Hybrid breeding in wheat: technologies to improve hybrid wheat seed production

Stigma and Glume Characteristics Synergistically Determine the Stigma Exsertion Rate in Thermo-Photo-Sensitive Genic Male Sterile Wheat

Wheat hybrids have been widely demonstrated to have remarkable heterosis or hybrid vigor in increasing yield potential and stability since the 1960s. Two-line hybrid wheat can achieve higher yields than local varieties, especially in marginal environments. However, the commercial application of hybrid wheat is hindered by higher seed costs, primarily due to lower yields in hybrid seed production. Stigma exsertion has been verified as a decisive factor in increasing rice's hybrid seed yield, but more investigation is needed in hybrid wheat breeding and production. In this study, four thermo-photo-sensitive genic male sterile lines, including K41S, K64S, K66S, and K68S, with different stigma exsertion rates (SERs) were used to compare the differences in floral architecture relative to stigma exsertion over two growing seasons. The results revealed that the K41S and K64S exhibited a relatively higher SER at 21.87% and 22.81%, respectively. No exserted stigma was observed in K66S, and K68S had an SER of only 0.82%. This study found that the stigma length, glume width and the length-width ratio of the glume were significantly correlated with the SER, with correlation coefficients of 0.46, -0.46 and 0.60, respectively. Other stigma features such as the branch angle, stretch width and hairbrush length, as well as the glume length, also had a weakly positive correlation with SER (r = 0.09-0.27). For K41S and K64S, the SER was significantly affected by the differences in the stigma branch angle and stigma stretch width among florets. A cross-pollination survey showed that the out-crossing ability of florets with an exserted stigma was about three times as high as that of florets with a non-exserted stigma. As a result, the stigma-exserted florets that accounted for 21.87% and 22.81% of the total florets in K41S and K64S produced 46.80% and 48.53% of the total cross-pollinated seeds in both sterile lines. These findings suggest that a longer stigma combined with a slender glume appears to be the essential floral feature of stigma exsertion in sterile wheat lines. It is expected that breeding and utilizing sterile lines with a higher SER would be a promising solution to cost-effective hybrid wheat seed production.

Identifying the seeds of heterotic pools for Southern and Eastern Africa from global elite spring wheat germplasm

Hybrid breeding can increase the competitiveness of wheat (Triticum aestivum L.) in Sub-Saharan Africa by fostering more public-private partnerships and promoting investment by the private sector. The benefit of hybrid wheat cultivars in South Africa has previously been demonstrated but due to the high cost of hybrid seed production, hybrid breeding has not received significant attention in the past decade. Considering the renewed commitment of the private sector to establish wheat as a hybrid crop globally, coupled with significant research investment into enhancement of outcrossing of wheat, hybrid wheat breeding in Southern and Eastern Africa should be revisited. Our study aimed to identify genetically distinct germplasm groups in spring wheat that would be useful in the establishment of heterotic pools targeting this region. Multi-environment yield testing of a large panel of F1 test hybrids, generated using global elite germplasm, was carried out between 2019 and 2020 in Argentina, Africa, Europe, and Australia. We observed significant genotype by environment interactions within our testing network, confirming the distinctiveness of African trial sites. Relatively high additive genetic variance was observed highlighting the contribution of parental genotypes to the grain yield of test hybrids. We explored the genetic architecture of these parents and the genetic factors underlying the value of parents appear to be associated with their genetic subgroup, with positive marker effects distributed throughout the genome. In testcrosses, elite germplasm from the International Maize and Wheat Improvement Center (CIMMYT) appear to be complementary to the genetically distinct germplasm bred in South Africa. The feasibility of achieving genetic gain via heterotic pool establishment and divergence, and by extension the viability of hybrid cultivars in Sub-Saharan Africa, is supported by the results of our study.

Diversity in bread and durum wheat stigma morphology and linkage of increased stigma length to dwarfing gene Rht14

KEY MESSAGE

The dwarfing allele Rht14 of durum wheat associates with greater stigma length, an important trait for hybrid breeding, whilst major dwarfing alleles Rht-B1b and Rht-D1b showed little to no effect. Although much understudied in wheat, the stigma is a crucial component for attaining grain set, the fundamental basis for yield, particularly in hybrid production systems where successful grain set relies on wind-driven pollen dispersal by the male parent and effective pollen capture by the female parent. Females with long stigma that exsert early are thought to be advantageous. Using glasshouse-grown lines, we examined variation in Total Stigma Length (TSL) across diverse panels comprising 27 durum and 116 bread wheat genotypes. Contrasting genotypes were selected for population development and genetic analysis. Quantitative trait loci (QTL) analysis was performed on a durum F2 population and a bread wheat recombinant inbred line (RIL) population. Contrasting with studies of anther length, we found no large effect on TSL of the GA-insensitive semi-dwarfing genes Rht-B1 and Rht-D1 in either durum or bread wheat. However, in durum cultivar Italo, we identified a region on chromosome 6A which is robustly associated with larger TSL and contains the Rht14 allele for reduced plant height, a trait that is favourable for female line development in hybrid systems. This dual effect locus explained 25.2 and 19.2% of TSL phenotypic variation in experiments across two growing seasons, with preliminary results suggesting this locus may increase TSL when transferred to bread wheat. In a bread wheat, RIL population minor QTL on 1A and 2A was indicated, but the strongest association was with Ppd-B1. Methods developed here, and the identification of a TSL-enhancing locus provides advances and further opportunities in the study of wheat stigma.

