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Colinear genomic regions in sugarcane (homoeologous BACs 265O22 and 51L01), rice (BAC 84L17), sorghum (BAC 110K05) and two homoeologous maize segments (Adh1 region and contig 276N13/123C01). Genes are indicated by gray boxes and shaded areas connect conserved genes. The figure is modified from of Ilic et al. (2003) and supplemented with the sugarcane data.
Source publication
Modern sugarcane (Saccharum spp.) is an important grass that contributes 60% of the raw sugar produced worldwide and has a high biofuel production potential. It was created about a century ago through hybridization of two highly polyploid species, namely S. officinarum and S. spontaneum. We investigated genome dynamics in this highly polyploid cont...
Context in source publication
Citations
... Knowledge of the global genome architecture of modern sugarcane cultivars is currently derived mainly from molecular cytogenetics 12,13,24,25 , genetic mapping 8,16,26 and haplotype sequence comparisons [27][28][29][30] . Our chromosome-scale R570 assembly provides the first fine-grain description of the genome architecture of modern sugarcane cultivars, a foundation to describe the patterns of genomic evolution and diversity within a neo-polyploid hybrid, a crucial resource for burgeoning sugarcane molecular breeding efforts. ...
Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide¹. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued². The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
... The first method is stable transformation modelled on the predominant method used for sugarcane (Saccharum ssp.; Silva et al. 2020), one of the closest relatives to sorghum (Saski et al. 2007;Cahoon et al. 2010). Sorghum is used as a genetic model to study sugarcane (Jannoo et al. 2007;Rokhsar et al. 2010) and was the key to annotating the complex sugarcane genome (Garsmeur et al. 2018). Because many sugarcane varieties are hybrids and do not produce seeds, the preferred explant in sugarcane transformation is leaf whorls, as frequently reported (Kumar et al. 2014;Wu et al. 2015;Zhang et al. 2015;Gao et al. 2016;Jung and Altpeter 2016;Sandhu et al. 2016). ...
Sorghum (Sorghum bicolor) is an emerging cereal crop in temperate climates due to its high drought tolerance and other valuable traits. Genetic transformation is an important tool for the improvement of cereals. However, sorghum is recalcitrant to genetic transformation which is almost only successful in warmer climates. Here, we test the application of two new techniques for sorghum transformation in temperate climates, namely transient transformation by Agrobacterium tumefaciens–mediated agroinfiltration and stable transformation using gold particle bombardment and leaf whorls as explants. We optimized the transient transformation method, including post-infiltration incubation of plants in the dark and using Agrobacterium grown on plates with a high cell density (OD600 = 2.0). Expression of the green fluorescence protein (GFP)-tagged endogenous sorghum gene SbDHR2 was achieved with low transformation efficiency, and our results point out a potential weakness in using this approach for localization studies. Furthermore, we succeeded in the production of callus and somatic embryos from leaf whorls, although no genetic transformation was accomplished with this method. Both methods show potential, even if they seem to be influenced by climatic conditions and therefore need further optimization to be applied routinely in temperate climates.
... Sugarcane is one of the most important economic crops with an annual value of US$90 billion and provides 80% of the world's sugar and 40% of ethanol [28]. Published genomic studies show that sugarcane and sorghum genomes are mostly collinear in the genic regions, sharing a common ancestor about 8-9 million years ago [29][30][31]. To date, no natural diploid sugarcane has been found, and sorghum (2n = 2x = 20) can be tentatively regarded as the hypothetical diploid sugarcane ancestor type. ...
Background
Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum , the most primitive and complex species in the genus Saccharum , has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear.
Results
In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012–46 (x = 9, hexaploid) and AP85–441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum . By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species.
Conclusions
Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum .
