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Homoeologous chromosome determination of Th. bessarabicum chromosome 3J using intron-targeted (IT) markers and characterization of spontaneous translocations T3JS·4JL and 3JS·4JL using ONPM#7 FISH. Plus sign indicates the presence of specific loci of Th. bessarabicum; minus sign indicates the absence of specific loci. Blue and red indicate markers that were in silico-mapped on the short arm and long arm, respectively, of homoeologous group 3 chromosomes. CS, Chinese Spring; MS301, CS-Th. bessarabicum amphiploid. The alien chromosomes were further validated after sequential GISH in Figs. S11 and S12
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Thinopyrum bessarabicum is an important genetic resource for wheat improvement by chromosome engineering. However, the present low-resolution karyotype limits identification of its chromosomes. Oligonucleotide probes to identify tandem repeats provide an efficient way to produce high-resolution karyotypes in many species. In this study, putative ta...
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Haynaldia villosa is a wild relative of wheat and a valuable gene resource for wheat improvement. Owing to the limited number of probes available for fluorescence in situ hybridization (FISH), the resolution at which the karyotype of H. villosa can be characterized is poor, hampering accurate characterization of small segmental alien introgressions...
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Citations
... Comparative analysis of copy number, nucleotide sequences, and localization on the chromosomes serves as a tool for basic phylogenetic and evolutionary studies of plants, including al., 1994;Kishii et al., 1999;AnamthawatJónsson et al., 2009;Han et al., 2017;Linc et al., 2017;Ruban, Badaeva, 2018;Said et al., 2018;Salina, Adonina, 2019;Dai et al., 2021;Wu et al., 2021;Chen C. et al., 2022;Kroupin et al., 2023;. Satellite repeats have found practical use as PCR markers and chromosomal markers for identifying introgres sions of alien genetic material containing valuable economic traits in the genomes of cultivated cereals (Li G. et al., 2016;Han et al., 2017;Liu L. et al., 2018;Chen J. et al., 2019). ...
... Tangible progress has been made in the study of Triticeae genomes, owing to the invention of wholegenome sequencing methods and bioinformatic algorithms for analyzing the data obtained (RabanusWallace, Stein, 2019; Gao et al., 2023). The rapid growth in the volume of information on genome wide sequences of Triticeae has significantly accelerated and simplified the search for repetitive DNA that can be used as chromosomal markers (Du et al., 2017;Said et al., 2018;Tang et al., 2018;Chen J. et al., 2019;Kroupin et al., 2019aKroupin et al., , 2022Lang et al., 2019a;Liu Q.L. et al., 2020;Wu et al., 2021Wu et al., , 2022. Due to the significant presence of repetitive DNA in the Triticeae genomes, information about satellite repeats can be obtained even through sequencing with low coverage. ...
Satellite repeats are a significant component of the genome of Triticeae and play a crucial role in the speciation. They are a valuable tool for studying these processes. Pseudoroegneria species play a special role among grasses, as they are considered putative donors of the St-genome in many polyploid species. The aim of this study was to compare the copy number of satellite repeats in the genomes of Triticeae species. Quantitative real-time PCR was applied to determine the copy numbers of 22 newly discovered satellite repeats revealed in the whole-genome sequences of Pseudoroegneria species and one additional repeat previously identified in the genome of Aegilops crassa . The study focused on seven species of Pseudoroegneria , three species of Thinopyrum , Elymus pendulinus , Ae. tauschii , Secale cereale , and Triticum aestivum . Based on the copy number level and coefficients of variation, we identified three groups of repeats: those with low variability between species (medium-copy CL82), those with medium variability (low- and medium-copy CL67, CL3, CL185, CL119, CL192, CL89, CL115, CL95, CL168), and those with high coefficients of variation (CL190, CL184, CL300, CL128, CL207, CL69, CL220, CL101, CL262, CL186, CL134, CL251, CL244). CL69 exhibited a specific high copy number in all Pseudoroegneria species, while CL101 was found in both Pseudoroegneria and Th. junceum , CL244 in Th. bessarabicum , CL184 in P. cognata and S. cereale . CL95, CL128, CL168, CL186, CL207, and CL300 exhibited higher copy numbers in P. cognata compared to other species; CL3, CL95, CL115, CL119, CL190, CL220, CL207, and CL300 in P. kosaninii ; CL89 in P. libanotica ; CL134 in P. geniculata . Our assessment of the copy number of new satellite repeats in the St-genome and the analysis of their amplification specificity between species can contribute to the molecular-genetic and chromosome markers used for evolutionary, phylogenetic, and population studies of Triticeae species.