Green Revolution dwarfing Rht genes negatively affected wheat floral traits related to cross-pollination efficiency

Hybrid breeding is a promising strategy to quickly improve wheat yield and stability. Due to the usefulness of the Rht 'Green Revolution' dwarfing alleles, it is important to gain a better understanding of their impact on traits related to hybrid development. Traits associated with cross-pollination efficiency were studied using Near Isogenic Lines carrying the different sets of alleles in Rht genes: Rht1 (semi-dwarf), Rht2 (semi-dwarf), Rht1 + 2 (dwarf), Rht3 (extreme dwarf), Rht2 + 3 (extreme dwarf), and rht (tall) during four growing seasons. Results showed that the extreme dwarfing alleles Rht2 + 3, Rht3, and Rht1 + 2 presented the greatest effects in all the traits analyzed. Plant height showed reductions up to 64% (Rht2 + 3) compared to rht. Decreases up to 20.2% in anther length and 33% in filament length (Rht2 + 3) were observed. Anthers extrusion decreased from 40% (rht) to 20% (Rht1 and Rht2), 11% (Rht3), 8.3% (Rht1 + 2), and 6.5% (Rht2 + 3). Positive correlations were detected between plant height and anther extrusion, anther, and anther filament lengths, suggesting the negative effect of dwarfing alleles. Moreover, the magnitude of these negative impacts depends on the combination of the alleles: Rht2 + 3 > Rht3/Rht1 + 2 > Rht2/Rht1 > rht (tall). Reductions were consistent across genotypes and environments with interactions due to magnitude effects. Our results indicate that Rht alleles are involved in multiple traits of interest for hybrid wheat production and the need to select alternative sources for reduced height/lodging resistance for hybrid breeding programs.

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages

BACKGROUND

Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored.

METHODS

In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages.

RESULTS

Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles.

CONCLUSION

These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.

From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma

Toxoplasma gondii causes morbidity, mortality, and disseminates widely via cat sexual stages. Here, we find T. gondii ornithine aminotransferase (OAT) is conserved across phyla. We solve TgO/GABA-AT structures with bound inactivators at 1.55 Å and identify an inactivator selective for TgO/GABA-AT over human OAT and GABA-AT. However, abrogating TgO/GABA-AT genetically does not diminish replication, virulence, cyst-formation, or eliminate cat's oocyst shedding. Increased sporozoite/merozoite TgO/GABA-AT expression led to our study of a mutagenized clone with oocyst formation blocked, arresting after forming male and female gametes, with "Rosetta stone"-like mutations in genes expressed in merozoites. Mutations are similar to those in organisms from plants to mammals, causing defects in conception and zygote formation, affecting merozoite capacitation, pH/ionicity/sodium-GABA concentrations, drawing attention to cyclic AMP/PKA, and genes enhancing energy or substrate formation in TgO/GABA-AT-related-pathways. These candidates potentially influence merozoite's capacity to make gametes that fuse to become zygotes, thereby contaminating environments and causing disease.

Heterosis in crop improvement

Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F1 hybrids over both inbred parents. The development of high-yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self-pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis-associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis-associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (Hordeum vulgare) as the model self-pollinating crop species, and a few heterosis-associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.

Selecting tropical wheat genotypes through combining ability analysis

The selection of parents to originate promising base populations, as well as the knowledge of the gene effects controlling agronomic traits by means of diallel, are useful to drive genetic gains in Brazilian tropical wheat breeding programs. The goals of this study were to select tropical wheat parents with a high frequency of favorable alleles and segregating populations with high potential to originate superior progenies through partial diallel analysis. Thus, 14 parents were divided in two groups and crossed in a 7 × 7 partial diallel scheme to originate 49 F1 combinations. After obtaining F2 generation, the populations and the parents were evaluated in the field in the summer of 2021. Days for heading, plant height, rust and yellow spot resistance, and grain yield were evaluated. The data were subjected to partial diallel analysis. There were significant effects of general combining ability for all traits. The specific combining ability effect was significant for days for heading and plant height. The additive gene effects were predominant over the non-additive ones. The parents with the highest frequency of favorable alleles for the traits evaluated were selected in each group. Four populations with high genetic potential to originate superior progenies were selected.

Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line

The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.

Combining ability analysis of yield and biomass allocation related traits in newly developed wheat populations

Increasing biomass allocation to the root system may increase soil-organic carbon stocks and confer drought adaptation in water-limited environments. Understanding the genetic bases and inheritance of biomass allocation is fundamental for drought tolerance breeding and soil health. The objective of this study was to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield and biomass allocation related traits in wheat to identify good combiners for breeding and enhanced carbon sequestration. Ten selected wheat genotypes were crossed in a full diallel mating design, and 90 F₂ families were generated and evaluated in the field and greenhouse under drought-stressed and non-stressed conditions. Significant differences were recorded among the tested families revealing substantial variation for plant height (PH), kernels per spike (KPS), root biomass (RB), shoot biomass (SB), total plant biomass (PB) and grain yield (GY). Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. Line BW162 had high yield and biomass production and can be used to transfer favourable genes to its progeny. The parental line LM75 maintained the general combining ability (GCA) effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study.

Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications

Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.

Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus

KEY MESSAGE

This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0 Mb (231.0-242 Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.

Genetic Mechanisms for Hybrid Breeding in Vegetable Crops

To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.

ROS accumulation-induced tapetal PCD timing changes leads to microspore abortion in cotton CMS lines

BACKGROUND

Cytoplasmic male sterility (CMS) is the basis of heterosis exploitation. CMS has been used to hybrid production in cotton, but its molecular mechanism remains unclear. CMS is associated with advanced or delayed tapetal programmed cell death (PCD), and reactive oxygen species (ROS) may mediate this process. In this study, we obtained Jin A and Yamian A, two CMS lines with different cytoplasmic sources.

RESULTS

Compared with maintainer Jin B, Jin A anthers showed advanced tapetal PCD with DNA fragmentation, producing excessive ROS which accumulated around the cell membrane, intercellular space and mitochondrial membrane. The activities of peroxidase (POD) and catalase (CAT) enzymes which can scavenge ROS were significantly decreased. However, Yamian A tapetal PCD was delayed with lower ROS content, and the activities of superoxide dismutase (SOD) and POD were higher than its maintainer. These differences in ROS scavenging enzyme activities may be caused by isoenzyme gene expressions. In addition, we found the excess ROS generated in Jin A mitochondria and ROS overflow from complex III might be the source in parallel with the reduction of ATP content.

CONCLUSION

ROS accumulation or abrogation were mainly caused by the joint action of ROS generation and scavenging enzyme activities transformation, which led to the abnormal progression of tapetal PCD, affected the development of microspores, and eventually contributed to male sterility. In Jin A, tapetal PCD in advance might be caused by mitochondrial ROS overproduction, accompanied by energy deficiency. The above studies will provide new insights into the cotton CMS and guide the follow-up research ideas.

A bifunctional selectable marker for wheat transformation contributes to the characterization of male-sterile phenotype induced by a synthetic Ms2 gene

KEY MESSAGE

An engineered selectable marker combining herbicide resistance and yellow fluorescence contributes to the characterization of male-sterile phenotype in wheat, the severity of which correlates with expression levels of a synthetic Ms2 gene. Genetic transformation of wheat is conducted using selectable markers, such as herbicide and antibiotic resistance genes. Despite their proven effectiveness, they do not provide visual control of the transformation process and transgene status in progeny, which creates uncertainty and prolongs screening procedures. To overcome this limitation, this study developed a fusion protein by combining gene sequences encoding phosphinothricin acetyltransferase and mCitrine fluorescent protein. The fusion gene, introduced into wheat cells by particle bombardment, enabled herbicide selection, and visual identification of primary transformants along with their progeny. This marker was then used to select transgenic plants containing a synthetic Ms2 gene. Ms2 is a dominant gene whose activation in wheat anthers leads to male sterility, but the relationship between the expression levels and the male-sterile phenotype is unknown. The Ms2 gene was driven either by a truncated Ms2 promoter containing a TRIM element or a rice promoter OsLTP6. The expression of these synthetic genes resulted in complete male sterility or partial fertility, respectively. The low-fertility phenotype was characterized by smaller anthers than the wild type, many defective pollen grains, and low seed sets. The reduction in the size of anthers was observed at earlier and later stages of their development. Consistently, Ms2 transcripts were detected in these organs, but their levels were significantly lower than those in completely sterile Ms2TRIM::Ms2 plants. These results suggested that the severity of the male-sterile phenotype was modulated by Ms2 expression levels and that higher levels may be key to activating total male sterility.

Characterisation of the complete mitochondrial genome of Taraxacum mongolicum revealed five repeat-mediated recombinations

We reported the mitochondrial genome of Taraxacum mongolicum for the first time. Five pairs of repeats that can mediate recombination were validated, leading to multiple conformations of genome. Taraxacum mongolicum belongs to the Asteraceae family and has important pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled the complete mitochondrial genome (mitogenome) of T. mongolicum using Illumina and Oxford Nanopore sequencing data. This genome corresponded to a circular molecule 304,467 bp long. It encodes 52 unique genes including 31 protein-coding, 3 ribosomal RNA (rRNA) and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, the existence of alternative conformations mediated by five repetitive sequences in the mitogenome was identified and validated. Recombination mediated by the inverted repeats resulted in two conformations. Conversely, recombination mediated by the two direct repeats broke one large circular molecule into two subgenomic circular molecules. Furthermore, we identified 12 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. Lastly, we identified a total of 278 RNA-editing sites in protein-coding sequences based on RNA-seq data. Among them, cox1 and nad5 gene has the most sites (21), followed by the nad2 gene with 19 sites. We successfully validated 213 predicted RNA-editing sites using PCR amplification and Sanger sequencing. This project reported the first mitogenome of T. mongolicum and demonstrated its multiple conformations generated by repeat-mediated recombination. This genome could provide critical information for the molecular breeding of T. mongolicum, and also be used as a reference genome for other species of the genus Taraxacum.

