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Silva JNB, Bueno RD, de Sousa TDJF, Xavier YPM, Silva LCC, Piovesan ND, Ribeiro C, Dal-Bianco M. Exploring SoySNP50K and USDA Germplasm Collection Data to Find New QTLs Associated with Protein and Oil Content in Brazilian Genotypes. Biochem Genet 2024:10.1007/s10528-024-10698-5. [PMID: 38358588 DOI: 10.1007/s10528-024-10698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Genetic diversity within a germplasm collection plays a vital role in the success of breeding programs. However, comprehending this diversity and identifying accessions with desirable traits pose significant challenges. This study utilized publicly available data to investigate SNP markers associated with protein and oil content in Brazilian soybeans. Through this research, twenty-two new QTLs (Quantitative Trait Loci) were identified, and we highlighted the substantial influence of Roanoke, Lee and Bragg ancestor on the genetic makeup of Brazilian soybean varieties. Our findings demonstrate that certain markers are being lost in modern cultivars, while others maintain or even increase their frequency. These observations indicate genomic regions that have undergone selection during soybean introduction in Brazil and could be valuable in breeding programs aimed at enhancing protein or oil content.
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Affiliation(s)
- Jessica Nayara Basílio Silva
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Rafael Delmond Bueno
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | | | - Yan Pablo Moreira Xavier
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Luiz Claudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil
| | - Newton Deniz Piovesan
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil.
- Departamento de Bioquímica E Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Yazaki J, Dal-Bianco M. In Situ Protein Microarray for Identifying the Geminivirus-Arabidopsis Interactome. Methods Mol Biol 2024; 2724:307-314. [PMID: 37987915 DOI: 10.1007/978-1-0716-3485-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The protein-protein interactions (PPI) by protein array technology complement other PPI assay technologies such as AP-MS and Y2H. The in situ protein array technology (NAPPA) enables low-cost, rapid, and comprehensive protein detection. It allows standardized and simultaneous assay of a wide range of proteins with a broad range of expression in cells. This technology facilitates the detection of protein-protein interactions within species and between heterologous species such as host-microbe. Here, we described the technique that identified a syntaxin-6 protein-mediated begomovirus infection using an array containing 4600 Arabidopsis genes. The protein microarray assay also identified several other viral protein-host protein interactions.
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Affiliation(s)
- Junshi Yazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan.
| | - Maximiller Dal-Bianco
- Plant Genetics and Biochemistry Laboratory, BIOAGRO, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
- Department of Biochemistry and Molecular Biology, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
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Rocha VDD, Dal'Sasso TCDS, Dal-Bianco M, Oliveira LOD. Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi. Fungal Genet Biol 2023; 169:103841. [PMID: 37797717 DOI: 10.1016/j.fgb.2023.103841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/06/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
Once deposited in the plant cell wall, pectin undergoes demethylesterification by endogenous pectin methylesterases (PMEs), which play various roles in growth and development, including defense against pathogen attacks. Pathogen PMEs can alter pectin's methylesterification pattern, increasing its susceptibility to degradation by other fungal pectinases and thus playing a critical role as virulence factors during early infection stages. To investigate the evolutionary history of PMEs in the Dothideomycetes class of fungi, we obtained genomic data from 15 orders (79 species) and added genomic data from 61 isolates of Corynespora cassiicola. Our analyses involved maximum likelihood phylogenies, gene genealogies, and selection analyses. Additionally, we measured PME gene expression levels of C. cassiicola using soybean as a host through RT-qPCR assays. We recovered 145 putative effector PMEs and 57 putative non-effector PMEs from across the Dothideomycetes. The PME gene family exhibits a small size (up to 5 members per genome) and comprises three major clades. The evolutionary patterns of the PME1 and PME2 clades were largely shaped by duplications and recurring gene retention events, while biased gene loss characterized the small-sized PME3 clade. The presence of five members in the PME gene family of C. cassiicola suggests that the family may play a key role in the evolutionary success of C. cassiicola as a polyphagous plant pathogen. The haplogroups Cc_PME1.1 and Cc_PME1.2 exhibited an accelerated rate of evolution, whereas Cc_PME2.1, Cc_PME2.2, and Cc_PME2.3 seem to be under strong purifying selective constraints. All five PME genes were expressed during infection of soybean leaves, with the highest levels during from six to eight days post-inoculation. The highest relative expression level was measured for CC_29_g7533, a member of the Cc_PME2.3 clade, while the remaining four genes had relatively lower levels of expression.
