The satellitome of Triticum aestivum cv. Chinese Spring consists of 36 satellite DNA (satDNA) families that were previously molecularly characterized and chromosomally mapped. The recent release of a complete gap-free telomere-to-telomere (T2T) assembly of the species offers a unique opportunity to refine the physical map and evolutionary interpretation of these sequences. Here, we re-evaluate the organization of the wheat satellitome by analyzing the T2T assembly with RepeatMasker and visualizing the results using the CHRISMAPP script. This research strengthens the notion that more than half of wheat satDNAs are connected to transposable elements (TEs) and enables us to propose a model of satDNA origin and evolution driven by TEs and other random genome sequences. By integrating T2T based physical mapping with previous FISH analyses, we refine the genomic distribution of tandem repeats, identify complex satellite organizations and length variants, and resolve several discrepancies between cytogenetic and genomic analyses. Finally, the detailed mapping of satDNA in centromeric and the subtelomeric regions highlight clear chromosome and subgenome specific patterns, suggesting potential roles of satellites in chromosome architecture. Together these findings provide the most complete and accurate satellitome map available for bread wheat, offering new insights into repeat evolution and genome organization in polyploid species. The organization of the different satellite DNA families that constitutes its satellitome is re-evaluated in light of the information provided by the new T2T assembly of the bread wheat genome, revealing relevant information about their origin and evolution, distribution, and role in centromeric and subtelomeric regions.

In this paper, we have performed an in-depth study of the complete set of the satellite DNA (satDNA) families (i.e. the satellitomes) in the genome of two barley species of agronomic value in a breeding framework, H. chilense (H1 and H7 accessions) and H. vulgare (H106 accession), which can be useful tools for studying chromosome associations during meiosis. The study has led to the analysis of a total of 18 satDNA families in H. vulgare, 25 satDNA families in H. chilense (accession H1) and 27 satDNA families in H. chilense (accession H7) that constitute 46 different satDNA families forming 36 homology groups. Our study highlights different important contributions of evolutionary and applied interests. Thus, both barley species show very divergent satDNA profiles, which could be partly explained by the differential effects of domestication versus wildlife. Divergence derives from the differential amplification of different common ancestral satellites and the emergence of new satellites in H. chilense, usually from pre-existing ones but also random sequences. There are also differences between the two H. chilense accessions, which support genetically distinct groups. The fluorescence in situ hybridization (FISH) patterns of some satDNAs yield distinctive genetic markers for the identification of specific H. chilense or H. vulgare chromosomes. Some of the satellites have peculiar structures or are related to transposable elements which provide information about their origin and expansion. Among these, we discuss the existence of different (peri)centromeric satellites that supply this region with some plasticity important for centromere evolution. These peri(centromeric) satDNAs and the set of subtelomeric satDNAs (a total of 38 different families) are analyzed in the framework of breeding as the high diversity found in the subtelomeric regions might support their putative implication in chromosome recognition and pairing during meiosis, a key point in the production of addition/substitution lines and hybrids.

BACKGROUND AND AIMS:Durum wheat, Triticum turgidum, and bread wheat, Triticum aestivum, are two allopolyploid species of very recent origin that have been subjected to intense selection programmes during the thousands of years they have been cultivated. In this paper, we study the durum wheat satellitome and establish a comparative analysis with the previously published bread wheat satellitome. METHODS:We revealed the durum wheat satellitome using the satMiner protocol, which is based on consecutive rounds of clustering of Illumina reads by RepeatExplorer2, and we estimated abundance and variation for each identified satellite DNA (satDNA) with RepeatMasker v4.0.5. We also performed a deep satDNA family characterization including chromosomal location by fluorescence in situ hybridization (FISH) in durum wheat and its comparison with FISH patterns in bread wheat. BLAST was used for trailing each satDNA in the assembly of durum wheat genome through NCBI's Genome Data Viewer and the genome assemblies of both species were compared. Sequence divergence and consensus turnover rate between homologous satDNA families of durum and bread wheat were estimated using MEGA11. KEY RESULTS:This study reveals that in an exceedingly short period, significant qualitative and quantitative changes have occurred in the set of satDNAs of both species, with expansions/contractions of the number of repeats and the loci per satellite, different in each species, and a high rate of sequence change for most of these satellites, in addition to the emergence/loss of satDNAs not shared between the two species analysed. These evolutionary changes in satDNA are common between species but what is truly remarkable and novel is that these processes have taken place in less than the last ~8000 years separating the two species, indicating an accelerated evolution of their satDNAs. CONCLUSIONS:These results, together with the relationship of many of these satellites with transposable elements and the polymorphisms they generate at the level of centromeres and subtelomeric regions of their chromosomes, are analysed and discussed in the context of the evolutionary origin of these species and the selection pressure exerted by humans throughout the history of their cultivation.