The Alpha Subunit of Mitochondrial Processing Peptidase Participated in Fertility Restoration in Honglian-CMS Rice

The cytoplasmic male sterility (CMS) and nuclear-controlled fertility restoration system is a favorable tool for the utilization of heterosis in plant hybrid breeding. Many restorer-of-fertility (Rf) genes have been characterized in various species over the decades, but more detailed work is needed to investigate the fertility restoration mechanism. Here, we identified an alpha subunit of mitochondrial processing peptidase (MPPA) that is involved in the fertility restoration process in Honglian-CMS rice. MPPA is a mitochondrial localized protein and interacted with the RF6 protein encoded by the Rf6. MPPA indirectly interacted with hexokinase 6, namely another partner of RF6, to form a protein complex with the same molecular weight as the mitochondrial F1F0-ATP synthase in processing the CMS transcript. Loss-of-function of MPPA resulted in a defect in pollen fertility, the mppa+/− heterozygotes showed semi-sterility phenotype and the accumulation of CMS-associated protein ORFH79, showing restrained processing of the CMS-associated atp6-OrfH79 in the mutant plant. Taken together, these results threw new light on the process of fertility restoration by investigating the RF6 fertility restoration complex. They also reveal the connections between signal peptide cleavage and the fertility restoration process in Honglian-CMS rice.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

Combined QTL mapping on bi-parental immortalized heterozygous populations to detect the genetic architecture on heterosis

From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB₁ and IB₂, representing the two directions of backcrossing) and F₂ (i.e., IF₂) populations can be developed. These populations are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB₁, IB₂, and IF₂) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB₁ and IB₂ are present, summation and subtraction are used. When IF₂ and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF₂ population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects.

Effect of Heavy Metal Stress on Phenolic Compounds Accumulation in Winter Wheat Plants

Heavy metal stress can lead to many adverse effects that inhibit cellular processes at various levels of metabolism, causing a decrease in plant productivity. In response to environmental stressors, phenolic compounds fulfill significant molecular and biochemical functions in plants. Increasing the biosynthesis of phenolic compounds in plants subjected to heavy metal stress helps protect plants from oxidative stress. A pot experiment was carried out to determine the effect of the accumulation of copper (Cu) and lead (Pb) salts at concentrations of 200, 500, and 1000 ppm on seed germination, the activity of enzymes in the phenylalanine ammonia-lyase pathway (PAL) and tyrosine ammonia-lyase (TAL), along with the total phenol and flavonoid contents in seedlings of hybrid Triticum aestivum L. (winter wheat) cultivars. The accumulation of heavy metals, especially Cu, had a negative impact on the seed germination process. The cultivar "Hyacinth" reacted most strongly to heavy metal stress, which was confirmed by obtaining the lowest values of the germination parameters. Heavy metal stress caused an increase in the activity of PAL and TAL enzymes and an increase in the accumulation of phenolic compounds. Under the influence of Cu, the highest activity was shown in cv. "Hyvento" (especially at 200 ppm) and, due to the accumulation of Pb, in cv. "Hyacinth" (1000 ppm) and cv. "Hyking" (200 ppm). The cultivar "Hyking" had the highest content of phenolic compounds, which did not increase with the application of higher concentrations of metals. In other cultivars, the highest content of total phenols and flavonoids was usually observed at the lowest concentration (200 ppm) of the tested heavy metals, Cu and Pb.

Genome-Wide Association Analysis for Hybrid Breeding in Wheat

Disclosure of markers that are significantly associated with plant traits can help develop new varieties with desirable properties. This study determined the genome-wide associations based on DArTseq markers for six agronomic traits assessed in eight environments for wheat. Moreover, the association study for heterosis and analysis of the effects of markers grouped by linkage disequilibrium were performed based on mean values over all experiments. All results were validated using data from post-registration trials. GWAS revealed 1273 single nucleotide polymorphisms with biologically significant effects. Most polymorphisms were predicted to be modifiers of protein translation, with only two having a more pronounced effect. Markers significantly associated with the considered set of features were clustered within chromosomes based on linkage disequilibrium in 327 LD blocks. A GWAS for heterosis revealed 1261 markers with significant effects.

Transcriptional gene silencing in bread wheat (Triticum aestivum L.) and its application to regulate male fertility for hybrid seed production

Transcriptional gene silencing (TGS) can offer a straightforward tool for functional analysis of plant genes, particularly in polyploid species such as wheat, where genetic redundancy poses a challenge in applying mutagenesis approaches, including CRISPR gene editing. In this study, we demonstrate efficient TGS in wheat, mediated by constitutive RNA expression of a promoter inverted repeat (pIR). pIR-mediated TGS of two anther-specific genes, TaMs45 and TaMs1, abolished their function resulting in male sterility. Whilst TGS of TaMs45 required transcriptional silencing of all three homoeologs, a B-genome-specific pIR for TaMs1 was sufficient to confer male sterility. We further show that the pIRs effect TGS of TaMs45 gene through DNA methylation of homologous promoter sequence, successfully suppressing transcription of all three homoeologs. Applying pIR-mediated TGS in wheat, we have generated a dominant male fertility system for production of hybrid seed and demonstrated the efficacy of this system under greenhouse and field conditions. This report describes the first successful TGS in wheat, whilst providing a dominant negative approach as alternative to gene knockout strategies for hybrid wheat breeding and seed production.

