Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China

While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa ‘Plena’ was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. ‘Fenghua’. Only R. ‘Jinbian’ and R. ‘Crimson Glory’ featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.

Detecting Major Introgressions in Wheat and their Putative Origins Using Coverage Analysis

Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex

The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco (Nicotiana tabacum) with counterparts from another angiosperm genus (Silene) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species (S. latifolia) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.

Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding

Genomic architecture facilitates chromosome recognition, pairing, and recombination. Telomeres and subtelomeres play an important role at the beginning of meiosis in specific chromosome recognition and pairing, which are critical processes that allow chromosome recombination between homologs (equivalent chromosomes in the same genome) in later stages. In plant polyploids, these terminal regions are even more important in terms of homologous chromosome recognition, due to the presence of homoeologs (equivalent chromosomes from related genomes). Although telomeres interaction seems to assist homologous pairing and consequently, the progression of meiosis, other chromosome regions, such as subtelomeres, need to be considered, because the DNA sequence of telomeres is not chromosome-specific. In addition, recombination operates at subtelomeres and, as it happens in rye and wheat, homologous recognition and pairing is more often correlated with recombining regions than with crossover-poor regions. In a plant breeding context, the knowledge of how homologous chromosomes initiate pairing at the beginning of meiosis can contribute to chromosome manipulation in hybrids or interspecific genetic crosses. Thus, recombination in interspecific chromosome associations could be promoted with the aim of transferring desirable agronomic traits from related genetic donor species into crops. In this review, we summarize the importance of telomeres and subtelomeres on chromatin dynamics during early meiosis stages and their implications in recombination in a plant breeding framework.

STUDY OF THE PASSIVITY LIMITS OF AUSTENITIC STAINLESS-STEEL IN H2S-CONTAINING BRINES USING MOTT-SCHOTTKY AND POINT DEFECT MODEL ANALYSIS

The objective of the study is to correlate the effects of H<sub>2</sub>S, and Cl<sup>-</sup> concentration on the passivity limits and the onset of localized corrosion, in UNS S31603 stainless steel by evaluating the changes in the semiconducting behavior exhibited by the passive layer. The study is accomplished experimentally by using a combination of direct and alternate current electrochemical methods, to study the passive layer formed by the stainless steel, in equilibrium with a gas phase at 2.8 MPa (400 psi) containing up to 60% mol of H<sub>2</sub>S (bal. CO<sub>2</sub>) at 25○</sup>C. The results obtained using the Mott-Schottky analysis indicate that the decrease of the passive layer stability formed on the UNS S31603 stainless steel is consistent with the increase in the electron donor carrier density. This is observed as the consequence of the effect of Cl<sup>-</sup> and H<sub>2</sub>S. In this context, the Cl<sup>-</sup> content in the brine was found to exert a larger effect than the H<sub>2</sub>S activity. The correlation with the evaluation of the passive layer using the Point Defect model suggest that both the polarizability and the rate of annihilation of the cation vacancies at the metal / film interface increase with the H<sub>2</sub>S content in the environment. This behavior can explain the increased content of Cl<sup>-</sup> and sulfides as main electron donor species, also the observable increase in the passive layer susceptibility to both stable and metastable pitting.

Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were detected between these two types of polyploid genotypes although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.

An unexpected donor in the adaptive introgression candidate Helianthus annuus subsp. texanus

Hybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis. Here we test this hypothesis using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We find that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson’s D and TreeMix) only find evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but non-zero introgression from H. debilis and significant introgression from H. argophyllus. Putative introgressions mainly occur in high recombination regions as predicted by theory if introgressed ancestry contains maladaptive alleles. To reconcile the disparate findings of our analyses, we discuss potential test-specific confounding features, including introgression from other taxa. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is likely independent of introgression.

Chromosome Manipulation for Plant Breeding Purposes

The transfer of genetic variability from related species into crops has been a main objective for decades in breeding programs. Breeders have used interspecific genetic crosses and alien introgression lines to achieve this goal, but the success is always dependent on the interspecific chromosome associations between the alien chromosomes and those from the crop during early meiosis. In this Special Issue, the strength of chromosome manipulation in a breeding framework is revealed through research and review papers that combine molecular markers, cytogenetics tools and other traditional breeding techniques. The papers and reviews included in this Special Issue “Chromosome manipulation for plant breeding purposes” describe the development and/or characterization of new plant material carrying desirable traits and the study of chromosome associations and recombination during meiosis. New tools to facilitate the transfer of desired traits from a donor species into a crop can be developed by expanding the knowledge of chromosome associations during meiosis.

Genome-Wide Identification and Expression Profile Analysis of the PHT1 Gene Family in Gossypium hirsutum and Its Two Close Relatives of Subgenome Donor Species

Phosphate transporter (PHT) is responsible for plant phosphorus (P) absorption and transport. PHT1 is a component of the high-affinity phosphate transporter system and plays pivotal roles in P absorption under P starvation conditions. However, in cotton, the number and identity of PHT1 genes that are crucial for P absorption from soil remain unclear. Here, genome-wide identification detected twelve PHT1 genes in Gossypium hirsutum and seven and eight PHT1 genes in two close relatives of the G. hirsutum genome—G. arboreum and G. raimondii, respectively. In addition, under low-phosphate treatment, the expressions of GaPHT1;3, GaPHT1;4, and GaPHT1;5 in roots were upregulated after 3 h of induction, and GhPHT1;3-At, GhPHT1;4-At, GhPHT1;5-At, GhPHT1;3-Dt, GhPHT1;4-Dt, and GhPHT1;5-Dt in the roots began to respond after 1 h of induction. Homologous pairs—GaPHT1;4 and GhPHT1;4-At; GaPHT1;5 and GhPHT1;5-At; GrPHT1;4 and GhPHT1;4-Dt, with GhPHT1;5-Dt and GhPHT1;5-At being syntenic—were all highly expressed in the roots under normal conditions. Among the genes highly expressed in the roots, GhPHT1;4-At, GhPHT1;5-At, GhPHT1;4-Dt and GhPHT1;5-Dt were continuously upregulated by P starvation. Therefore, it is concluded that these four genes might be key genes for P uptake in cotton roots. The results of this study provide insights into the mechanisms of P absorption and transport in cotton.

Overcoming Back Electron Transfer Facilitates the Implementation of Electron Donor-Acceptor Complexes in Catalysis

Electron donor-acceptor (EDA) complexes can controllably generate radicals under mild conditions through selective photoexcitation events. However, unproductive reactivity from fast deactivation of the photoexcited complexes through back electron transfer has slowed the development of EDA complexes in synthetic methodology. Here, we disclose the study of EDA complexes derived from 2-methoxynaphthalene donor and acylated ethyl isonicotinate <i>N</i>-oxide acceptor that undergo a fast N–O bond fragmentation event upon photoexcitation. This reaction design not only overcomes the limitations of back electron transfer but also enables the regeneration of the donor species, representing a rare example EDA photochemistry in a catalytic regime. The synthetic utility is demonstrated through visible light-driven radical trifluoromethylation and Minisci alkylation reactions. The scalability of the EDA complex promoted reaction evidenced by the successful multigram-scale trifluoromethylation of methyl N-Boc pyrrole-2-carboxylate in a continuous flow manifold.