EDITORIAL article Front. Plant Sci., 04 January 2024Sec. Plant Systematics and Evolution Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1335981

The nonpathogenic strain Fusarium oxysporum FO12 has been characterized as an effective biological control agent against Verticillium dahliae in olive. Nevertheless, the endophytic role of FO12 in herbaceous hosts is still uncertain. Thus, the aim of this study was to demonstrate the nonpathogenic character of FO12 in eight V. dahliae-susceptible herbaceous hosts and to evaluate its ability to promote plant growth. To this end, plants of each host were grown in pots filled with sterile peat moss and inoculated by irrigation with a conidial suspension of FO12 (106 conidia ml−1) two times—at sowing and at the emergence of the first true leaves. Many plants irrigated with sterile distilled water were included as controls. Sampling was conducted at 7, 14, 21, and 28 days after the second inoculation. The fresh weight and length of the aerial parts, roots, and whole plants were determined at each sampling time. Fungal colonization was assessed via quantitative and qualitative methods, including microbiological isolation from roots and stems and confocal laser scanning microscopy (CLSM) imaging at each sampling time. FO12 exhibited the ability to endophytically colonize the roots and stems of the inoculated plants. However, the effect on growth and the degree of colonization varied depending on the host. FO12 did not exert any evident pathogenic effects or negative effects on plant growth or development. The growth of the eggplant, lettuce, and tomato plants in the FO12 treatment group was similar to that in the control group, whereas the relative area under the growth progress curve was significantly greater than that in the control group for plant length in cotton and cucumber; for root fresh weight in pepper, sunflower, and wheat; and for plant fresh weight in sunflower and wheat. These results highlight the need to continue researching the interaction between FO12 and V. dahliae in a wider range of plant species of agronomic interest.

In bread wheat ( Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread wheat satellitome to shed light on the molecular organization of wheat subtelomeres. Our results revealed that the 2.53% of bread wheat genome is composed by satDNA and subtelomeres are particularly enriched in such DNA sequences. Thirty-four satellite DNA (21 for the first time in this work) have been identified, analyzed and cytogenetically validated. Many of the satDNAs were specifically found at particular subtelomeric chromosome regions revealing the asymmetry in subtelomere organisation among the wheat subgenomes, which might play a role in proper homologous recognition and pairing during meiosis. An integrated physical map of the wheat satellitome was also constructed. To the best of our knowledge, our results show that the combination of both cytogenetics and genome research allowed the first comprehensive analysis of the wheat satellitome, shedding light on the complex wheat genome organization, especially on the polymorphic nature of subtelomeres and their putative implication in chromosome recognition and pairing during meiosis.

The use of wild species as a source of genetic variability is a valued tool in the framework of crop breeding. Hordeum chilense Roem. et Schult is a wild barley species that can be a useful genetic donor for sustainable wheat breeding which carries genes conferring resistance to some diseases or increasing grain quality, among others. Septoria tritici blotch (STB), caused by the Zymoseptoria tritici fungus, is one of the most important wheat diseases worldwide, affecting both bread and durum wheat and having a high economic impact. Resistance to STB has been previously described in H. chilense chromosome 4Hch. In this study, we have developed introgression lines for H. chilense chromosome 4Hch in durum wheat using interspecific crosses, advanced backcrosses, and consecutive selfing strategies. Alien H. chilense chromosome segments have been reduced in size by genetic crosses between H. chilense disomic substitution lines in durum wheat and durum wheat lines carrying the Ph1 deletion. Hordeum chilense genetic introgressions were identified in the wheat background through several plant generations by fluorescence in situ hybridisation (FISH) and simple sequence repeat (SSR) markers. An STB infection analysis has also been developed to assess STB resistance to a specific H. chilense chromosome region. The development of these H. chilense introgression lines with moderate to high resistance to STB represents an important advance in the framework of durum breeding and can be a valuable tool for plant breeders.