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Affiliation(s)
| | | | - Maximiller Dal-Bianco
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Luiz Orlando de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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Pinto VB, Vidigal PMP, Dal-Bianco M, Almeida-Silva F, Venancio TM, Viana JMS. Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta). Sci Rep 2023; 13:19400. [PMID: 37938583 PMCID: PMC10632369 DOI: 10.1038/s41598-023-46810-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/06/2023] [Indexed: 11/09/2023] Open
Abstract
Aluminum (Al) toxicity limits crop production worldwide. Although studies have identified genes associated with Al tolerance in crops, a large amount of data remains unexplored using other strategies. Here, we searched for single substitutions and InDels across differentially expressed genes (DEGs), linked DEGs to Al-tolerance QTLs reported in the literature for common maize, and investigated the alternative splicing regulated by Al3+ toxicity. We found 929 substitutions between DEGs in Al-tolerant and 464 in Al-sensitive inbred lines, of which 165 and 80 were non-synonymous, respectively. Only 12 NS variants had deleterious predicted effect on protein function in Al-tolerant and 13 in Al-sensitive. Moreover, 378 DEGs were mapped in Al-QTL regions for the Al-tolerant and 213 for the Al-sensitive. Furthermore, Al stress is primarily regulated at the transcriptional level in popcorn. Important genes identified, such as HDT1, SWEET4a, GSTs, SAD9, PIP2-2, CASP-like 5, and AGP, may benefit molecular assisted popcorn breeding or be useful in biotechnological approaches. These findings offer insights into the mechanisms of Al tolerance in popcorn and provide a 'hypothesis-free' strategy for identifying and prioritizing candidate genes that could be used to develop molecular markers or cultivars resilient to acidic soils.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-000, Brazil.
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | | | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas/BIOAGRO. UFV, Viçosa, MG, 36570-000, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
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Yoshida CHP, Pacheco AC, de Marcos Lapaz A, de Souza Ferreira C, Dal-Bianco M, Viana JMS, Ribeiro C. Tolerance mechanisms to aluminum in popcorn inbred lines involving aluminum compartmentalization and ascorbate-glutathione redox pathway. Planta 2023; 257:28. [PMID: 36592255 DOI: 10.1007/s00425-022-04062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Inbred line 11-133 of popcorn showed the lowest apoplast Al and total Al concentrations and Al-lumogallion complex, associated with a more efficient antioxidant system, mainly due to glutathione metabolism. Popcorn (Zea mays L. var. everta) is largely intended for human consumption. About 40% of the world's arable soils are acidic. In soils acidic, aluminum (Al) ionizes producing the trivalent cation, which is highly toxic to plants. Hence, this work aimed to: (1) evaluate the Al toxicity sites and its effect on the structure of the root tips, (2) quantify Al concentrations in the apoplast and symplast of the roots, and (3) to elucidate the modulation on the activity of antioxidant enzymes and metabolites of the ascorbate-glutathione cycle in two popcorn inbred lines (ILs) 11-133 and 11-60, classified as tolerant and sensitive to this metal, respectively. Aluminum toxicity did not affect the shoot growth; however, there was a yellowing of the oldest leaf blade only in 11-60. The better performance of 11-133 is related to lower apoplastic and total Al concentrations and Al accumulation in the root associated with a lower fluorescence of Al-lumogallion complex at the root tip, indicating the presence of mechanisms of chelation with this metal. Consequently, this IL showed less change in root morphoanatomy and lower reactive oxygen species and malondialdehyde content, which are associated with a more efficient enzymatic and non-enzymatic system, mainly due to the higher content of the glutathione metabolite and the higher activities of superoxide dismutase, monodehydroascorbate reductase, dehydroascorbate reductase, γ-glutamylcysteine synthetase, and glutathione peroxidase enzymes. Thus, these findings illustrated above indicate how internal mechanisms of detoxification respond to Al in popcorn, which can be used as tolerance biomarkers.
