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... El conocimiento de genomas complejos, como es el caso de la caña de azúcar, se benefició a partir de un gran número de descubrimientos en otros cereales y la disponibilidad de mapas genéticos de sorgo, maíz y arroz (Souza y col., 2001). Sin embargo, una de las mayores contribuciones lo constituye el resultado del Proyecto de Secuencias Expresadas en Caña de Azúcar (SUCEST del inglés -Sugarcane Expressed Sequence Tags") financiado por el consorcio brasileño ONSA (-Organization for Nucleotide Sequencing & Analysis") (Arruda, 2001). En dicho Proyecto participaron 74 grupos de secuenciación y a través de las ESTs (-Expressed Sequence Tags‖), herramienta económica y rápida que brinda información acerca de los genes que se expresan en ciertos tejidos o tipos de células en organismos multicelulares, se lograron secuenciar alrededor de 50 000 genes únicos (Vettore y col., 2001), que representaron el 38% de las 237 954 ESTs identificados en 26 librerías genómicas de ADNc en diferentes órganos, tejidos y distintos estados de desarrollo de las plantas. ...
... En caña de azúcar se determinaron las principales rutas metabólicas del etileno, ácido abscísico, auxinas, giberelinas y jasmonatos. Se llevó a cabo la búsqueda de secuencias con homología a genes relacionados con los mecanismos de traducción de señales, desarrollo, regulación de genes, reparación de ADN, respuesta a estrés biótico y abiótico, constitución de organelos y metabolismo (Santelli y Siviero, 2001;Carraro y col., 2001;Arruda, 2001;Pan, 2006). ...
... A group from South Africa began an EST collection for cultivar Nco376 (Carson and Botha, 2000). A huge number of ESTs have been produced and deposited in the EST database (Arruda, 2001;Bower et al., 2005;Casu et al., 2003Casu et al., , 2004Ma et al., 2004;Vettore et al., 2003). The largest achievement in EST collection was the Brazilian ONSA consortium's Sugarcane EST Project (SUCEST) which contained 237 954 ESTs from 37 cDNA libraries derived from different organs and tissues sampled at different developmental stages (Simpson and Perez, 1998;Vettore et al., 2001; http://sucest.lad.ic.unicamp.br/en/). ...
... Microarray analysis of sugarcane genotypes that varied in sucrose content revealed that many of the genes associated with high sucrose content showed overlap with drought data sets, but appeared to be mostly independent from abscisic acid signalling [12]. A large expressed sequence tag (EST) study of the sugarcane transcriptome and physiological, developmental and tissue-specific gene regulation was initiated in Brazil [13]. Sugarcane cultivars differing in both maximum sucrose accumulation (in Brix) capacity and accumulation dynamics during growth and culm maturation were studied cDNA microarrays and developmentally regulated genes related to hormone signalling, stress response, sugar transport, lignin biosynthesis and fibre content were identified [12]. ...
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Background: Sugarcane is a major crop of the tropics cultivated mainly for its high sucrose content. The crop is genetically less explored due to its complex polyploid genome. Sucrose synthesis and accumulation are complex processes influenced by physiological, biochemical and genetic factors, and the growth environment. The recent focus on the crop for fibre and biofuel has led to a renewed interest on understanding the molecular basis of sucrose and biomass traits. This transcriptome study aimed to identify genes that are associated with and differentially regulated during sucrose synthesis and accumulation in the mature stage of sugarcane. Patterns of gene expression in high and low sugar genotypes as well as mature and immature culm tissues were studied using RNA-Seq of culm transcriptomes. Results: In this study, 28 RNA-Seq libraries from 14 genotypes of sugarcane differing in their sucrose content were used for studying the transcriptional basis of sucrose accumulation. Differential gene expression studies were performed using SoGI (Saccharum officinarum Gene Index, 3.0), SAS (sugarcane assembled sequences) of sugarcane EST database (SUCEST) and SUGIT, a sugarcane Iso-Seq transcriptome database. In total, about 34,476 genes were found to be differentially expressed between high and low sugar genotypes with the SoGI database, 20,487 genes with the SAS database and 18,543 genes with the SUGIT database at FDR < 0.01, using the Baggerley's test. Further, differential gene expression analyses were conducted between immature (top) and mature (bottom) tissues of the culm. The DEGs were functionally annotated using GO classification and the genes consistently associated with sucrose accumulation were identified. Conclusions: The large number of DEGs may be due to the large number of genes that influence sucrose content or are regulated by sucrose content. These results indicate that apart from being a primary metabolite and storage and transport sugar, sucrose may serve as a signalling molecule that regulates many aspects of growth and development in sugarcane. Further studies are needed to confirm if sucrose regulates the expression of the identified DEGs or vice versa. The DEGs identified in this study may lead to identification of genes/pathways regulating sucrose accumulation and/or regulated by sucrose levels in sugarcane. We propose identifying the master regulators of sucrose if any in the future.
