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The diagram illustrates the characterization of Chrs 1–, 2–, 7–, and 8–derived chromosomes in LC05-136. A The diagram illustrates the characterization of a given chromosome based on multiple painting probe FISH. Each bar represents a chromosome. Green color represents the FISH signal of chromosome 1 painting (CP1) probe. Magenta color represents the FISH signal of spontaneum–specific painting (SsP) probe. The chromosomes with CP1 signal were identified by CP1 FISH. After FISH using SsP probe, six cases (a1–a6) could be found based on the SsP signal pattern in the chromosome with CP1 signal. A chromosome with overlapping whole-chromosome signal of CP1 and SsP represents the entire S. spontaneum chromosome (a1). A chromosome with only whole-chromosome CP1 signal represents the entire S. officinarum chromosome (a2). A chromosome with whole-chromosome CP1 signal and SsP signals from a chromosomal fragment represents interspecific recombination between homoeologous chromosomes (a3). A chromosome with fragmental signals from both CP1 and SsP represents interspecific recombination between nonhomoeologous chromosomes (a4). A chromosome with whole-chromosome SsP signal but CP1 signal from a chromosomal fragment represents translocation of S. spontaneum chromosome (a5). A chromosome with only CP1 signal from a chromosomal fragment represents translocation of S. officinarum chromosome (a6). B The diagram illustrates the characterization of Chrs 1–, 2–, 7–, and 8–derived chromosomes in LC05-136
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Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40–128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Te...
Citations
... Accurate identification of individual chromosomes and structural chromosomal rearrangements is essential for a comprehensive understanding of the evolutionary relationships among species (Ferguson-Smith and Trifonov 2007;Rosin et al. 2021;Wang et al. 2022). Not until very recently, plant cytogenetics research has been restricted to the use of traditional FISH probes, such as large-insert genomic DNA BAC (Bacterial Artificial Chromosomes) clones and repetitive DNA sequences, including tandem and dispersed repeats (Liu et al. 2020). ...
Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus.
Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species.
... The monoploid sugarcane genome is estimated to be 382 Mb in size (Garsmeur et al., 2018) while the polyploid sugarcane nuclear genome is about 10 Gb (D'Hont and Glaszmann, 2001;Hoarau et al., 2001;Le Cunff et al., 2008) The genomes of S. officinarum LA Purple and S. spontaneum SES208 were explored by earlier studies beginning from 1996 (D'Hont et al., 1996). Recently, genomes of S. spontaneum, S. officinarum and the hybrid genotype R570 were explored (Zhang et al., 2018;Wang et al., 2022;Zhang et al., 2022). However, the entire polyploid sugarcane genome is not sequenced yet due to the inherent genome complexity resulting from the varied contributions of two to three progenitor genomes (Pompidor et al., 2021), recombination, repetitive content, and alternative splicing (Thirugnanasambandam et al., 2018). ...
Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.
... Pioneering studies on mitotic chromosomes have established that the constitution of modern varieties consists of approximately 75%-80% S. officinarum, 10%-25% S. spontaneum and 10%-15% recombinant chromosomes (D'Hont et al., 1996;Piperidis et al., 2010;Piperidis & D'Hont, 2020). However, using S. spontaneum-specific chromosome probes, Wang, Cheng, et al. (2022) It would be interesting, in the near future, to focus on immunolocalisation of the axis and synaptonemal complex proteins in the parental contributors of sugarcane to characterise their role in stabilising sugarcane meiosis. Future work could also focus on the pairing partner switches observed at pachytene that could be confirmed and visualised in greater detail, as was the case in Arabidopsis arenosa (Morgan & Wegel, 2020). ...
