in haploids, but the cell percentage comprising stomata did not change. These results confirm the direct correlation between ploidy content and cell size in plants, and suggest that reduced cell expansion predominantly explains DNA content equivalence between haploid and diploid samples, confounding efforts to develop a haploid detection method using DNA content.

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.

Effect of F1 and F2 generations on genetic variability and working steps of doubled haploid production in maize

For doubled haploid (DH) production in maize, F1 generation has been the most frequently used for haploid induction due to facility in the process. However, using F2 generation would be a good alternative to increase genetic variability owing to the additional recombination in meiosis. Our goals were to compare the effect of F1 and F2 generations on DH production in tropical germplasm, evaluating the R1-navajo expression in seeds, the working steps of the methodology, and the genetic variability of the DH lines obtained. Sources germplasm in F1 and F2 generations were crossed with the tropicalized haploid inducer LI-ESALQ. After harvest, for both induction crosses were calculated the haploid induction rate (HIR), diploid seed rate (DSR), and inhibition seed rate (ISR) using the total number of seeds obtained. In order to study the effectiveness of the DH working steps in each generation, the percentage per se and the relative percentage were verified. In addition, SNP markers were obtained for genetic variability studies. Results showed that the values for HIR, ISR, and DSR were 1.23%, 23.48%, and 75.21% for F1 and 1.78%, 15.82%, and 82.38% for F2, respectively. The effectiveness of the DH working step showed the same percentage per se value (0.4%) for F1 and F2, while the relative percentage was 27.2% for F1 and 22.4% for F2. Estimates of population parameters in DH lines from F1 were higher than F2. Furthermore, population structure and kinship analyses showed that one additional generation was not sufficient to create new genotype subgroups. Additionally, the relative efficiency of the response to selection in the F1 was 31.88% higher than F2 due to the number of cycles that are used to obtain the DH. Our results showed that in tropical maize, the use of F1 generation is recommended due to a superior balance between time and genetic variability.

Genome-wide association study to identify genomic regions influencing spontaneous fertility in maize haploids

Efficient production and use of doubled haploid lines can greatly accelerate genetic gains in maize breeding programs. One of the critical steps in standard doubled haploid line production is doubling the haploid genome using toxic and costly mitosis-inhibiting chemicals to achieve fertility in haploids. Alternatively, fertility may be spontaneously restored by natural chromosomal doubling, although generally at a rate too low for practical applications in most germplasm. This is the first large-scale genome-wise association study to analyze spontaneous chromosome doubling in haploids derived from tropical maize inbred lines. Induction crosses between tropicalized haploid inducers and 400 inbred lines were made, and the resulting haploid plants were assessed for haploid male fertility which refers to pollen production and haploid fertility which refers to seed production upon self-fertilization. A small number of genotypes were highly fertile and these fertility traits were highly heritable. Agronomic traits like plant height, ear height and tassel branch number were positively correlated with fertility traits. In contrast, haploid induction rate of the source germplasm and plant aspect were not correlated to fertility traits. Several genomic regions and candidate genes were identified that may control spontaneous fertility restoration. Overall, the study revealed the presence of large variation for both haploid male fertility and haploid fertility which can be potentially exploited for improving the efficiency of doubled haploid derivation in tropical maize germplasm.

DeepSort: deep convolutional networks for sorting haploid maize seeds

BACKGROUND

Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize line has accelerated the pace of development of superior commercial seed varieties and has been transforming the agricultural industry. In this technique the chromosomes of the haploid seeds are doubled and taken forward in the process while the diploids marked for elimination. Traditionally, selective visual expression of a molecular marker within the embryo region of a maize seed has been used to manually discriminate diploids from haploids. Large scale production of inbred maize lines within the agricultural industry would benefit from the development of computer vision methods for this discriminatory task. However the variability in the phenotypic expression of the molecular marker system and the heterogeneity arising out of the maize genotypes and image acquisition have been an enduring challenge towards such efforts.

RESULTS

In this work, we propose a novel application of a deep convolutional network (DeepSort) for the sorting of haploid seeds in these realistic settings. Our proposed approach outperforms existing state-of-the-art machine learning classifiers that uses features based on color, texture and morphology. We demonstrate the network derives features that can discriminate the embryo regions using the activations of the neurons in the convolutional layers. Our experiments with different architectures show that the performance decreases with the decrease in the depth of the layers.

CONCLUSION

Our proposed method DeepSort based on the convolutional network is robust to the variation in the phenotypic expression, shape of the corn seeds, and the embryo pose with respect to the camera. In the era of modern digital agriculture, deep learning and convolutional networks will continue to play an important role in advancing research and product development within the agricultural industry.