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Affiliation(s)
| | - Ana Claudia Pacheco
- Departamento de Agronomia, Universidade do Oeste Paulista, Presidente Prudente, São Paulo, 19067-175, Brazil
| | - Allan de Marcos Lapaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Clayton de Souza Ferreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | | | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
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Ribeiro C, de Marcos Lapaz A, de Freitas-Silva L, Ribeiro KVG, Yoshida CHP, Dal-Bianco M, Cambraia J. Aluminum promotes changes in rice root structure and ascorbate and glutathione metabolism. Physiol Mol Biol Plants 2022; 28:2085-2098. [PMID: 36573146 PMCID: PMC9789240 DOI: 10.1007/s12298-022-01262-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In acidic soil, aluminum (Al) ionizes into trivalent cation and becomes highly toxic to plants. Thus, the objectives of this work were (i) to evaluate the Al concentration and identify sites of Al toxicity and its effect on the structure on rice root tips and (ii) to elucidate the adjustments involved in the activities/contents of enzymes/compounds in the roots against Al. For this, two genotypes with contrasting Al tolerance were used. Our results showed that the root length of the tolerant genotype was not affected after Al exposure. We also observed that both the genotypes used strategies to avoid Al uptake, such as the overlap of P and Al in the tolerant genotype and the presence of border cells in the sensitive genotype, which proved inefficient. In the tolerant genotype, other external Al detoxification mechanisms may have contributed to the lower Al concentration in roots and lower fluorescence of the Al-lumogallion complex. Additionally, both genotypes present the activation of key enzymes to decrease oxidative stress, such as CAT, POX, APX, and DHAR, and a more reducing redox environment, mainly due to the increase in the AA/DHA ratio. However, higher total ascorbate, AA, total glutathione, and GSH contents associated with higher SOD, GPX, and GR activities contributed to the reduction of oxidative stress in the tolerant genotype after Al exposure. Furthermore, there was a strong association between the sensitive genotype to Al concentration, O2 •- content, and MDA amount; therefore, these traits can be used as sensitivity indicators in Al studies.
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Affiliation(s)
- Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900 Brazil
| | - Allan de Marcos Lapaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais Brazil
| | | | | | | | - Maximiller Dal-Bianco
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais Brazil
| | - José Cambraia
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900 Brazil
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Silva LCC, Mayrink DB, Bueno RD, Piovesan ND, Ribeiro C, Dal-Bianco M. Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. Biochem Genet 2022; 60:937-952. [PMID: 34554351 DOI: 10.1007/s10528-021-10135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.
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Affiliation(s)
- Luiz Cláudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil.
| | | | - Rafael Delmond Bueno
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Newton Deniz Piovesan
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Alves da Silva A, Oliveira Silva C, do Rosario Rosa V, Silva Santos MF, Naomi Kuki K, Dal-Bianco M, Delmond Bueno R, Alves de Oliveira J, Santos Brito D, Costa AC, Ribeiro C. Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean. PeerJ 2022; 10:e13118. [PMID: 35321407 PMCID: PMC8935993 DOI: 10.7717/peerj.13118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.