Engineering Apomixis: Clonal Seeds Approaching the Fields

Apomixis is a form of reproduction leading to clonal seeds and offspring that are genetically identical to the maternal plant. While apomixis naturally occurs in hundreds of plant species distributed across diverse plant families, it is absent in major crop species. Apomixis has a revolutionary potential in plant breeding, as it could allow the instant fixation and propagation though seeds of any plant genotype, most notably F₁ hybrids. Mastering and implementing apomixis would reduce the cost of hybrid seed production, facilitate new types of hybrid breeding, and make it possible to harness hybrid vigor in crops that are not presently cultivated as hybrids. Synthetic apomixis can be engineered by combining modifications of meiosis and fertilization. Here, we review the current knowledge and recent major achievements toward the development of efficient apomictic systems usable in agriculture.

Hybrid Seed Set in Relation with Male Floral Traits, Estimation of Heterosis and Combining Abilities for Yield and Its Components in Wheat (Triticum aestivum L.)

Breeding hybrids with maximum heterosis requires efficient cross-pollination and an improved male sterility system. Renewed efforts have been made to dissect the phenotypic variation and genetic basis of hybrid floral traits, although the potential of tailoring the appropriate flower design on seed setting is less known. To this end, elite wheat genotypes were crossed using a chemical hybridizing agent at different doses. A total of 23 hybrids were developed from a partial diallel design; and planted in an alpha lattice design with their parents at two locations in Morocco, for two years, to evaluate for yield components, heterosis and combining abilities. The 13.5 L ha^-1 dose induced a maximum level of sterility (95%) and seed set showed large phenotypic variation and high heritability. In parallel, seed set showed tight correlation with pollen mass (0.97), visual anther extrusion (0.94) and pollen shedding (0.91) (p < 0.001), allowing direct selection of the associated traits. Using the combined data, mid-parent heterosis ranges were -7.64-14.55% for biomass (BM), -8.34-12.51% for thousand kernel weight (TKW) and -5.29-26.65% for grain yield (YLD); while best-parent heterosis showed ranges of -11.18-7.20%, -11.35-11.26% and -8.27-24.04% for BM, TKW and YLD, respectively. The magnitude of general combining ability (GCA) variance was greater than the specific combining ability (SCA) variance suggesting a greater additive gene action for BM, TKW and YLD. The favorable GCA estimates showed a simple method to predict additive effects contributing to high heterosis and thus could be an effective approach for the selection of promising parents in early generations.

Profiling Cultivars Development in Kersting's Groundnut [Macrotyloma geocarpum (Harms) Maréchal and Baudet] for Improved Yield, Higher Nutrient Content, and Adaptation to Current and Future Climates

Kersting's groundnut [Macrotyloma geocarpum (Harms.) Maréchal and Baudet], Fabaceae, is an important source of protein and essential amino acids. As a grain legume species, it also contributes to improving soil fertility through symbiotic nitrogen fixation. However, the crop is characterized by a relatively low yield (≤500 kg/ha), and limited progress has been made so far, toward the development of high-yielding cultivars that can enhance and sustain its productivity. Recently, there was an increased interest in alleviating the burdens related to Kersting's groundnut (KG) cultivation through the development of improved varieties. Preliminary investigations assembled germplasms from various producing countries. In-depth ethnobotanical studies and insightful investigation on the reproductive biology of the species were undertaken alongside morphological, biochemical, and molecular characterizations. Those studies revealed a narrow genetic base for KG. In addition, the self-pollinating nature of its flowers prevents cross-hybridization and represents a major barrier limiting the broadening of the genetic basis. Therefore, the development of a research pipeline to address the bottlenecks specific to KG is a prerequisite for the successful expansion of the crop. In this paper, we offer an overview of the current state of research on KG and pinpoint the knowledge gaps; we defined and discussed the main steps of breeding for KG' cultivars development; this included (i) developing an integrated genebank, inclusive germplasm, and seed system management; (ii) assessing end-users preferences and possibility for industrial exploitation of the crop; (iii) identifying biotic and abiotic stressors and the genetic control of responsive traits to those factors; (iv) overcoming the cross-pollination challenges in KG to propel the development of hybrids; (v) developing new approaches to create variability and setting adequate cultivars and breeding approaches; (vi) karyotyping and draft genome analysis to accelerate cultivars development and increase genetic gains; and (vii) evaluating the adaptability and stability of cultivars across various ecological regions.

A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Secale cereale L.)

Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.