... tauri on one pair of chromosomes, and minor signals were observed in various regions of the remaining chromosomes (Figure 1). The localization of the CL119-like repeats in Triticeae species is characterized by distal, subtelomeric, and terminal localization on chromosomes (Tables 2 and S1) [51,[63][64][65][66]. These repeats have also been found on B chromosomes of rye and Aegilops [67,68], except for pAcPR5, which is distributed across all P genome chromosomes of A. cristatum [69]. ...
... bessarabicum, while in the latter species, the signals were the strongest. Given the conserved nature of localization and its distribution in many species of Triticeae, as well as the similarity of the CL244 terminal repeat to the Spelt52.1 repeats from Ae. Speltoides [70], pSc200 and pSc7235 from S. cereale [71,72], and BSCL1 and DP4J27982 from Th. bessarabicum [66,73], it can be assumed that CL244 refers to ancient repeats that arose before the divergence of the hypothetical ancient genome into separate genomes. ...
... Supplementary Materials: The following supporting information can be downloaded at https:// www.mdpi.com/article/10.3390/plants12244169/s1. References [46,47,50,51,[60][61][62][63][64][65][66][67][68][69][70][74][75][76][77][78][79][85][86][87][88][89][90][91] are cited in the supplementary materials. Supplementary Tables: Table S1: Results of the homology search for new St genome terminal satellite repeats with known Triticeae repeats. ...
Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.
... Unlike for Th. elongatum, a signal only on one arm is observed for chromosomes 2 and 7 of Th. bessarabicum, on both arms for group 3, and on the short arm and polymorphically on the long arm for group 5 (Grewal et al. 2018;Chen et al. 2019;Badaeva et al. 2019;Singh et al. 2020). ...
... Interstitial signals can be detected on the long arm of groups 2 and 5 and on the short arm of groups 6 and 7. The brightest band is typical to the terminal region of the long arm of group 5 (Grewal et al. 2018;Chen et al. 2019;Badaeva et al. 2019;Singh et al. 2020;Dai et al. 2021). Singh et al. (2019) used labeled oligo probes pSc119.2-1 ...
... Th. bessarabicum karyotype and ideograms were developed using oligo multiplex #1 (TAMRA-labeled pAs1-3 + pAs1-4 + pAs1-6 and FAM-labeled (GAA) 10 ) supplemented with FAM-labeled DP4J27982, based on a series of Chinese spring introgression lines. Chen et al. (2019) used the OLIGO7 bioinformatics algorithm to identify eight abundant tandem repeats with terminal or subterminal localization (BSCL1, BSCL242; BSCL5, BSCL75; BSCL158) or with additional interstitial localization (BSCL135; BSCL184; BSCL156) on chromosomes. The BSCL135 (similar to pTa-713 and producing the strongest and most widely distributed signals on all chromosomes) and BSCL242 (specific to subterminal region of 7JL) repeats, together with a mixture of different variants of oligoprobes pAs1, AFA, pSc119.2, ...
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for “classical” wheat probes (pSc119.2 and Afa family) and “universal” repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
... Despite the significant progress made in genome sequencing, the number of DNA probes employed in FISH analysis of cereal species is still very limited. In addition to pSc119.2 and pAs1 probes that have traditionally been used for chromosome identification and phylogenetic studies of the Triticeae since the middle 80 th (Bedbrook et al., 1980;Rayburn and Gill, 1986), several new DNA sequences have been isolated from nuclear DNA and used as probes in FISH analysis of wheat and Aegilops as well as of other grass species (Kato et al., 2004(Kato et al., , 2011Komuro et al., 2013;Chen et al., 2019;Xi et al., 2019). ...
... However, the genome of Ae. crassa has not yet been sequenced, which certainly limits the possibilities of its comprehensive study. From the other side, even unassembled reads can be used to search for new tandem satellite repeats from which chromosomal markers can be developed (Koo et al., 2016;Du et al., 2017;Liu et al., 2018b;Chen et al., 2019;Kroupin et al., 2019b;Nikitina et al., 2020). In particular, comparative genome analysis has been successfully used to obtain specific chromosomal markers for the detection of alien chromosomes in wheat addition lines Liu et al., 2018a) and for identification of Y subgenome in Roegneria (Wu et al., 2021). ...