... However, markerassisted selection (MAS) has arisen as a powerful tool to facilitate genetic manipulation through the identification of candidate genes for various traits of sugarcane and to develop saturated genetic maps. Molecular markers such as RAPD (al-Janabi et al. 1993), RFLP (Lu et al. 1994;da Silva et al. 1995), AFLP (Barbosa et al. 2003) and SSR (Selvi et al. 2003) have already been used in sugarcane for genotyping as well as genetic mapping and efforts have been made to develop molecular markers using these techniques (Lu et al. 1994;Glaszmann et al. 1997;Alix et al. 1998;Jannoo et al. 2007). ...
... However, markerassisted selection (MAS) has arisen as a powerful tool to facilitate genetic manipulation through the identification of candidate genes for various traits of sugarcane and to develop saturated genetic maps. Molecular markers such as RAPD (al-Janabi et al. 1993), RFLP (Lu et al. 1994;da Silva et al. 1995), AFLP (Barbosa et al. 2003) and SSR (Selvi et al. 2003) have already been used in sugarcane for genotyping as well as genetic mapping and efforts have been made to develop molecular markers using these techniques (Lu et al. 1994;Glaszmann et al. 1997;Alix et al. 1998;Jannoo et al. 2007). ...
Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.
... A comparative study among grass genomes for their conserved segments indicated a high degree of collinearity among them (Moore 1995;Gale and Devos 1998), such as observed between Sorghum and sugarcane (Grivet et al. 1994;Dillon et al. 2007;Garsmeur et al. 2018). Collinearity could occur in terms of high sequence identity (95.2%), orthologous gene match (85%), reasonably low chromosome rearrangements (Grivet et al. 1994;Dufour et al. 1997;Guimarães et al. 1997;Ming et al. 1998;Wang et al. 2010), high conservation of gene order and close evolutionary relationship (Jannoo et al. 2007;Garsmeur et al. 2011). The near-complete genome information of Sorghum bicolor (Paterson et al. 2009), having a genome size of about 730 MB, could therefore be exploited in sugarcane, as a template to identify genes lying in the vicinity of QTLs. ...
... Till date, only a monoploid mosaic genome sequence for commercial cultivar R570 and an allele-defined Saccharum spontaneum genome were reported (Garsmeur et al. 2018;Zhang et al. 2018). Alternatively, recent advancements in sequencing techniques had paved the way for sequencing of several crops with less complex genomes, such as Sorghum genome, that exhibits a high degree of micro-collinearity with sugarcane genome (Ming et al. 1998;Jannoo et al. 2007;Wang et al. 2010;Garsmeur et al. 2011). Genome sequence of haploid S. spontaneum (AP85-441) shows an estimated 90% similarity in the genes and 80% similarity in gene order with Sorghum bicolor genome (Zhang et al. 2018). ...
Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop.
... Sugarcane has a high level of synteny and collinearity with sorghum (Garsmeur et al., 2011;Kim et al., 2013;Mancini et al., 2018;de Setta et al., 2014;Vilela et al., 2017), diverging from sorghum 6-9 million years ago (MYA) and from Miscanthus 8-9 MYA. In addition, sugarcane has undergone two whole-genome duplications (WGDs) after divergence, while Miscanthus has since undergone one WGD ( Jannoo et al., 2007;Paterson et al., 2004;Zhang et al., 2018). Sugarcane also shares collinearity and low genomic rearrangements with maize, rice, and Brachypodium (Ming et al., 1998). ...
... spontaneum recombinant chromosomes. In the SP80-3280 hybrid, which has 112 chromosomes (Sforça et al., 2019), a representative gene space (Tomkins et al., 1999) Adh1 region Jannoo et al. (2007) BAC clones from R570 sugarcane cultivar (Tomkins et al., 1999) and four selfed R570 individuals Bru1 region Le Cunff et al. (2008) BAC clones from R570 sugarcane cultivar (Tomkins et al., 1999) Multiple regions Wang et al. (2010) BAC clones from R570 sugarcane cultivar (Tomkins et al., 1999) and four selfed R570 individuals (Le Cunff et al., 2008) Bru1 region Garsmeur et al. (2011) BAC clones from R570 sugarcane cultivar (Tomkins et al., 1999) Multiple regions Berkman et al. ...