Mitochondrial genes are involved in the fertility transformation of the thermosensitive male-sterile line YS3038 in wheat

Heterosis can improve the stress resistance, quality, and yield of crops, and the male sterility of wheat can be utilized to accelerate the breeding process of hybrid. To determine whether mitochondrial genes are involved in the fertility of K-type cytoplasmic male-sterile (CMS) line and the YS-type thermosensitive male-sterile (TMS) line in wheat, we sequenced and assembled the mitochondrial genomes of K519A, 519B, and YS3038 by next-generation sequencing (NGS). The non-synonymous mutations were analyzed, and the first-generation sequencing was conducted to verify the non-synonymous mutation sites. Furthermore, the expression patterns of genes with non-synonymous mutations were analyzed. Finally, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to test the functions of the candidate genes. The results revealed that the mitochondrial genomes of K519A, 519B, and YS3038 were 420,543, 433,560, and 452,567 bp in length, respectively. Besides, 33, 31, and 37 protein-coding genes were identified in K519A, 519B, and YS3038, respectively. There were 14 protein-coding genes and 83 open reading frame (ORF) sequences that differed between K519A and 519B and 10 protein-coding genes and 122 ORF sequences that differed between K519A and YS3038. At the binucleate stage, seven genes (nad6, ORF256, ORF216, ORF138, atp6, nad3, and cox1) were downregulated in K519A compared with 519B, and 10 genes (nad6, atp6, cox3, atp8, nad3, cox1, rps3, ORF216, ORF138, and ORF224) were downregulated in YS3038 compared with K519A. Besides, six genes (nad6, ORF138, cox3, cox1, rps3, and ORF224) were downregulated under fertile conditions relative to sterile conditions in YS3038. Gene silencing analysis showed that the silencing of cox1 significantly reduced the seed setting rate of YS3038, indicating that the cox1 gene may be involved in the fertility transformation of YS3038.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01252-x.

MS1 is essential for male fertility by regulating the microsporocyte cell plate expansion in soybean

Male sterility is an essential trait in hybrid seed production, especially for monoclinous and autogamous food crops. Soybean male-sterile ms1 mutant has been known for more than 50 years and could be instrumental in making hybrid seeds. However, the gene responsible for the male-sterile phenotype has remained unknown. Here, we report the map-based cloning and characterization of the MS1 gene in soybean. MS1 encodes a kinesin protein and localizes to the nucleus, where it is required for the male meiotic cytokinesis after telophase II. We further substantiated that MS1 colocalizes with microtubules and is essential for cell plate formation in soybean male gametogenesis through immunostaining. Both ms1 and CRISPR/Cas9 knockout mutants show complete male sterility but are otherwise phenotypically normal, making them perfect tools for producing hybrid seeds. The identification of MS1 has the practical potential for assembling the sterility system and speeding up hybrid soybean breeding.

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.

Genetic Mapping of ms1s, a Recessive Gene for Male Sterility in Common Wheat

The utilization of heterosis is an important way to improve wheat yield, and the production of wheat hybrid seeds mainly relies on male-sterile lines. Male sterility in line 15 Fan 03 derived from a cross of 72,180 and Xiaoyan 6 is controlled by a single recessive gene. The gene was mapped to the distal region of chromosome 4BS in a genetic interval of 1.4 cM and physical distance of 6.57 Mb between SSR markers Ms4BS42 and Ms4BS199 using an F₂ population with 1205 individuals. Sterile individuals had a deletion of 4.57 Mb in the region presumed to carry the Ms1 locus. The allele for sterility was therefore named ms1s. Three CAPS markers were developed and verified from the region upstream of the deleted fragment and can be used for ms1s marker-assisted selection in wheat hybrid breeding. This work will enrich the utilization of male sterility genetic resources.

Male Fertility Genes in Bread Wheat (Triticum aestivum L.) and Their Utilization for Hybrid Seed Production

Hybrid varieties can provide the boost needed to increase stagnant wheat yields through heterosis. The lack of an efficient hybridization system, which can lower the cost of goods of hybrid seed production, has been a major impediment to commercialization of hybrid wheat varieties. In this review, we discuss the progress made in characterization of nuclear genetic male sterility (NGMS) in wheat and its advantages over two widely referenced hybridization systems, i.e., chemical hybridizing agents (CHAs) and cytoplasmic male sterility (CMS). We have characterized four wheat genes, i.e., Ms1, Ms5, TaMs26 and TaMs45, that sporophytically contribute to male fertility and yield recessive male sterility when mutated. While Ms1 and Ms5 are Triticeae specific genes, analysis of TaMs26 and TaMs45 demonstrated conservation of function across plant species. The main features of each of these genes is discussed with respect to the functional contribution of three sub-genomes and requirements for complementation of their respective mutants. Three seed production systems based on three genes, MS1, TaMS26 and TaMS45, were developed and a proof of concept was demonstrated for each system. The Tams26 and ms1 mutants were maintained through a TDNA cassette in a Seed Production Technology-like system, whereas Tams45 male sterility was maintained through creation of a telosome addition line. These genes represent different options for hybridization systems utilizing NGMS in wheat, which can potentially be utilized for commercial-scale hybrid seed production.

An Assessment of the Factors Influencing the Prediction Accuracy of Genomic Prediction Models Across Multiple Environments

The effects of climate change create formidable challenges for breeders striving to produce sufficient food quantities in rapidly changing environments. It is therefore critical to investigate the ability of multi-environment genomic prediction (GP) models to predict genomic estimated breeding values (GEBVs) in extreme environments. Exploration of the impact of training set composition on the accuracy of such GEBVs is also essential. Accordingly, we examined the influence of the number of training environments and the use of environmental covariates (ECs) in GS models on four subsets of n = 500 lines of the soybean nested association mapping (SoyNAM) panel grown in nine environments in the US-North Central Region. The ensuing analyses provided insights into the influence of both of these factors for predicting grain yield in the most and the least extreme of these environments. We found that only a subset of the available environments was needed to obtain the highest observed prediction accuracies. The inclusion of ECs in the GP model did not substantially increase prediction accuracies relative to competing models, and instead more often resulted in negative prediction accuracies. Combined with the overall low prediction accuracies for grain yield in the most extreme environment, our findings highlight weaknesses in current GP approaches for prediction in extreme environments, and point to specific areas on which to focus future research efforts.

