Inheritance and genetic mapping of two nuclear genes involved in nuclear-cytoplasmic incompatibility in peas (Pisum sativum L.)

Gene-Based Resistance to Erysiphe Species Causing Powdery Mildew Disease in Peas (Pisum sativum L.)

Globally powdery mildew (PM) is one of the major diseases of the pea caused by Erysiphe pisi. Besides, two other species viz. Erysiphe trifolii and Erysiphe baeumleri have also been identified to infect the pea plant. To date, three resistant genes, namely er1, er2 and Er3 located on linkage groups VI, III and IV respectively were identified. Studies have shown the er1 gene to be a Pisum sativum Mildew resistance Locus 'O' homologue and subsequent analysis has identified eleven alleles namely er1-1 to er1-11. Despite reports mentioning the breakdown of er1 gene-mediated PM resistance by E. pisi and E. trifolii, it is still the most widely deployed gene in PM resistance breeding programmes across the world. Several linked DNA markers have been reported in different mapping populations with varying linkage distances and effectiveness, which were used by breeders to develop PM-resistant pea cultivars through marker assisted selection. This review summarizes the genetics of PM resistance and its mechanism, allelic variations of the er gene, marker linkage and future strategies to exploit this information for targeted PM resistance breeding in Pisum.

Discordant evolution of organellar genomes in peas (Pisum L.)

Plastids and mitochondria have their own small genomes, which do not undergo meiotic recombination and may have evolutionary fates different from each other and that of the nuclear genome. For the first time, we sequenced mitochondrial genomes of pea (Pisum L.) from 42 accessions mostly representing diverse wild germplasm from throughout the wild pea geographical range. Six structural types of the pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant, implying not less than six events of hybridisation between diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles could have been driven by plastid-nuclear incompatibility, which is known to be widespread in crosses involving wild peas and affects organellar inheritance. The topology of the phylogenetic tree based on nucleotide sequences of a nuclear gene, His5, encoding a histone H1 subtype, corresponded to the current taxonomy and resembled that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin, resulting from crosses of peas related to those presently inhabiting the eastern Mediterranean in a broad sense. These results highlight the roles of hybridisation and cytonuclear conflict in shaping plant microevolution.

Genetic and Molecular Genetic Basis of Nuclear-Plastid Incompatibilities

Genetic analysis of nuclear-cytoplasm incompatibilities is not straightforward and requires an elaborated experimental design. A number of species have been genetically studied, but notable advances in genetic mapping of nuclear loci involved in nuclear-plastid incompatibility have been achieved only in wheat and pea. This review focuses on the study of the genetic background underlying nuclear-plastid incompatibilities, including cases where the molecular genetic basis of such incompatibility has been unveiled, such as in tobacco, Oenothera, pea, and wheat.

The role of the testa during the establishment of physical dormancy in the pea seed

BACKGROUND

A water-impermeable testa acts as a barrier to a seed's imbibition, thereby imposing dormancy. The physical and functional properties of the macrosclereids are thought to be critical determinants of dormancy; however, the mechanisms underlying the maintenance of and release from dormancy in pea are not well understood.

METHODS

Seeds of six pea accessions of contrasting dormancy type were tested for their ability to imbibe and the permeability of their testa was evaluated. Release from dormancy was monitored following temperature oscillation, lipid removal and drying. Histochemical and microscopic approaches were used to characterize the structure of the testa.

KEY RESULTS

The strophiole was identified as representing the major site for the entry of water into non-dormant seeds, while water entry into dormant seeds was distributed rather than localized. The major barrier for water uptake in dormant seeds was the upper section of the macrosclereids, referred to as the 'light line'. Dormancy could be released by thermocycling, dehydration or chloroform treatment. Assays based on either periodic acid or ruthenium red were used to visualize penetration through the testa. Lipids were detected within a subcuticular waxy layer in both dormant and non-dormant seeds. The waxy layer and the light line both formed at the same time as the establishment of secondary cell walls at the tip of the macrosclereids.

CONCLUSIONS

The light line was identified as the major barrier to water penetration in dormant seeds. Its outer border abuts a waxy subcuticular layer, which is consistent with the suggestion that the light line represents the interface between two distinct environments - the waxy subcuticular layer and the cellulose-rich secondary cell wall. The mechanistic basis of dormancy break includes changes in the testa's lipid layer, along with the mechanical disruption induced by oscillation in temperature and by a decreased moisture content of the embryo.

Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes

Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions. The positions of three accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, two accessions, from the Black Sea area of Turkey and Georgia, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. We suppose these unusual plastid genomes to be ancient lineages ascending to a 'missing link' between P. fulvum and P. sativum, represented by accession Pe 013 from Turkey. Accessions with common pea appearance but deeply diverged plastids could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas.

When Two Rights Make a Wrong: The Evolutionary Genetics of Plant Hybrid Incompatibilities

Hybrids between flowering plant species often exhibit reduced fitness, including sterility and inviability. Such hybrid incompatibilities create barriers to genetic exchange that can promote reproductive isolation between diverging populations and, ultimately, speciation. Additionally, hybrid breakdown opens a window into hidden molecular and evolutionary processes occurring within species. Here, we review recent work on the mechanisms and origins of hybrid incompatibility in flowering plants, including both diverse genic interactions and chromosomal incompatibilities. Conflict and coevolution among and within plant genomes contributes to the evolution of some well-characterized genic incompatibilities, but duplication and drift also play important roles. Inversions, while contributing to speciation by suppressing recombination, rarely cause underdominant sterility. Translocations cause severe F₁ sterility by disrupting meiosis in heterozygotes, making their fixation in outcrossing sister species a paradox. Evolutionary genomic analyses of both genic and chromosomal incompatibilities, in the context of population genetic theory, can explicitly test alternative scenarios for their origins.

Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry

Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking).

A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)

The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.

Nuclear-cytoplasmic conflict in pea (Pisum sativum L.) is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits

In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized.

Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.

Wild peas vary in their cross-compatibility with cultivated pea (Pisum sativum subsp. sativum L.) depending on alleles of a nuclear-cytoplasmic incompatibility locus

KEY MESSAGE

Divergent wild and endemic peas differ in hybrid sterility in reciprocal crosses with cultivated pea depending on alleles of a nuclear 'speciation gene' involved in nuclear-cytoplasmic compatibility.

BACKGROUND

In hybrids between cultivated and wild peas, nuclear-cytoplasmic conflict frequently occurs. One of the nuclear genes involved, Scs1, was earlier mapped on Linkage Group III.

RESULTS

In reciprocal crosses of seven divergent pea accessions with cultivated P. sativum, some alleles of Scs1 manifested incompatibility with an alien cytoplasm as a decrease in pollen fertility to about 50 % in the heterozygotes and lack of some genotypic classes among F2 segregants. Earlier, we defined monophyletic evolutionary lineages A, B, C and D of pea according to allelic state of three markers, from nuclear, plastid and mitochondrial genomes. All tested representatives of wild peas from the lineages A and C exhibited incompatibility due to Scs1 deleterious effects in crosses with testerlines of P. sativum subsp. sativum (the common cultivated pea) at least in one direction. A wild pea from the lineage B and a cultivated pea from the lineage D were compatible with the testerline in both directions. The tested accession of cultivated P. abyssinicum (lineage A) was partially compatible in both directions. The Scs1 alleles of some pea accessions even originating from the same geographic area were remarkably different in their compatibility with cultivated Pisum sativum cytoplasm.

CONCLUSION

Variability of a gene involved in reproductive isolation is of important evolutionary role and nominate Scs1 as a speciation gene.

Does the mode of plastid inheritance influence plastid genome architecture?

Plastid genomes show an impressive array of sizes and compactnesses, but the forces responsible for this variation are unknown. It has been argued that species with small effective genetic population sizes are less efficient at purging excess DNA from their genomes than those with large effective population sizes. If true, one may expect the primary mode of plastid inheritance to influence plastid DNA (ptDNA) architecture. All else being equal, biparentally inherited ptDNAs should have a two-fold greater effective population size than those that are uniparentally inherited, and thus should also be more compact. Here, we explore the relationship between plastid inheritance pattern and ptDNA architecture, and consider the role of phylogeny in shaping our observations. Contrary to our expectations, we found no significant difference in plastid genome size or compactness between ptDNAs that are biparentally inherited relative to those that are uniparentally inherited. However, we also found that there was significant phylogenetic signal for the trait of mode of plastid inheritance. We also found that paternally inherited ptDNAs are significantly smaller (n = 19, p = 0.000001) than those that are maternally, uniparentally (when isogamous), or biparentally inherited. Potential explanations for this observation are discussed.