... Between the late 1990's and the beginning of the 2000's, the completion of a big multi-institutional Brazilian project on Sugarcane ESTs Project (SUCEST) (312), raised the enthusiasm on the possibilities of molecular breeding and genetic transformation processes in providing plants able to tap productivity levels never seen before. Enthusiastically, one director of a big sugarcane research center declared: "We believe there is no ceiling in productivity, theoretically" (313). ...
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Humanity is facing a pressing need to decarbonize the atmosphere in order to avoid catastrophic consequences. Sugar cane holds great potential to move towards a sustainable bioenergy production, as it is one of the most efficient biomass producing plants. However, the stagnant worldwide sugarcane yield is a menace to the fulfillment of its prospected contribution. Although promises abound of reaching that goal with new productive cultivars, there is a bottleneck not yet acknowledged: a dependable resilience of the cultivars. Resilience is a key factor in any agricultural crop and the genetic constitution of conventional sugarcane clearly shows why it fails in it. In a century-old sugarcane breeding system, one drive has prevailed: despite the cultivars having high concentration of sugar, they must consist of low fiber (12 ±2%), as allegedly the mills can operate with high efficiency. To accomplish this tradeoff, the sugary ancestral Saccharum officinarum contributes with nearly 85% to the genome of the cultivars, while the fibrous and resilient ancestral S. spontaneum complements the rest. With this composition, it has met the feedstock quality imposed by the industry, but the level of resilience is prejudiced. As result, the productivity of sugarcane has levelled off worldwide and the only chance of a leap forward is to break this captive dogmatism with energy cane: a plant with a higher contribution of the genome of S. spontaneum. With this gene influx, the resultant plant has higher resilience; the higher the genome contribution of this ancestral, the higher its resilience. This new hybrid type with high fiber content can definitively upgrade the biomass agroindustry, due to both its higher resilience and heterosis for biomass productivity and other favorable characteristics, thus giving a valuable contribution to CO2 mitigation.
... A complete description of the (SUCEST) database (http://sucest.lad.dcc.unicamp.br) can be found in Arruda (2001). ...
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Sugarcane is a very important crop that grows associated with diazotrophic and plant hormone-producing endophytic bacteria, such as Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and H. rubrisubalbicans. In this interaction, bacteria colonize the intercellular spaces and vascular tissues of most plant organs, promoting plant growth without inducing disease symptoms or nodule formation. Probably, plant genetic factors control the processes involved in plant colonization by these endophytes. The signaling pathways by which sugarcane plants can decipher bacterial signals and respond properly for a successful association are still not clearly understood. Here, we searched the sugarcane database for all expressed sequence tags (ESTs) preferentially or exclusively expressed in cDNA libraries constructed from sugarcane plants inoculated with G. diazotrophicus and H. rubrisubalbicans. Two such data sets of ESTs were generated in the infected libraries and ESTs from both data sets were functionally organized. For all categories, ESTs candidates to be involved in different processes of plant/bacteria signaling were identified, suggesting that the initial steps of colonization are actively controlled by the plant in the sugarcane/diazotrophic endophyte association.
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Sugarcane (Saccharum spp hybrid) is grown across the continents, principally for white sugar and bioethanol. It is a C4 plant, generates highest amount of biomass among the cultivated crops, and meets nearly 80% of the global white sugar requirement. The modern cultivated sugarcane is a derivative of Saccharum officinarum (noble canes) and the wild relative, S. spontaneum. Worldwide, breeding strategies have improved sugarcane yield till 1970s and later cane yield remained static across the countries. Many biotic constraints seriously affect productivity of the crop which is specific to cane growing countries. Among the diseases, smut, ratoon stunting, yellow leaf and mosaic are the major constraints in most of the countries. The diseases like red rot and wilt seriously affect cane production in South and South East Asian countries with many historic red rot epiphytotics causing huge crop losses in India. Similarly, the phytoplasma diseases, grassy shoot and white leaf are serious constraints in Asian region. Recently, the diseases like rusts, pokkah boeng, red stripe etc. emerged as major diseases in different countries. Among the insect pests, stalk borers are ubiquitous in nature with serious economic losses and each country or region has unique group of borer pests. Apart from the borer pests, many sucking pests and root grub are also of serious concern to sugarcane cultivation. Among the management strategies, host resistance is successfully exploited against various diseases and healthy seed, heat treatment, and chemicals are the other management strategies adopted in tandem. In case of insect pests, an integrated management is followed with more emphasis on biological control and chemicals depending on the pests and the location. Though remarkable gains were achieved through breeding strategies, complex polyploidy hinders genetic advancements for various traits in sugarcane. Recently, various genomic tools, especially transcriptomics were applied to understand gene functions and molecular markers are partially successful. Although, genetic transformation was successful in developing many transgenic lines against various biotic constraints, application of genome editing is in nascent stage due to multiple alleles. Overall, the various biotic constraints are managed through host resistance and other strategies in an integrated approach. Genomic applications have helped to understand genomes of the crop and pathogens/insects and, host resistance and genetic engineering supports trait improvement.