High-resolution mapping of the Mov-1 locus in wheat by combining radiation hybrid (RH) and recombination-based mapping approaches

This work reports a quick method that integrates RH mapping and genetic mapping to map the dominant Mov-1 locus to a 1.1-Mb physical interval with a small number of candidate genes. Bread wheat is an important crop for global human population. Identification of genes and alleles controlling agronomic traits is essential toward sustainably increasing crop production. The unique multi-ovary (MOV) trait in wheat holds potential for improving yields and is characterized by the formation of 2-3 grains per spikelet. The genetic basis of the multi-ovary trait is known to be monogenic and dominant in nature. Its precise mapping and functional characterization is critical to utilizing this trait in a feasible manner. Previous mapping efforts of the locus controlling multiple ovary/pistil formation in the hexaploid wheat have failed to produce a consensus for a particular chromosome. We describe a mapping strategy integrating radiation hybrid mapping and high-resolution genetic mapping to locate the chromosomal position of the Mov-1 locus in hexaploid wheat. We used RH mapping approach using a panel of 188 lines to map the Mov-1 locus in the terminal part of long arm of wheat chromosome 2D with a map resolution of 1.67 Mb/cR₁₅₀₀. Then using a genetic population of MOV × Synthetic wheat of F₂ lines, we delineated the Mov-1 locus to a 1.1-Mb physical region with a small number of candidate genes. This demonstrates the value of this integrated strategy to mapping dominant genes in wheat.

Assessing the Suitability of Elite Lines for Hybrid Seed Production and as Testers in Wide Crosses With Wheat Genetic Resources

The use of genetic resources in breeding is considered critical to ensure future selection gain, but the absence of important adaptation genes often masks the breeding value of genetic resources for grain yield. Testing genetic resources in a hybrid background has been proposed as a solution to obtain unbiased estimates of breeding values for grain yield. In our study, we evaluated the suitability of European wheat elite lines for implementing this hybrid strategy, focusing on maximizing seed yield in hybrid production and reducing masking effects due to susceptibility to lodging, yellow rust, and leaf rust of genetic resources. Over a 3-year period, 63 wheat elite female lines were crossed with eight male plant genetic resources in a multi-environment field experiment to evaluate seed yield on the female side. Then, the resulting hybrids and their parents were tested for plant height, lodging, and susceptibility to yellow rust and leaf rust in a further field experiment at multiple locations. We found that seed yield was strongly influenced by the elite wheat line choice in addition to environment and observed substantial differences among elite tester lines in their ability to reduce susceptibility to lodging, yellow rust, and leaf rust when the hybrid strategy was implemented. Consequently, breeders can significantly increase the amount of hybrid seed produced in wide crosses through appropriate tester choice and adapt genetic resources of wheat with the hybrid strategy to the modern cropping system.

Plant breeding: Revealing the secrets of cytoplasmic male sterility in wheat

While cytoplasmic male sterility is used for breeding in many crops, it has proved difficult to implement in wheat. A new study identifying the key molecules and their mode of action in cytoplasmic male sterility provides new opportunities for wheat breeding.

Breeding for drought and heat tolerance in wheat

Many approaches have been adopted to enhance the heat and drought tolerance of wheat with mixed success. An assessment of the relative merits of different strategies is presented. Wheat is the most widely grown crop globally and plays a key role in human nutrition. However, it is grown in environments that are prone to heat and drought stress, resulting in severely reduced yield in some seasons. Increased climate variability is expected to have a particularly adverse effect of wheat production. Breeding for stable yield across both good and bad seasons while maintaining high yield under optimal conditions is a high priority for most wheat breeding programs and has been a focus of research activities. Multiple strategies have been explored to enhance the heat and drought tolerance of wheat including extensive genetic analysis and modify the expression of genes involved in stress responses, targeting specific physiological traits and direct selection under a range of stress scenarios. These approaches have been combined with improvements in phenotyping, the development of genetic and genomic resources, and extended screening and analysis techniques. The results have greatly expanded our knowledge and understanding of the factors that influence yield under stress, but not all have delivered the hoped-for progress. Here, we provide an overview of the different strategies and an assessment of the most promising approaches.

Hotter, drier, CRISPR: the latest edit on climate change

Integrating CRISPR/Cas9 genome editing into modern breeding programs for crop improvement in cereals. Global climate trends in many agricultural regions have been rapidly changing over the past decades, and major advances in global food systems are required to ensure food security in the face of these emerging challenges. With increasing climate instability due to warmer temperatures and rising CO₂ levels, the productivity of global agriculture will continue to be negatively impacted. To combat these growing concerns, creative approaches will be required, utilising all the tools available to produce more robust and tolerant crops with increased quality and yields under more extreme conditions. The integration of genome editing and transgenics into current breeding strategies is one promising solution to accelerate genetic gains through targeted genetic modifications, producing crops that can overcome the shifting climate realities. This review focuses on how revolutionary genome editing tools can be directly implemented into breeding programs for cereal crop improvement to rapidly counteract many of the issues affecting agriculture production in the years to come.