Marker-Assisted Breeding of Improved Maternal Haploid Inducers in Maize for the Tropical/Subtropical Regions

For efficient production of doubled haploid (DH) lines in maize, maternal haploid inducer lines with high haploid induction rate (HIR) and good adaptation to the target environments is an important requirement. In this study, we present second-generation Tropically Adapted Inducer Lines (2GTAILs), developed using marker assisted selection (MAS) for qhir1, a QTL with a significant positive effect on HIR from the crosses between elite tropical maize inbreds and first generation Tropically Adapted Inducers Lines (TAILs). Evaluation of 2GTAILs for HIR and agronomic performance in the tropical and subtropical environments indicated superior performance of 2GTAILs over the TAILs for both HIR and agronomic performance, including plant vigor, delayed flowering, grain yield, and resistance to ear rots. One of the new inducers 2GTAIL006 showed an average HIR of 13.1% which is 48.9% higher than the average HIR of the TAILs. Several other 2GTAILs also showed higher HIR compared to the TAILs. While employing MAS for qhir1 QTL, we observed significant influence of the non-inducer parent on the positive effect of qhir1 QTL on HIR. The non-inducer parents that resulted in highest mean HIR in the early generation qhir1+ families also gave rise to highest numbers of candidate inducers, some of which showed transgressive segregation for HIR. The mean HIR of early generation qhir1+ families involving different non-inducer parents can potentially indicate recipient non-inducer parents that can result in progenies with high HIR. Our study also indicated that the HIR associated traits (endosperm abortion rate, embryo abortion rate, and proportion of haploid plants among the inducer plants) can be used to differentiate inducers vs. non-inducers but are not suitable for differentiating inducers with varying levels of haploid induction rates. We propose here an efficient methodology for developing haploid inducer lines combining MAS for qhir1 with HIR associated traits.

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.

Tapping the genetic diversity of landraces in allogamous crops with doubled haploid lines: a case study from European flint maize

Using landraces for broadening the genetic base of elite maize germplasm is hampered by heterogeneity and high genetic load. Production of DH line libraries can help to overcome these problems. Landraces of maize (Zea mays L.) represent a huge reservoir of genetic diversity largely untapped by breeders. Genetic heterogeneity and a high genetic load hamper their use in hybrid breeding. Production of doubled haploid line libraries (DHL) by the in vivo haploid induction method promises to overcome these problems. To test this hypothesis, we compared the line per se performance of 389 doubled haploid (DH) lines across six DHL produced from European flint landraces with that of four flint founder lines (FFL) and 53 elite flint lines (EFL) for 16 agronomic traits evaluated in four locations. The genotypic variance ([Formula: see text]) within DHL was generally much larger than that among DHL and exceeded also [Formula: see text] of the EFL. For most traits, the means and [Formula: see text] differed considerably among the DHL, resulting in different expected selection gains. Mean grain yield of the EFL was 25 and 62% higher than for the FFL and DHL, respectively, indicating considerable breeding progress in the EFL and a remnant genetic load in the DHL. Usefulness of the best 20% lines was for individual DHL comparable to the EFL and grain yield (GY) in the top lines from both groups was similar. Our results corroborate the tremendous potential of landraces for broadening the narrow genetic base of elite germplasm. To make best use of these "gold reserves", we propose a multi-stage selection approach with optimal allocation of resources to (1) choose the most promising landraces for DHL production and (2) identify the top DH lines for further breeding.

Identification of in vivo induced maternal haploids in maize using seedling traits

In vivo haploid induction in high frequency followed by efficient identification of haploids are important components of deriving completely homozygous doubled haploid (DH) lines in maize. Several genetic marker systems were proposed and/or used for identification of in vivo maternal haploids in maize, such as R1-nj (Navajo), high oil, red root and transgenic markers. In this study, we propose a new method of haploid/diploid identification based on natural differences in seedling traits of haploids and diploids, which can be used in any induction cross independently of the genetic marker systems. Using confirmed haploids and diploids from five different populations, the study established that haploid and diploid seedlings exhibit significant differences for seedling traits, particularly radicle length (RL), coleoptile length (CL), and number of lateral seminal roots (NLSR). In six populations that exhibited complete inhibition of the commonly used R1-nj (Navajo) marker, we could effectively differentiate haploids from diploids by visual inspection of the seedling traits. In the haploid seed fraction identified based on R1-nj marker in ten populations, false positives were reduced several-fold by early identification of haploids at seedling stage using the seedling traits. We propose that seedling traits may be integrated at the haploid identification stage, especially in populations that are not amenable to use of genetic markers, and for improving the efficiency of DH line production by reducing the false positives.

Fine mapping of qhir8 affecting in vivo haploid induction in maize

The QTL qhir8 affecting in vivo haploid induction in maize was mapped to a 789 kb region, embryo abortion rate and segregation ratios were analyzed, linkage markers for MAS were developed. The doubled-haploid (DH) technology has become an important tool for line development in modern maize breeding. However, the genetic basis of haploid induction remains elusive. In previous QTL mapping research, qhir8 besides qhir1 significantly affected haploid induction rate (HIR). Our objective was to fine map qhir8 and assess its effect on HIR, segregation distortion (SD) and embryo abortion (EmA). A total of 3989 F2 plants from the cross of inducers CAUHOI and UH400 were screened for recombinants in the qhir8 region. F2 plants and F3 plants from selfing progenies of 34 recombinant F2 plants were evaluated for HIR, SD and EmA. In parallel, we developed 31 new markers providing good coverage of the qhir8 region. We confirmed that qhir8 has an increasing effect on HIR and EmA, but not on SD. Moreover, we successfully narrowed down the qhir8 locus to a 789 kb region flanked by markers 4292232 and umc1867.

Haploids: Constraints and opportunities in plant breeding

The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F2 plants are the most suitable for the induction of DH lines than F1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye and wheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resources with DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to national programs or small-medium private seed for the exploitation of DH technology in plant breeding.