Sugarcane
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ABSTRACT:
PROVIDER: PRJNA810923 | ENA |
REPOSITORIES: ENA
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Project description:To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including one F1 population derived from cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.
2019-12-17 | GSE128450 | GEO
Project description:Genome-wide association studies reveal the genetic loci of sugarcane leaf angles at different developmental stages
| PRJNA810929 | ENA
Project description:In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues. There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane. During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively. Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively. Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h). A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed. Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed. Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves.
2008-07-01 | GSE11934 | GEO
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress. Screenning of sRNA transcriptome of sugarcane plants under drougth stress
2012-11-24 | E-GEOD-42483 | biostudies-arrayexpress
Project description:By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it was possible to address unique characteristics in each of them. Four-month-old leaves showed a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to four-month-old internodes. It was possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which was assumed to be linked to cuticle formation. The data generated enriched the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants
2018-01-05 | PXD007893 | Pride
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.
2012-11-24 | GSE42483 | GEO
Project description:Transcriptional profiling of sugarcane leaf (+1) was collected from drought-prone areas at 42 and 117 days after the last rainfall when plants were 6- and 9-month-old, respectively. Sample hybridization (non-irrigated treatment against irrigated control) was performed to monitor gene expression in a two-color Agilent custom microarray. Our goal was to investigate the effect of mild and severe water stress on the transcriptomes of drought-sensitive (IACSP97-7065) and -tolerant (IACSP94-2094) sugarcane genotypes.
2021-11-05 | GSE187416 | GEO
Project description:In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues. There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane. During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively. Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively. Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h). A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed. Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed. Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves. Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006. Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o. Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest. The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base. Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK). At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany). Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.
2008-07-01 | E-GEOD-11934 | biostudies-arrayexpress
Project description:We report the deep sequencing of small RNA populations derived from apex, internode 3, internode 6, internode 16, leaf +3, calli and suspesion cells from sugarcane cultivar Q117
2013-12-13 | GSE53304 | GEO
Project description:This study was to determine quantitative proteome changes in sugarcane cultivars LCP 85-384 (resistance to leaf scald) and ROC20 (susceptible to leaf scald) to understand the molecular insights into defense mechanism of sugarcane against X. albilineans using a high-throughput iTRAQ-based technique
2020-05-26 | PXD015930 | Pride