The modern cultivars of sugarcane (Saccharum spp.) are highly polyploid and accumulate aneuploidies due to their history of domestication, genetic improvement and interspecific hybrid origin involving the domesticated sweet species Saccharum officinarum (‘noble cane’) and the wild Saccharum spontaneum, both with an evolutionary history of polyploidy. The first hybrids were backcrossed with S. officinarum, and selection from progenies in subsequent generations established the genetic basis of modern cultivars. Saccharum genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture and cytogenetics. Herein, we conducted a comparative analysis of the meiotic behaviour of representatives of the parentals S. officinarum and S. spontaneum, and the commercial variety, SP80‐3280. S. officinarum, an octoploid species, exhibited regular meiotic behaviour. In contrast, S. spontaneum and SP80‐3280 exhibited several abnormalities from metaphase I to the end of division. We reported and typified, for the first time, the occurrence of peri‐ and paracentric inversions. Using in‐situ hybridisation techniques, we were able to determine how pairing association occurred at diakinesis, the origin of lagging chromosomes and, in particular, the mitotic chromosome composition of SP80‐3280. Interestingly, S. spontaneum and recombinant chromosomes showed the most marked tendency to produce laggards in both divisions. Future attempts to advance knowledge on sugarcane genetics and genomics should take meiotic chromosome behaviour information into account.
... Sugarcane hybrids are typical polyploid plants and have undergone an improvement process in which S. officinarum (noble cane) were crossed with S. spontaneum (wild cane) to generate hybrid offspring; then, these sugarcane hybrids were backcrossed with S. officinarum successively to obtain high sugar content and production features [1]. Modern sugarcane hybrids combine the high sugar content of S. officinarum and the excellent traits of S. spontaneum, such as high resistance to stress, high tillering, and perennial root, which are of great value for the crop to satisfy worldwide increasing demand for table sugar. ...
Modern sugarcane cultivars (Saccharum spp. hybrids) are the major contributors to sucrose and bioenergy in the world. The global changes in gene expression and the molecular mechanism of heterosis between modern sugarcane hybrids and their parents remain to be elucidated. In this study, we performed a comparative transcriptome analysis between hybrids and their parents using the Illumina RNA-Seq method to understand the differences in transcript expression after hybridization. The results show that (1) introduction of the S. spontaneum lineage resulted in significant upregulation of biotic and abiotic stress resistance genes in S. hybrids, including hexokinase (HXK) genes, pathogenesis-related protein (PR1) genes, coronatine-insensitive protein (COI-1), jasmonate ZIM domain-containing protein (JAZ) genes, and serine/threonine protein kinase 2 (SnRK2) genes. (2) Transgressive genes in hybrids were mainly concentrated in the synthesis pathways of biotin and vitamin B6, helping establish advantages in terms of stress resistance, antioxidant activity, and growth. (3) Glutathione-S-transferase (GST) was likely to enhance stress resistance in hybrids, and corresponding genes were key positive selection genes in processes, including round-robin selection and other adaptations. In this study, we propose explanations for heterosis in sugarcane hybrids from a transcriptomic perspective, in addition to identifying candidate genes to aid in the improvement of sugarcane cultivars.
... A complete census of chromosomal numbers has been attempted with sugar cane. 25,45 Much of the research indicated that there is significant variation in the number of chromosomes based on this plant's geographic location, as shown in Figure 2. Sugar cane is an excellent system for studying the evolutionary patterns of chromosome number and genome size evolution among monocots because this group has an unusually high diversity of chromosome 47,48 numbers (n = 20−131). The species are perennial and distributed in the tropical ecosystem worldwide 19 to adapt under a tropical environment with C 4 photosynthesis, 49 creating a more suitable crop under climate change conditions with ease of reproduction/hybridization of the different species among the Saccharum genus for creating new traits. ...
