Interspecific and intergeneric hybridization and chromosomal engineering of Brassicaceae crops

A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe

Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) ⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.

Embryo Rescue in Plant Breeding

Embryo rescue (ER) techniques are among the oldest and most successful in vitro tissue culture protocols used with plant species. ER refers to a series of methods that promote the development of an immature or lethal embryo into a viable plant. Intraspecific, interspecific, or intergeneric crosses allow the introgression of important alleles of agricultural interest from wild species, such as resistance or tolerance to abiotic and biotic stresses or morphological traits in crops. However, pre-zygotic and post-zygotic reproductive barriers often present challenges in achieving successful hybridization. Pre-zygotic barriers manifest as incompatibility reactions that hinder pollen germination, pollen tube growth, or penetration into the ovule occurring in various tissues, such as the stigma, style, or ovary. To overcome these barriers, several strategies are employed, including cut-style or graft-on-style techniques, the utilization of mixed pollen from distinct species, placenta pollination, and in vitro ovule pollination. On the other hand, post-zygotic barriers act at different tissues and stages ranging from early embryo development to the subsequent growth and reproduction of the offspring. Many crosses among different genera result in embryo abortion due to the failure of endosperm development. In such cases, ER techniques are needed to rescue these hybrids. ER holds great promise for not only facilitating successful crosses but also for obtaining haploids, doubled haploids, and manipulating the ploidy levels for chromosome engineering by monosomic and disomic addition as well substitution lines. Furthermore, ER can be used to shorten the reproductive cycle and for the propagation of rare plants. Additionally, it has been repeatedly used to study the stages of embryonic development, especially in embryo-lethal mutants. The most widely used ER procedure is the culture of immature embryos taken and placed directly on culture media. In certain cases, the in vitro culture of ovule, ovaries or placentas enables the successful development of young embryos from the zygote stage to maturity.

Applications of In Vitro Tissue Culture Technologies in Breeding and Genetic Improvement of Wheat

Sources of new genetic variability have been limited to existing germplasm in the past. Wheat has been studied extensively for various agronomic traits located throughout the genome. The large size of the chromosomes and the ability of its polyploid genome to tolerate the addition or loss of chromosomes facilitated rapid progress in the early study of wheat genetics using cytogenetic techniques. At the same time, its large genome size has limited the progress in genetic characterization studies focused on diploid species, with a small genome and genetic engineering procedures already developed. Today, the genetic transformation and gene editing procedures offer attractive alternatives to conventional techniques for breeding wheat because they allow one or more of the genes to be introduced or altered into an elite cultivar without affecting its genetic background. Recently, significant advances have been made in regenerating various plant tissues, providing the essential basis for regenerating transgenic plants. In addition, Agrobacterium-mediated, biolistic, and in planta particle bombardment (iPB) gene delivery procedures have been developed for wheat transformation and advanced transgenic wheat development. As a result, several useful genes are now available that have been transferred or would be helpful to be transferred to wheat in addition to the current traditional effort to improve trait values, such as resistance to abiotic and biotic factors, grain quality, and plant architecture. Furthermore, the in planta genome editing method will significantly contribute to the social implementation of genome-edited crops to innovate the breeding pipeline and leverage unique climate adaptations.

Intergeneric hybridization of marguerite (Argyranthemum frutescens (L.) Sch. Bip.) and Roman chamomile (Chamaemelum nobile (L.) All.) using ovule culture and confirmation of hybridity

To introduce useful characteristics such as fragrance into Argyranthemum frutescens (L.) and to expand the variation, we conducted crosses using A. frutescens as the seed parent and Chamaemelum nobile (L.) All. as the pollen parent. All the tested cross combinations between the three strains of A. frutescens and one strain of C. nobile produced embryos, and healthy plants were obtained by ovule culture. The obtained plantlets had a white ray floret, and the leaf shape was intermediate to those of the parents. The individuals obtained from this cross were subjected to two methods to determine hybridity: flow cytometry analyses and cleaved amplified polymorphic sequence (CAPS) markers. For the CAPS marker, we selected the internal transcribed spacer (ITS) region, which is highly variable among the genera, as the region to be amplified. We selected restriction enzymes BmgT120 I and Afl II, which selectively cut common sequences in the genus Argyranthemum, based on the sequence analysis of one parent strain each of A. frutescens and C. nobile and alignment with known sequences of related species. Flow cytometry analyses and CAPS markers revealed that the individuals obtained from the cross between A. frutescens and C. nobile are intergeneric hybrids. In addition, these established methods were capable of quickly and reliably identifying hybrids between A. frutescens and C. nobile. This report shows for the first time that crossbreeding between A. frutescens (seed parent) and C. nobile (pollen parent) is possible, and further development of Argyranthemum breeding, such as the expansion of variation by intergeneric crosses, is expected.

Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis

The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.

Development and Characteristics of Interspecific Hybrids between Brassica oleracea L. and B. napus L

Interspecific hybridization between B. oleracea inbred lines of head cabbage, Brussels sprouts, kale and B. taurica and inbred lines of rapeseed (B. napus L.) were performed aiming at the development of the new sources of genetic variability of vegetable Brassicas. Using conventional crossings and the embryo-rescue techniques the following interspecific hybrids were developed: 11 genotypes of F1 generation, 18 genotypes of F2 and F1 × F2 generations (produced after self- and cross-pollination of interspecific F1 hybrids), 10 plants of the BC1 generation (resulted from crossing head cabbage cytoplasmic male-sterile lines with interspecific hybrids of the F2 and F1 generations) and 8 plants of BC1 × (F1 × F2). No viable seeds of the BC2 generation (B. oleracea) were obtained due to the strong incompatibility and high mortality of embryos. The morphological characteristics during the vegetative and generative stages, pollen characteristics, seed development and propagation, nuclear DNA contents and genome compositions of interspecific hybrids were analyzed. All the interspecific F1 hybrids were male-fertile with a majority of undeveloped and malformed pollen grains. They showed intermediate values for morphological traits and nuclear DNA contents and had nearly triploid chromosomal numbers (27 to 29) compared with parental lines. The F2 generation had a doubled nuclear DNA content, with 52 and 56 chromosomes, indicating their allohexaploid nature. F2 hybrids were characterized by a high heterosis of morphological characteristics, viable pollen and good seed development. F1 × F2 hybrids were male-fertile with a diversified DNA content and intermediate pollen viability. BC1 plants were male-sterile with an intermediate nuclear DNA content between the F2 and head cabbage, having 28 to 38 chromosomes. Plants of the BC1 × (F1 × F2) generation were in majority male-fertile with 38–46 chromosomes, high seed set, high heterosis and intermediate values for morphological traits. The obtained interspecific hybrids are valuable as new germplasm for improving Brassica-breeding programs.

Tapping Pennisetum violaceum, a Wild Relative of Pearl Millet (Pennisetum glaucum), for Resistance to Blast (caused by Magnaporthe grisea) and Rust (caused by Puccinia substriata var. indica)

Blast (Magnaporthe grisea) and rust (Puccinia substriata var. indica) are the two important foliar diseases of pearl millet (Pennisetum glaucum (L.) R. Br.) that can be best managed through host plant resistance. For identification of diverse sources of blast and rust resistance, 305 accessions of Pennisetum violaceum, a wild relative of pearl millet, were screened under greenhouse conditions against five pathotype-isolates of M. grisea and a local isolate of P. substriata var. indica collected from ICRISAT farm, Patancheru, India. Based on the mean blast score (1 to 9 scale), 17 accessions (IP 21525, 21531, 21536, 21540, 21594, 21610, 21640, 21706, 21711, 21716, 21719, 21720, 21721, 21724, 21987, 21988, and 22160) were found resistant (score ≤3.0) to all five pathotypes, and 24 accessions were resistant to four pathotypes of M. grisea. As there was variability for rust resistance within some accessions, individual rust-resistant (<5% severity) plants from 17 accessions were selected, grown in pots and advanced to next generation by selfing, and rescreened for three to four generations following pedigree selection to develop rust-resistant genetic stocks. Single plant selections from nine accessions (IP 21629, 21645, 21658, 21660, 21662, 21711, 21974, 21975, and 22038) were found highly resistant to rust (0% rust severity) after four generations of pedigree selection and subsequent screening. Some of the blast-resistant accessions and rust-resistant genetic stocks are being utilized in a prebreeding program at ICRISAT for introgressing resistance genes from the wild into the parental lines of cultivated and potential pearl millet hybrids and varieties.