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Various abiotic stresses adversely affect the normal growth and development of the sugarcane crop and lead to decreased sugarcane productivity. Abiotic stress tolerance in sugarcane is regulated by many regulatory genes such as transcription factors and kinases that enable plants to withstand unfavorable conditions. Advancements in the sugarcane genome sequencing and genetic mapping will assist in pinpointing the locations of genes or markers related to abiotic stress tolerance. MicroRNAs also play important regulatory roles in sugarcane stress tolerance. Different proteins expressed in responses to various abiotic stresses allow the operation of the many molecular pathways involved in stress responses. Differential proteome analysis under stress conditions allows identification and utilization of new candidate genes for developing new cultivars by using them in breeding programs. Use of CRISPR-mediated genome editing techniques is likely to be the technique of choice for engineering abiotic stress tolerance in sugarcane.
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Sugarcane (Saccharum spp. hybrids), with its complex polyploid genome, is not well understood at the genetic level. Partial sequencing of anonymous cDNA clones is a widely used technique for gene identification. These partial cDNA sequences, or Expressed Sequence Tags (ESTs) have potential application for the identification of important genes for genetic manipulation. This study aimed to initiate the preliminary development of an EST database for sugarcane and thereby gain some potentially useful information on sugarcane gene sequences. A nondirectional cDNA library has been constructed from sugarcane leaf roll (meristematic region) tissue. Two hundred fifty clones have been randomly selected, subjected to single-pass sequencing from the 5' end of the vector, and identified by sequence similarity searches against gene sequences in international databases. Of the 250 leaf roll clones, 26% exhibit similarity to known plant genes, 50% to non-plant genes, while 24% represent new gene sequences. Analysis of the identified clones indicated sequence similarity to a broad diversity of genes encoding proteins such as enzymes, structural proteins, and regulatory factors. A significant proportion of genes identified in the leaf roil were involved in processes related to protein synthesis and protein modification, as would be expected in meristematic tissues. These results present a successful application of EST analysis in sugarcane and provide a preliminary indication of gene expression in leaf roll tissue.
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Sugarcane cultivars are polyploid, aneuploid, interspecific hybrids between the domesticated species Saccharum officinarum and the wild relative S. spontaneum. Cultivar chromosome numbers range from 100 to 130 with approximately 10% contributed by S. spontaneum. We have undertaken a mapping study on the progeny of a selfed cultivar, R570, to analyze this complex genome structure. A set of 128 restriction fragment length polymorphism probes and one isozyme was used. Four hundred and eight markers were placed onto 96 cosegregation groups, based on linkages in coupling only. These groups could tentatively be assembled into 10 basic linkage groups on the basis of common probes. Origin of markers was investigated for 61 probes and the isozyme, leading to the identification of 80 S. officinarum and 66 S. spontaneum derived markers, respectively. Their distribution in cosegregation groups showed better map coverage for the S. spontaneum than for the S. officinarum genome fraction and occasional recombination between the two genomes. The study of repulsions between markers suggested the prevalence of random pairing between chromosomes, typical of autopolyploids. However, cases of preferential pairing between S. spontaneum chromosomes were also detected. A tentative Saccharum map was constructed by pooling linkage information for each linkage group.
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The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German x S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 x S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple x S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into "homologous groups" based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.
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Modern cultivated sugarcane is a complex aneuploid polyploid with an estimated genome size of 3000 Mb. Although most traits in sugarcane show complex inheritance, a rust locus showing monogenic inheritance has been documented. In order to facilitate cloning of the rust locus, we have constructed a bacterial artificial chromosome (BAC) library for the cultivar R570. The library contains 103,296 clones providing 4.5 sugarcane genome equivalents. A random sampling of 240 clones indicated an average insert size of 130 kb allowing a 98% probability of recovering any specific sequence of interest. High-density filters were gridded robotically using a Genetix Q-BOT in a 4 × 4 double-spotted array on 22.5-cm(2) filters. Each set of five filters provides a genome coverage of 4x with 18,432 clones represented per filter. Screening of the library with three different barley chloroplast gene probes indicated an exceptionally low chloroplast DNA content of less than 1%. To demonstrate the library's potential for map-based cloning, single-copy RFLP sugarcane mapping probes anchored to nine different linkage groups and three different gene probes were used to screen the library. The number of positive hybridization signals resulting from each probe ranged from 8 to 60. After determining addresses of the signals, clones were evaluated for insert size and HindIII-fingerprinted. The fingerprints were then used to determine clone relationships and assemble contigs. For comparison with other monocot genomes, sugarcane RFLP probes were also used to screen a Sorghum bicolor BAC library and two rice BAC libraries. The rice and sorghum BAC clones were characterized for insert size and fingerprinted, and the results compared to sugarcane. The library was screened with a rust resistance RFLP marker and candidate BAC clones were subjected to RFLP fragment matching to identify those corresponding to the same genomic region as the rust gene.