Genome editing of polyploid crops: prospects, achievements and bottlenecks

Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.

Spikelet movements, anther extrusion and pollen production in wheat cultivars with contrasting tendencies to cleistogamy

BACKGROUND

Cleistogamic flowers are a main barrier in pollen dispersal for cross-pollination necessary in wheat hybrid breeding. The aim of our study was to gain new knowledge on the biology of wheat flowering, in particular on the differences between the cleisto- and chasmogamic forms which has certainly cognitive significance, but it can also be used in practice when seeking a female and male ideotypes for cross hybridization.

RESULTS

We characterized the most significant features defining the flowering specificity in two wheat cultivars with contrasting tendency to cleistogamy: Piko (chasmogamous) and Dacanto (cleistogamous). In the field observations we assessed diurnal pattern of anther extrusion and anther extrusion capacity. For the first time we adapted the time lapse method for measuring kinetics of the spikelet movement and 3-D image correlation technique for the non-invasive measurements of potential deformations of the spikelet lemmas. We found that the two cultivars differ in the potential of pollen dispersion for-cross-pollination and in the spikelet kinetics. We also described some anatomical traits that can have potential functional role in floret opening. None of the cultivars showed any symptoms of lemma surface deformation.

CONCLUSIONS

The cleistogamic and chasmogamic wheat cultivars differ significantly in the potential for pollen dispersion for cross-pollination, which is mainly related to anther extrusion capacity. Although none of these features differentiated the cultivars clearly, we assume, based on spikelet kinetics and the lack of lemmas surface deformation, that the water transport and turgor of cells is essential for the floret opening and anther extrusion in wheat. The search for parental ideotype should be supported by marker assisted selection, e.g. based of polymorphisms in genes related to aquaporin biosynthesis.

Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko

Hybrid breeding in wheat has the potential to boost yields. An efficient hybrid seed production system requires elite pollinators; however, such germplasm is limited among modern cultivars. Piko, a winter wheat (Triticum aestivum L.) cultivar, has been identified as a superior pollinator and has been used in Europe. Piko has favourable pollinator traits for anther extrusion, anther length, pollen mass and hybrid seed set. However, the genetic factors responsible for Piko's favourable traits are largely unknown. Here, we report on the genetic analysis of a Piko-derived F2 mapping population. We confirmed that Piko's Rht-D1a allele for tall stature is associated with large anthers and high anther extrusion. However, Rht-D1 was not found to be associated with anther filament length, confirmed by near isogenic lines. Piko's photoperiod sensitive Ppd-B1b allele shows an association with increased spike length, more spikelets and spike architecture traits, while the insensitive Ppd-B1a allele is linked with high anther extrusion and larger anthers. We identified an anther extrusion quantitative trait locus (QTL) on chromosome 6A that showed significantly biased transmission of the favourable Piko allele amongst F2 progenies. The Piko allele is completely absent in the distal 6AS region and the central 6A region revealed a significantly lower ratio (<8%) of F2 with homozygous Piko alleles. Our study provided further evidence for the effects of Rht-D1 and Ppd-B1 loci on multiple pollinator traits and a novel anther extrusion QTL that exhibits segregation distortion.

Deciphering the dynamic gene expression patterns of pollen abortion in a male sterile line of Avena sativa through transcriptome analysis at different developmental stages

BACKGROUND

Male sterility (MS) has important applications in hybrid seed production, and the abortion of anthers has been observed in many plant species. While most studies have focused on the genetic factors affecting male sterility, the dynamic gene expression patterns of pollen abortion in male sterile lines have not been fully elucidated. In addition, there is still no hybrid oat that is commercially planted due to the lack of a suitable system of male sterility for hybrid breeding.

RESULTS

In this study, we cultivated a male sterile oat line and a near-isogenic line by crossbreeding to elucidate the expression patterns of genes that may be involved in sterility. The first reported CA male sterile (CAMS) oat line was used for cross-testing and hybridization experiments and was confirmed to exhibit a type of nuclear sterility controlled by recessive genes. Oat stamens of two lines were sampled at four different developmental stages separately. Paired-end RNA sequencing was performed for each sample and generated 252.84 Gb sequences. There were 295,462 unigenes annotated in public databases in all samples, and we compared the histological characteristics and transcriptomes of oat stamens from the two oat lines at different developmental stages. Our results demonstrate that the sterility of the male sterile oat line occurs in the early stage of stamen development and is primarily attributable to abnormal meiosis and the excessive accumulation of superoxide.

CONCLUSIONS

To the best of our knowledge, this study is the first to decipher the dynamic expression profiles of pollen abortion CAMS and CA male fertile (CAMF) oat lines, which may represent a valuable resource for further studies attempting to understand pollen abortion and anther development in oats.

The genetic basis of cytoplasmic male sterility and fertility restoration in wheat

Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.

Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach

BACKGROUND

The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach.

RESULTS

More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs.

CONCLUSIONS

Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.