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Affiliation(s)
- Adinan Alves da Silva
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cíntia Oliveira Silva
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | - Kacilda Naomi Kuki
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Maximiller Dal-Bianco
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Rafael Delmond Bueno
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Danielle Santos Brito
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alan Carlos Costa
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cleberson Ribeiro
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Hua S, Dal-Bianco M, Chen ZH. Editorial: Crop Yield and Quality Response to the Interaction Between Environment and Genetic Factors. Front Genet 2022; 13:823279. [PMID: 35368712 PMCID: PMC8971661 DOI: 10.3389/fgene.2022.823279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Shuijin Hua,
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO and Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Vicosa, Brazil
| | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Gouveia-Mageste BC, Martins LGC, Dal-Bianco M, Machado JPB, da Silva JCF, Kim AY, Yazaki J, dos Santos AA, Ecker JR, Fontes EPB. A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV. Plant Physiol 2021; 187:158-173. [PMID: 34618135 PMCID: PMC8418432 DOI: 10.1093/plphys/kiab252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/09/2021] [Indexed: 06/13/2023]
Abstract
Because of limited free diffusion in the cytoplasm, viruses must use active transport mechanisms to move intracellularly. Nevertheless, how the plant single-stranded DNA begomoviruses hijack the host intracytoplasmic transport machinery to move from the nucleus to the plasmodesmata remains enigmatic. Here, we identified nuclear shuttle protein (NSP)-interacting proteins from Arabidopsis (Arabidopsis thaliana) by probing a protein microarray and demonstrated that the cabbage leaf curl virus NSP, a facilitator of the nucleocytoplasmic trafficking of viral (v)DNA, interacts in planta with an endosomal vesicle-localized, plant-specific syntaxin-6 protein, designated NSP-interacting syntaxin domain-containing protein (NISP). NISP displays a proviral function, unlike the syntaxin-6 paralog AT2G18860 that failed to interact with NSP. Consistent with these findings, nisp-1 mutant plants were less susceptible to begomovirus infection, a phenotype reversed by NISP complementation. NISP-overexpressing lines accumulated higher levels of vDNA than wild-type. Furthermore, NISP interacted with an NSP-interacting GTPase (NIG) involved in NSP-vDNA nucleocytoplasmic translocation. The NISP-NIG interaction was enhanced by NSP. We also showed that endosomal NISP associates with vDNA. NISP may function as a docking site for recruiting NIG and NSP into endosomes, providing a mechanism for the intracytoplasmic translocation of the NSP-vDNA complex toward and from the cell periphery.
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Affiliation(s)
- Bianca Castro Gouveia-Mageste
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Laura Gonçalves Costa Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - João Paulo Batista Machado
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
- Agronomy Institute, Universidade Federal de Viçosa, Campus Florestal, Florestal, Minas Gerais 35690-000, Brazil
| | - José Cleydson Ferreira da Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Alice Y. Kim
- Genomic Analysis Laboratory, Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Junshi Yazaki
- Genomic Analysis Laboratory, Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan
| | - Anésia Aparecida dos Santos
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
- Departament of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Joseph R. Ecker
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute of Biological Studies, La Jolla, California 92037, USA
| | - Elizabeth Pacheco Batista Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
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Hua S, Dal-Bianco M, Chen ZH. Editorial: Regulation and Manipulation of Nutrient-Controlling Genes in Crops. Front Genet 2020; 11:164. [PMID: 32174979 PMCID: PMC7056896 DOI: 10.3389/fgene.2020.00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/12/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO and Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Vicosa, Brazil
| | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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12
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Silva LCC, Bueno RD, da Matta LB, Pereira PHS, Mayrink DB, Piovesan ND, Sediyama CS, Fontes EPB, Cardinal AJ, Dal-Bianco M. Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar. Theor Appl Genet 2018; 131:1099-1110. [PMID: 29397403 DOI: 10.1007/s00122-018-3061-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation. Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.
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Affiliation(s)
- Luiz Claudio Costa Silva
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Rafael Delmond Bueno
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Danyelle Barbosa Mayrink
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Newton Deniz Piovesan
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Andrea J Cardinal
- Crop Science Department, North Carollina State University, Raleigh, NC, 27695, USA
- Syngenta Biotechnology, Inc, 3054 Cornwallis Rd., Research Triangle Park, NC, 27709, USA
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO and Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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13
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Silva JCF, Carvalho TFM, Basso MF, Deguchi M, Pereira WA, Sobrinho RR, Vidigal PMP, Brustolini OJB, Silva FF, Dal-Bianco M, Fontes RLF, Santos AA, Zerbini FM, Cerqueira FR, Fontes EPB. Geminivirus data warehouse: a database enriched with machine learning approaches. BMC Bioinformatics 2017; 18:240. [PMID: 28476106 PMCID: PMC5420152 DOI: 10.1186/s12859-017-1646-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/25/2017] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. RESULTS Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. CONCLUSIONS The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.