Developmental Stage and Shape of Embryo Determine the Efficacy of Embryo Rescue in Introgressing Orange/Yellow Color and Anthocyanin Genes of Brassica Species

Vegetables in Brassica are some of the world's most commonly cultivated plants and have a wide range of consumable plant organs. Improvement of this group of vegetables is limited at the species level due to limited genetic variability. Interspecies hybridization could be a powerful alternate tool for broadening the genetic variability of target traits. Embryo rescue technique is necessarily practiced in interspecies hybridization for protecting embryos from premature abortion. However, its success depends on the age of ovaries, shape of embryos, and the effect of female genotype. In this study, we carried out a wide range of interspecies crossing for introgressing target traits (orange/yellow color in cabbage and anthocyanin in Chinese cabbage) and optimizing the appropriate age of ovaries, the shape of embryo, and the suitable genotypes of such crosses. We observed that 15 DAP (days after pollination) was the best for embryo rescue in the diploid-diploid (Brassica rapa × B. oleracea) crosses, while 20 DAP was optimum for amphidiploid-diploid (B. napus/B. juncea × B. rapa) crosses. Cotyledonary shape of embryos and genotypes of amphidiploid species were the best for successful plant regeneration in interspecies crosses. We successfully selected plants with desired orange/yellow inner leaves for cabbage and higher anthocyanin in Chinese cabbage. The results of this study have the potential to be applied for the efficient production of interspecific hybrids and to develop Brassica vegetables with new traits, which could have potential for the enrichment of the human diet.

A quartet pollen phenotype identified in a population of Brassica interspecific hybrids shows incomplete penetrance and variable response to temperature

Quartet pollen, where pollen grains remain attached to each other post-meiosis, is useful for tetrad analysis, crossover assessment and centromere mapping. We observed the quartet pollen phenotype for the first time in the agriculturally significant Brassica genus, in an experimental population of allohexaploid Brassica hybrids derived from the cross (Brassica napus × B. carinata) × B. juncea followed by two self-pollination generations. Quartet pollen production was assessed in 144 genotypes under glasshouse conditions, following which a set of 16 genotypes were selected to further investigate the effect of environment (warm: 25 °C and cold: 10 °C temperatures) on quartet pollen production in growth cabinets. Under glasshouse phenotyping conditions, only 92 out of 144 genotypes produced enough pollen to score: of these, 30 did not produce any observable quartet pollen, while 62 genotypes produced quartet pollen at varying frequencies. Quartet pollen production appeared quantitative and did not clearly fall into phenotypic or qualitative categories indicative of major gene expression. No consistent effect of temperature on quartet pollen production was identified, with some genotypes producing more and some producing less quartet pollen under different temperature treatments. The genetic heterogeneity and frequent pollen infertility of this population prevents strong conclusions being made. However, it is clear that the quartet phenotype in this Brassica population does not show complete penetrance and shows variable (likely genotype-specific) response to temperature stress. In future, identification of quartet phenotypes in Brassica would perhaps best be carried out via screening of diploid (e.g. B. rapa) TILLING populations.

Development of an intergeneric hybrid between Oryza sativa L. and Leersia perrieri (A. Camus) Launert

An intergeneric hybrid was successfully developed between Oryza sativa L. (IRRI 154) and Leersia perrieri (A. Camus) Launert using embryo rescue technique in this study. A low crossability value (0.07%) implied that there was high incompatibility between the two species of the hybrid. The F1 hybrid showed intermediate phenotypic characteristics between the parents but the plant height was very short. The erect plant type resembled the female parent IRRI 154 but the leaves were similar to L. perrieri. Cytological analysis revealed highly non-homology between chromosomes of the two species as the F1 plants showed 24 univalents without any chromosome pairing. The F1 hybrid plant was further confirmed by PCR analysis using the newly designed 11 indel markers showing polymorphism between O. sativa and L. perrieri. This intergeneric hybrid will open up opportunities to transfer novel valuable traits from L. perrieri into cultivated rice.

The production and characterization of a BoFLC2 introgressed Brassica rapa by repeated backcrossing to an F1

Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.

Wide Hybridization Between Oat and Pearl Millet

Wide hybridization is a one of the important techniques in plant breeding. Oat (Avena sativa L.) and pearl millet (Pennisetum glaucum L.) belong to different subfamilies of Poaceae. In generally, such distant relative species show uniparental chromosome elimination after successful fertilization. However, all seven pearl millet chromosomes are retained beside the genome of oat during embryogenesis. Hybrid seedlings develop, but show necrosis after light irradiation. Here, a detailed protocol for wide hybridization between oat and pearl millet is described.

The role of mitochondria in plant development and stress tolerance

Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.