Sugarcane (Saccharum spp. hybrids) is an essential crop in the world for sugar and bioenergy production. However, genetic studies in sugarcane are complex due to its high ploidy levels and unbalanced chromosome numbers. Nevertheless, a significant improvement can be addressed in sugarcane breeding programs using information from omics (transcriptomics, proteomics, and metabolomics) resources. In this context, the chapter will point to the main applications of molecular markers and possible associations with the phenotype to increase gene detection accuracy, including allele dosage information, complex networks, and sophisticated genome models to predict genetic gains.
... Ten BAC clones from the sugarcane cultivar R570 library developed by Tomkins et al. (1999) and identified by Jannoo et al. (2007) as corresponding to hom(oe)ologous chromosome segments bearing the Adh1 gene were sequenced. Mate-pair libraries of ten BAC clones were produced and sequenced using the 454 method (FLX Titanium, Roche) and assembled with Newbler (Roche). ...
... Sequences were submitted to the EMBL database under the following accession numbers (BAC clone names in parentheses; Sh, Saccharum hybrid): HG531786 (Sh102M23), HG531788 (Sh111P05), HG531792 (Sh172H13), HG531793 (Sh182G15), HG531794 (Sh186P07), HG531797 (Sh192N12), HG531798 (Sh206M17), HG531799 (Sh209M19), HG531802 (Sh242M02) and HG531804 (Sh245F09). Two additional hom(oe)ologous BAC clones, Sh051L01 and Sh265O22 (accession numbers AM403006 and AM403007), were previously sequenced using the Sanger method (Jannoo et al., 2007). ...
... Gene predictions were manually curated using Artemis software as described in Garsmeur et al. (2011). Genes were numbered according to Jannoo et al. (2007) and de Setta et al. (2014) for the Adh1 and Rpa1 regions, respectively. Large transposable elements (TEs) were annotated in the Adh1 region as described in Garsmeur et al. (2011) and for the Rpa1 region the annotation from de Setta et al. (2014) was updated. ...
Background and aims:
Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.
Methods:
To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.
Key results:
The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.
Conclusions:
This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.
... The importance of understanding the mechanisms of nodal root development is further supported by sugarcane, which diverged from sorghum 6-9 MYA and is more closely related to sorghum than maize [81][82][83]. Sugarcane is primarily propagated vegetatively, which occurs when a piece of stem, termed a sett, is planted in the soil and the root system is derived from nodes only. Sugarcane shows remarkable plasticity in nodal root phenotypes, with roots that emerge from the sett showing fine, highly branched architectures, whereas the roots that emerge from the new shoot are thick and reminiscent of the nodal roots in maize and sorghum [84]. ...
Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots–subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.
... Therefore, the shared control of brace roots and flowering time (Supplemental Table 5) may not be unique to maize. Sugarcane diverged from sorghum 6-9 MYA and is more closely related to sorghum than maize, (Paterson et al., 2004;Jannoo et al., 2007;Thirugnanasambandam et al., 2018). Sugarcane differs from other members of Andropogoneae in that it is primarily propagated vegetatively, which means that the root system is entirely nodal-derived. ...
Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, there are two types of post-embryonic roots - subterranean nodal roots (crown roots) and aerial nodal roots (brace roots). Recent research in maize demonstrates that aerial nodal roots play an important role in crop anchorage. However, most studies have been unsuccessful at teasing apart the relationship between phase change, flowering time, and brace root development. Though less is known about function, other members of the Poaceae have documented aerial nodal roots including sorghum, sugarcane, setaria. To meet the demands of a growing population, the development and function of aerial nodal roots in crops must be better characterized. Here, we summarize recent research demonstrating 1) the importance aerial nodal roots in maize anchorage, 2) the fundamental association between phase change, flowering time, and brace roots in maize, and 3) the limited knowledge of brace root development and function in other members of Poaceae. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.
