Control of sucrose accumulation in sugarcane (<i>Saccharum</i> spp. hybrids) involves miRNA‐mediated regulation of genes and transcription factors associated with sugar metabolism

Miao, Wang; Li, Aomei; Liao, Fang; Qin, Cui-Xian; Chen, Zhongliang; Zhou, Li; Li, Yang–Rui; Li, Xiaofeng; Lakshmanan, Prakash; Huang, Dongliang

doi:10.1111/gcbb.12909

Cited by 17 publications

(11 citation statements)

References 77 publications

(118 reference statements)

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“…Sugarcane sucrose content improvement by conventional breeding programme is concerningly low due to the complex genetic background and slow introgression of exogenous genes [ 36 ]. To explore molecular breeding strategies for sugar content improvement, we are studying the molecular basis of sucrose accumulation in sugarcane [ 13 , 16 , 18 , 19 ], with the ultimate aim of identifying potential molecular targets for variety improvement. Recently, we have developed a proteomic dataset developed for sucrose accumulation studies, and it is used in this study.…”

Section: Discussionmentioning

confidence: 99%

“…However, little success has been made so far in relation to identifying key genetic elements that control sucrose accumulation, which will help develop molecular breeding strategies for sugarcane. Some previous studies in sugarcane have identified candidate genes likely to be involved in sugar accumulation, but the molecular mechanism sugar accumulation in this crop remains unknown [ 12 – 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

Chen

Qin

et al. 2022

BMC Genomics

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Background Sugarcane is the most important sugar crop, contributing > 80% of global sugar production. High sucrose content is a key target of sugarcane breeding, yet sucrose improvement in sugarcane remains extremely slow for decades. Molecular breeding has the potential to break through the genetic bottleneck of sucrose improvement. Dissecting the molecular mechanism(s) and identifying the key genetic elements controlling sucrose accumulation will accelerate sucrose improvement by molecular breeding. In our previous work, a proteomics dataset based on 12 independent samples from high- and low-sugar genotypes treated with ethephon or water was established. However, in that study, employing conventional analysis, only 25 proteins involved in sugar metabolism were identified . Results In this work, the proteomics dataset used in our previous study was reanalyzed by three different statistical approaches, which include a logistic marginal regression, a penalized multiple logistic regression named Elastic net, as well as a Bayesian multiple logistic regression method named Stochastic search variable selection (SSVS) to identify more sugar metabolism-associated proteins. A total of 507 differentially abundant proteins (DAPs) were identified from this dataset, with 5 of them were validated by western blot. Among the DAPs, 49 proteins were found to participate in sugar metabolism-related processes including photosynthesis, carbon fixation as well as carbon, amino sugar, nucleotide sugar, starch and sucrose metabolism. Based on our studies, a putative network of key proteins regulating sucrose accumulation in sugarcane is proposed, with glucose-6-phosphate isomerase, 2-phospho-D-glycerate hydrolyase, malate dehydrogenase and phospho-glycerate kinase, as hub proteins. Conclusions The sugar metabolism-related proteins identified in this work are potential candidates for sucrose improvement by molecular breeding. Further, this work provides an alternative solution for omics data processing.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

Chen

Qin

et al. 2022

BMC Genomics

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“…The expressions of 5 genes related to sex determination and differentiation were selected randomly, and their expressions were quantified by qRT-PCR, as described previously [ 40 ]. The reactions were performed as follows: 95 °C for 3 min, followed by 45 cycles of denaturation at 95 °C for 10 s, then annealing at 57 °C for 10 s and extension at 72℃ for 20 s. The elongation factor 1-alpha gene (Unigene19366_All) obtained from this transcriptome data was used as a reference.…”

Section: Methodsmentioning

confidence: 99%

“…Transcriptome sequencing provides detailed information on all RNA molecules, such as mRNA, tRNA rRNA and noncoding RNAs [ 38 ]. It has been used for the screening of genes associated with various traits in sugarcane, such as sucrose accumulation [ 39 , 40 ], smut resistance [ 41 , 42 ] and the response to low nitrogen [ 43 ]. Transcriptome analysis was also used for the identification of sex-determining genes in many insects, such as Plutella xylostella [ 44 ], Phlebotominae sand flies [ 45 ], whitefly [ 46 ], Sogatella furcifera [ 47 ] and Zeugodacus tau (Walker) [ 48 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling Reveals Genes Related to Sex Determination and Differentiation in Sugarcane Borer (Chilo sacchariphagus Bojer)

Wei

et al. 2022

Insects

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Chilo sacchariphagus Bojer is an important sugarcane pest globally. Along with genetic modification strategies, the sterile insect technique (SIT) has gained more attention as an environment-friendly method for pest control. The identification of key genes associated with sex determination and differentiation will provide important basic information for this control strategy. As such, the transcriptome sequencing of female and male adults was conducted in order to understand the sex-biased gene expression and molecular basis of sex determination and differentiation in this species. A total of 60,429 unigenes were obtained; among them, 34,847 genes were annotated. Furthermore, 11,121 deferentially expressed genes (DEGs) were identified, of which 8986 were male-biased and 2135 were female-biased genes. The male-biased genes were enriched for carbon metabolism, peptidase activity and transmembrane transport, while the female-biased genes were enriched for the cell cycle, DNA replication, and the MAPK signaling pathway. In addition, 102 genes related to sex-determination and differentiation were identified, including the protein toll, ejaculatory bulb-specific protein, fruitless, transformer-2, sex-lethal, beta-Catenin, sox, gata4, beta-tubulin, cytosol aminopeptidase, seminal fluid, and wnt4. Furthermore, transcription factors such as myb, bhlh and homeobox were also found to be potentially related to sex determination and differentiation in this species. Our data provide new insights into the genetic elements associated with sex determination and differentiation in Chilo sacchariphagus, and identified potential candidate genes to develop pest-control strategies.

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“…7,8 Therefore, improvements in sugar cane yield and sugar content have been extremely slow for decades compared to other crops. 6,9,10 Wild species of sugar cane and its relatives are important germplasms for breeding due to their strong ratoonability, fast growth rate, drought tolerance, and disease resistance. 11,12 Thus, to broaden the genetic background of modern sugar cane, breeders have attempted to enrich sugar cane genome through introgression with sugar cane relatives, including Tripidium, Narenga, Sclerostachya, Erianthus, and Miscanthus, to further improve yield and sugar content as well as resistance/tolerance to biotic and abiotic stress.…”

Section: ■ Introductionmentioning

confidence: 99%

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

Zhang,

Huang,

Zhang

et al. 2023

J. Agric. Food Chem.

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Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yieldrelated markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

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Control of sucrose accumulation in sugarcane (Saccharum spp. hybrids) involves miRNA‐mediated regulation of genes and transcription factors associated with sugar metabolism

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 17 publications

References 77 publications

Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

Transcriptome Profiling Reveals Genes Related to Sex Determination and Differentiation in Sugarcane Borer (Chilo sacchariphagus Bojer)

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

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