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Affiliation(s)
- Jose Cleydson F Silva
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Marcos F Basso
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Michihito Deguchi
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Welison A Pereira
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Roberto R Sobrinho
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pedro M P Vidigal
- Núcleo de Biomoléculas, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Anésia A Santos
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Francisco Murilo Zerbini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabio R Cerqueira
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Engenharia de Produção, Universidade Federal Fluminense, Petrópolis, Rio de Janeiro, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil. .,Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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14
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Reis PAB, Carpinetti PA, Freitas PP, Santos EG, Camargos LF, Oliveira IH, Silva JCF, Carvalho HH, Dal-Bianco M, Soares-Ramos JR, Fontes EPB. Functional and regulatory conservation of the soybean ER stress-induced DCD/NRP-mediated cell death signaling in plants. BMC Plant Biol 2016; 16:156. [PMID: 27405371 PMCID: PMC4943007 DOI: 10.1186/s12870-016-0843-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/01/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The developmental and cell death domain (DCD)-containing asparagine-rich proteins (NRPs) were first identified in soybean (Glycine max) as transducers of a cell death signal derived from prolonged endoplasmic reticulum (ER) stress, osmotic stress, drought or developmentally-programmed leaf senescence via the GmNAC81/GmNAC30/GmVPE signaling module. In spite of the relevance of the DCD/NRP-mediated signaling as a versatile adaptive response to multiple stresses, mechanistic knowledge of the pathway is lacking and the extent to which this pathway may operate in the plant kingdom has not been investigated. RESULTS Here, we demonstrated that the DCD/NRP-mediated signaling also propagates a stress-induced cell death signal in other plant species with features of a programmed cell death (PCD) response. In silico analysis revealed that several plant genomes harbor conserved sequences of the pathway components, which share functional analogy with their soybean counterparts. We showed that GmNRPs, GmNAC81and VPE orthologs from Arabidopsis, designated as AtNRP-1, AtNRP-2, ANAC036 and gVPE, respectively, induced cell death when transiently expressed in N. benthamiana leaves. In addition, loss of AtNRP1 and AtNRP2 function attenuated ER stress-induced cell death in Arabidopsis, which was in marked contrast with the enhanced cell death phenotype displayed by overexpressing lines as compared to Col-0. Furthermore, atnrp-1 knockout mutants displayed enhanced sensitivity to PEG-induced osmotic stress, a phenotype that could be complemented with ectopic expression of either GmNRP-A or GmNRP-B. In addition, AtNRPs, ANAC036 and gVPE were induced by osmotic and ER stress to an extent that was modulated by the ER-resident molecular chaperone binding protein (BiP) similarly as in soybean. Finally, as putative downstream components of the NRP-mediated cell death signaling, the stress induction of AtNRP2, ANAC036 and gVPE was dependent on the AtNRP1 function. BiP overexpression also conferred tolerance to water stress in Arabidopsis, most likely due to modulation of the drought-induced NRP-mediated cell death response. CONCLUSION Our results indicated that the NRP-mediated cell death signaling operates in the plant kingdom with conserved regulatory mechanisms and hence may be target for engineering stress tolerance and adaptation in crops.