Rice (Oryza sativa L.) is a very important cereal worldwide, since it is the staple food for more than half of the world's population. Iron (Fe) deficiency is among the most important agronomical concerns in calcareous soils where rice plants may suffer from this deficiency. Current production systems are based on the use of high-yielding varieties and the application of large quantities of agrochemicals, which can cause major environmental problems. The use of beneficial rhizosphere microorganisms is considered a relevant sustainable alternative to synthetic fertilizers. The main goal of this study was to determine the ability of the nonpathogenic strain Fusarium oxysporum FO12 to induce Fe-deficiency responses in rice plants and its effects on plant growth and Fe chlorosis. Experiments were carried out under hydroponic system conditions. Our results show that the root inoculation of rice plants with FO12 promotes the production of phytosiderophores and plant growth while reducing Fe chlorosis symptoms after several days of cultivation. Moreover, Fe-related genes are upregulated by FO12 at certain times in inoculated plants regardless of Fe conditions. This microorganism also colonizes root cortical tissues. In conclusion, FO12 enhances Fe-deficiency responses in rice plants, achieves growth promotion, and reduces Fe chlorosis symptoms.

FO12 strain enhances Fe deficiency responses in cucumber plants, probably through the production of ethylene and NO in the subapical regions of the roots. Rhizosphere microorganisms can elicit induced systemic resistance (ISR) in plants. This type of resistance involves complex mechanisms that confer protection to the plant against pathogen attack. Additionally, it has been reported by several studies that ISR and Fe deficiency responses are modulated by common pathways, involving some phytohormones and signaling molecules, like ethylene and nitric oxide (NO). The aim of this study was to determine whether the nonpathogenic strain of Fusarium oxysporum FO12 can induce Fe deficiency responses in cucumber (Cucumis sativus L.) plants. Our results demonstrate that the root inoculation of cucumber plants with the FO12 strain promotes plant growth after several days of cultivation, as well as rhizosphere acidification and enhancement of ferric reductase activity. Moreover, Fe-related genes, such as FRO1, IRT1 and HA1, are upregulated at certain times after FO12 inoculation either upon Fe-deficiency or Fe-sufficient conditions. Furthermore, it has been found that this fungus colonizes root cortical tissues, promoting the upregulation of ethylene synthesis genes and NO production in the root subapical regions. To better understand the effects of the FO12 strain on field conditions, cucumber plants were inoculated and cultivated in a calcareous soil under greenhouse conditions. The results obtained show a modification of some physiological parameters in the inoculated plants, such as flowering and reduction of tissue necrosis. Overall, the results suggest that the FO12 strain could have a great potential as a Fe biofertilizer and biostimulant.

Barley ( Hordeum vulgare ) is one of the most popular cereal crops globally. Although it is a diploid species, (2 n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.

The increasing human population demands an increase in crop yields that must be implemented through breeding programmes to ensure a more efficient and sustainable production of agro-food products. In the framework of breeding, genetic crosses are developed between cultivated species such as wheat and their relative species that are used as genetic donors to transfer desirable agronomic traits into the crop. Unfortunately, interspecific associations between chromosomes from the donor species and the cultivar are rare during meiosis, the process to produce gametes in organisms with sexual reproduction, hampering the transfer of genetic variability into wheat. In addition, little is known about how homologous (equivalent) chromosomes initiate interaction and recognition within the cell nucleus to enter meiosis. In this context, we aim to get insight into wheat chromatin structure, particularly the distribution of homologous chromosomes within the cell nucleus and their putative interactions in premeiotic stages to facilitate chromosome associations and recombination at the beginning of meiosis. Cytogenetics allows the study of both the structure and the behaviour of chromosomes during meiosis and is key in plant breeding. In this study we visualized an extra pair of barley homologous chromosomes in a wheat genetic background to study the spatial distribution, arrangements and interactions occurring exclusively between this pair of homologous chromosomes during premeiosis using fluorescence in situ hybridization (FISH). Our results suggest that homologous chromosomes can initiate interactions in premeiotic stages that could facilitate the processes of specific chromosome recognition and association occurring at the onset of meiosis.

Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.

Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.