Sugar cane (Saccharum spp. hybrids) is a major crop for sugar and renewable bioenergy worldwide, grown in arid and semiarid regions. China, the world's fourth-largest sugar producer after Brazil, India, and the European Union, all share ∼80% of the global production, and the remaining ∼20% of sugar comes from sugar beets, mostly grown in the temperate regions of the Northern Hemisphere, also used as a raw material in production of bioethanol for renewable energy. In view of carboxylation strategies, sugar cane qualifies as one of the best C 4 crop. It has dual CO 2 concentrating mechanisms located in its unique Krantz anatomy, having dimorphic chloroplasts located in mesophylls and bundle sheath cells for integrated operation of C 4 and C 3 carbon fixation cycles, regulated by enzymes to upgrade/sustain an ability for improved carbon assimilation to acquire an optimum carbon economy by producing enhanced plant biomass along with sugar yield under elevated temperature and strong irradiance with improved water-use efficiency. These superior intrinsic physiological carbon metabolisms encouraged us to reveal and recollect the facts for moving ahead with the molecular approaches to reveal the expression of proteogenomics linked with plant productivity under abiotic stress during its cultivation in specific agrizones globally.
... Multiple chromosome-marking by oligo-FISH probes also has been developed for cucumber and potato and served in comparative karyotype analysis within the genera of Cucumis (Han et al., 2015) and Solanum . Also, chromosome barcoding has been achieved in maize (Braz et al., 2020;, beans (de Oliveira Bustamante et al., 2021), oats , wheat , rice (Liu et al., 2020a), and sugarcane (Piperidis, D'Hon, 2020;Wang et al., 2022). ...
Please use the following format when citing the article: Stakelienė V., Pašakinskienė I. 2022. Fluorescent in situ hybridisation in plants: new ways to link DNA sequence resources and chromosome loci-a review. Zemdirbyste-Agriculture, 109 (2): 171-178. Abstract Fluorescent in situ hybridisation (FISH) that allows chromosome DNA labelling has revolutionised plant molecular cytogenetics. With the development of FISH techniques, diverse opportunities to explore and understand the structure, origin, and evolution of plant karyotype have emerged. This review aims to summarize and discuss the latest advances in the application of the FISH technique in crop plants and some wild species. Variable patterns of the genome rearrangements in the newly made distant hybrids are covered as well as contribution of genomic in situ hybridisation (GISH) in revealing allopolyploid species phylogeny at the evolutionary scale. Currently, oligo-FISH increased chromosome loci detection and visualisation at a precision never recorded before. This approach requires skills in computational analysis of DNA resources and oligo-probe design. The advantages of synthetic bulked oligo-FISH probes for genome mapping and gene localisation are emphasised in this review. This technique significantly compliments DNA sequencing data, highlights new findings in chromosome collinearity, and shows some unusual instances of plant genome plasticity.
The modern cultivars of sugarcane ( Saccharum spp.) are highly polyploid and accumulate aneuploidies due to their history of domestication, genetic improvement and interspecific hybrid origin involving the domesticated sweet species S. officinarum ('noble cane') and the wild S. spontaneum , both with an evolutionary history of polyploidy. The first hybrids were backcrossed with S. officinarum , and selection from progenies in subsequent generations established the genetic basis of modern cultivars. Saccharum genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture and cytogenetics. Herein, we conducted a comparative analysis of the meiotic behavior of representatives of the parentals S. officinarum and S. spontaneum , and the commercial variety, SP80-3280. S. officinarum , an octoploid species, exhibited regular meiotic behavior. In contrast, S. spontaneum and SP80-3280 exhibited several abnormalities from metaphase I to the end of division. We reported and typified, for the first time, the occurrence of peri- and paracentric inversions. Using in-situ hybridization techniques, we were able to determine how pairing association occurred at diakinesis and, in particular, the chromosome composition of SP80-3280. Our findings have implications for sugarcane genetic mapping, genomics, and for studies on resynthesized polyploids.
The Saccharum genus comprises species with large and variable chromosome numbers, leading to challenges in genomic studies and breeding improvement. Cytogenetics, including classical and molecular approaches, has played a central role in deciphering the genome structure, classification, and evolution of the genus Saccharum. The application of fluorescence in situ hybridization using oligonucleotide probes significantly improved our understanding of the complex genomes of Saccharum species. This paper reviews the application and progress of cytogenetic techniques in Saccharum. Future applications of cytogenetics are discussed, as they could benefit both genomic studies and breeding of sugarcane as well as other plants with complex genomes.