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Affiliation(s)
- Pedro A. B. Reis
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Paola A. Carpinetti
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Paula P.J. Freitas
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Eulálio G.D. Santos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Luiz F. Camargos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Igor H.T. Oliveira
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - José Cleydson F. Silva
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Humberto H. Carvalho
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Maximiller Dal-Bianco
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Juliana R.L. Soares-Ramos
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
| | - Elizabeth P. B. Fontes
- />Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG Brazil
- />National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG Brazil
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15
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Silva PA, Silva JCF, Caetano HDN, Machado JPB, Mendes GC, Reis PAB, Brustolini OJB, Dal-Bianco M, Fontes EPB. Comprehensive analysis of the endoplasmic reticulum stress response in the soybean genome: conserved and plant-specific features. BMC Genomics 2015; 16:783. [PMID: 26466891 PMCID: PMC4606518 DOI: 10.1186/s12864-015-1952-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/23/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the relevance of the eukaryotic endoplasmic reticulum (ER)-stress response as an integrator of multiple stress signals into an adaptive response, knowledge about these ER-mediated cytoprotective pathways in soybean (Glycine max) is lacking. Here, we searched for genes involved in the highly conserved unfolded protein response (UPR) and ER stress-induced plant-specific cell death signaling pathways in the soybean genome. METHODS Previously characterized Arabidopsis UPR genes were used as prototypes for the identification of the soybean orthologs and the in silico assembly of the UPR in soybean, using eggNOG v4.0 software. Functional studies were also conducted by analyzing the transcriptional activity of soybean UPR transducers. RESULTS As a result of this search, we have provided a complete profile of soybean UPR genes with significant predicted protein similarities to A. thaliana UPR-associated proteins. Both arms of the plant UPR were further examined functionally, and evidence is presented that the soybean counterparts are true orthologs of previously characterized UPR transducers in Arabidopsis. The bZIP17/bZI28 orthologs (GmbZIP37 and GmbZIP38) and ZIP60 ortholog (GmbZIP68) from soybean have similar structural organizations as their Arabidopsis counterparts, were induced by ER stress and activated an ERSE- and UPRE-containing BiP promoter. Furthermore, the transcript of the putative substrate of GmIREs, GmbZIP68, harbors a canonical site for IRE1 endonuclease activity and was efficiently spliced under ER stress conditions. In a reverse approach, we also examined the Arabidopsis genome for components of a previously characterized ER stress-induced cell death signaling response in soybean. With the exception of GmERD15, which apparently does not possess an Arabidopsis ortholog, the Arabidopsis genome harbors conserved GmNRP, GmNAC81, GmNAC30 and GmVPE sequences that share significant structural and sequence similarities with their soybean counterparts. These results suggest that the NRP/GmNAC81 + GmNAC30/VPE regulatory circuit may transduce cell death signals in plant species other than soybean. CONCLUSIONS Our in silico analyses, along with current and previous functional data, permitted generation of a comprehensive overview of the ER stress response in soybean as a framework for functional prediction of ER stress signaling components and their possible connections with multiple stress responses.
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Affiliation(s)
- Priscila Alves Silva
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Hanna D N Caetano
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Joao Paulo B Machado
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Giselle C Mendes
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Pedro A B Reis
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Otavio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions and Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
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Dal-Bianco M, Carneiro MS, Hotta CT, Chapola RG, Hoffmann HP, Garcia AAF, Souza GM. Sugarcane improvement: how far can we go? Curr Opin Biotechnol 2011; 23:265-70. [PMID: 21983270 DOI: 10.1016/j.copbio.2011.09.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/26/2011] [Accepted: 09/13/2011] [Indexed: 01/05/2023]
Abstract
In recent years, efforts to improve sugarcane have focused on the development of biotechnology for this crop. It has become clear that sugarcane lacks tools for the biotechnological route of improvement and that the initial efforts in sequencing ESTs had limited impact for breeding. Until recently, the models used by breeders in statistical genetics approaches have been developed for diploid organisms, which are not ideal for a polyploid genome such as that of sugarcane. Breeding programs are dealing with decreasing yield gains. The contribution of multiple alleles to complex traits such as yield is a basic question underlining the breeding efforts that could only be addressed by the development of specific tools for this grass. However, functional genomics has progressed and gene expression profiling is leading to the definition of gene networks. The sequencing of the sugarcane genome, which is underway, will greatly contribute to numerous aspects of research on grasses. We expect that both the transgenic and the marker-assisted route for sugarcane improvement will contribute to increased sugar, stress tolerance, and higher yield and that the industry for years to come will be able to rely on sugarcane as the most productive energy crop.
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Affiliation(s)
- Maximiller Dal-Bianco
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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