... The A subgenome chromosomes of wheat were classified using additional probe combination GAA n and pTa-535 according to Komuro et al. (2013); chromosomes of Ae. tauschii were classified as suggested by Badaeva et al. (2002Badaeva et al. ( , 2019a and Zhao et al. (2018), Ae. crassa as in Abdolmalaki et al. (2019), and Badaeva et al. (2021). Th. bessarabicum chromosomes were classified according to Grewal et al. (2018), Badaeva et al. (2019b), and Chen et al. (2019). ...
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D¹D¹XcrXcr and 2n = 6x = 42, D¹D¹XcrXcrD²D², respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D¹ and D² subgenomes of Ae. crassa were contributed by Aegilopstauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D¹ or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
... Total genomic DNA of D. villosum was used as a probe for genomic in situ hybridization (GISH) following Zhang et al. (2012). Procedures of FISH and sequential GISH were conducted as described in Huang et al. (2018) and Chen et al. (2019), respectively. Chromosomes were visualized under an Olympus BX60 or BX53 microscope (Olympus Inc., Japan), and images were captured through a SPOT CCD (SPOT Cooled Color Digital, Olympus DP72 or DP80) camera (Olympus Inc., Japan) and analysed using the image program Photoshop ® (Adobe Inc., USA). ...
Background and aims:
Dasypyrum villosum (2n = 2x = 14) harbors potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow genetic base of wheat. A better solution for this issue is to utilize diversified D. villosum accessions as genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information of the species. Using cytogenetic and molecular tools we analyzed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat.
Methods:
A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. The polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content (CPIC) were used in genetic diversity analysis.
Key results:
Consensus karyotypes of D. villosum were developed, and the homoeologous status of individual D. villosum chromosomes relative to wheat were determined. The tandem repeat probes of pSc119.2, (GAA)10 and AFA family produced high-resolution signals not only showing different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids.
Conclusions:
Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination - chromosome engineering - allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.
Key message
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat.
Abstract
Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection (CWMCC) and Shanxi Province wheat collection (SXPWC) were used for chromosome analysis using oligonucleotide probe multiple (ONPM) FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. Genome wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a DH population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.
Modern hexaploid wheat (Triticum aestivum L.; AABBDD) has evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy have played important roles in wheat evolution. How these variations occur and their role in expanding the genetic diversity of modern wheat remain largely unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variations that occur during the early generations of existence. SHW lines derived by crossing durum wheat ‘Langdon’ with 12 Ae. tauschii accessions were analyzed using oligonucleotide probe multiplex fluorescence in situ hybridization (FISH) of metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorizes them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes, but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in the SHW lines detected in this study may indicate that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.
Mycobiota of Podolyanka and Poliska 90 winter wheat varieties seeds was found to be represented mainly by fungi of the Alternaria, Fusarium, Penicillium, Aspergillus, Chaetomium, Trichothecium genera which are characterized by various levels of pathogenicity, depending on the physiological and biochemical properties the host variety. Signifcant increase is air temperature and relative humidity during the wheat flowering and milking stage of grain ripening contributed to the spread of micromycetes of the genus Alternaria Nees. (50 %). The seeds the affected by fungi Alternaria were physiologically underdeveloped, had low energy and germination, which averaged 40 %. Plants form such seeds lag behind in growth and development. It is established that the physiological and biochemical mechanism of Podolyanka winter wheat variety stimulates mycelium radial growth and intensity of fungi Alternaria sporulation indicating the rapid reproduction of micromycetes, which contributes to the contamination of agrophytocenoses by propagative structures of the pathogen. However, the intensity of spore formation and the rate of mycelium radial growth on Poliska 90 variety seeds, was signifcantly lower. This fact gives reason to believe that the physiological and biochemical mechanism of the Poliska 90 variety plants is able to restrain the intensity of the genus Alternaria micromycetes spore formation at an ecologically safe level. It was found that the seeds of the Podolyanka and Poliska 90 winter wheat varieties are low in protein content and have high humidity. In terms of raw gluten content, they are classifed in the quality group 3. Isolates of fungi the genus Alternaria developed more intensively on the Podolyanka winter wheat variety grain, which is characterized by a lower content of protein and gluten. However the development of fungi was signifcantly lower on the Poliska 90 variety grain, which is characterized by a slightly higher content of protein and gluten. System-ecological approach to the improvement of agroecosystems in organic farming can be carried out using indicators of the variety physiological and biochemical properties interaction with physiological properties of phytopathogenic fungi, namely sporulation intensity and mycelial radial growth rate. This can increase the level of biosafety in agroecosystems and improve the quality of plant raw materials. Key words: the frequency of occurrence, mycelium radial growth, sporulation intensity, phytosanitary optimization, wheat winter agrphytocenoses.