Bread wheat is an allohexaploid that behaves as a diploid during meiosis, the cell division process to produce the gametes occurring in organisms with sexual reproduction. Knowledge of the mechanisms implicated in meiosis can contribute to facilitating the transfer of desirable traits from related species into a crop like wheat in the framework of breeding. It is particularly interesting to shed light on the mechanisms controlling correct pairing between homologous (equivalent) chromosomes and recombination, even more in polyploid species. The Ph1 (Pairing homoeologous 1) locus is implicated in recombination. In this work, we aimed to study whether homoeologous (equivalent chromosomes from different genomes) Hordeum chilense (wild barley) and H. vulgare (cultivated barley) chromosomes can associate and recombine during meiosis in the wheat background in the absence of the Ph1 locus. For this, we have developed H. chilense and H. vulgare double monosomic addition lines for the same and for different homoeology group in wheat in the ph1b mutant background. Using genomic in situ hybridization, we visualized the two (wild and cultivated) barley chromosomes during meiosis and we studied the processes of recognition, association, and recombination between homoeologous chromosomes in the absence of the Ph1 locus. Our results showed that the Ph1 locus does not prevent homoeologous chromosome pairing but it can regulate recombination.

Stress caused by drought and salinity may compromise growth and productivity of olive (Olea europaea L.) tree crops. Several studies have reported the use of beneficial rhizobacteria to alleviate symptoms produced by these stresses, which is attributed in some cases to the activity of 1-aminocyclopropane-1-carboxylic acid deaminase (ACD). A collection of beneficial olive rhizobacteria was in vitro screened for ACD activity. Pseudomonas sp. PICF6 displayed this phenotype and sequencing of its genome confirmed the presence of an acdS gene. In contrast, the well-known root endophyte and biocontrol agent Pseudomonas simiae PICF7 was defective in ACD activity, even though the presence of an ACD-coding gene was earlier predicted in its genome. In this study, an unidentified deaminase was confirmed instead. Greenhouse experiments with olive ‘Picual’ plants inoculated either with PICF6 or PICF7, or co-inoculated with both strains, and subjected to drought or salt stress were carried out. Several physiological and biochemical parameters increased in stressed plants (i.e., stomatal conductance and flavonoids content), regardless of whether or not they were previously bacterized. Results showed that neither PICF6 (ACD positive) nor PICF7 (ACD negative) lessened the negative effects caused by the abiotic stresses tested, at least under our experimental conditions.

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.

Pseudomonas simiae PICF7 is an indigenous inhabitant of the olive (Olea europaea L.) rhizosphere/root endosphere and an effective biocontrol agent against Verticillium wilt of olive (VWO), caused by the soil-borne fungus Verticillium dahliae. This study aimed to evaluate the potential involvement of selected phenotypes of strain PICF7 in root colonization ability and VWO biocontrol. Therefore, a random transposon-insertion mutant bank of P. simiae PICF7 was screened for the loss of phenotypes likely involved in rhizosphere/soil persistence (copper resistance), root colonization (biofilm formation) and plant growth promotion (phytase activity). Transposon insertions in genes putatively coding for the transcriptional regulator CusR or the chemotaxis protein CheV were found to affect copper resistance, whereas an insertion in fleQ gene putatively encoding a flagellar regulatory protein hampered the ability to form a biofilm. However, these mutants displayed the same antagonistic effect against V. dahliae as the parental strain. Remarkably, two mutants impaired in biofilm formation were never found inside olive roots, whereas their ability to colonize the root exterior and to control VWO remained unaffected. Endophytic colonization of olive roots was unaltered in mutants impaired in copper resistance and phytase production. Results demonstrated that the phenotypes studied were irrelevant for VWO biocontrol.

Crested wheatgrass (Agropyron cristatum L. Gaertn., genome P), included in the Triticeae tribe (family Poaceae), is one of the most important grasses in temperate regions. It has been valued as a donor of important agronomic traits for wheat improvement, including tolerance to cold, drought, and high salinity, as well as resistance to leaf rust, stripe rust, and powdery mildew. For successful incorporation of beneficial alleles into wheat, it is essential that recombination between wheat and A. cristatum chromosomes occurs. In this work, we analysed chromosome associations during meiosis in wheat lines carrying chromosome introgressions from A. cristatum chromosomes 5P and 6P in the presence and absence of Ph1 locus using fluorescence in situ hybridisation. The results showed that the Ph1 locus does not affect chromosome associations between A. cristatum and wheat chromosomes because there were no interspecific chromosome associations; therefore, no recombination between chromosomes from wheat and Agropyron were observed in the absence of the Ph1 locus. The 5P and 6P A. cristatum chromosomes do not have a suppressor effect on the Ph1 locus. Wheat univalents in metaphase I suggest that Agropyron chromosomes might carry genes having a role in wheat homologous chromosome associations. Putative effect of the Agropyron genes on wheat chromosome associations does not interact with the Ph1 locus.

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.

Meiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.