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Sathyabhama M, Viswanathan R, Prasanth CN, Malathi P, Sundar AR. Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses. PLANT CELL REPORTS 2022; 41:1461-1476. [PMID: 35415786 DOI: 10.1007/s00299-022-02870-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/22/2022] [Indexed: 02/05/2023]
Abstract
KEY MESSAGE The differential compatibility responses of sugarcane to Colletotrichum falcatum pathotypes depend on the nature of both host primary defence signalling cascades and pathogen virulence. The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from ~ 54,699,263 raw reads, while 4022 contigs were assembled from ~ 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+, BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest clade to the perfect stage of C. falcatum (G. tucumanensis).
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Affiliation(s)
- M Sathyabhama
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
- Department of Biotechnology, PSG College of Arts and Science, Coimbatore, 641014, India
| | - R Viswanathan
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - C N Prasanth
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - P Malathi
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - A Ramesh Sundar
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. 3 Biotech 2022; 12:48. [PMID: 35127303 PMCID: PMC8787009 DOI: 10.1007/s13205-022-03113-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/08/2022] [Indexed: 02/05/2023] Open
Abstract
Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03113-6.
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Affiliation(s)
- C. Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - R. Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - P. Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - A. Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
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Shabbir R, Javed T, Afzal I, Sabagh AE, Ali A, Vicente O, Chen P. Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses. AGRONOMY 2021; 11:1042. [DOI: 10.3390/agronomy11061042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.
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Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Expression Analyses of Resistance-Associated Candidate Genes During Sugarcane-Colletotrichum falcatum Went Interaction. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-00976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Nandakumar M, Malathi P, Sundar AR, Rajadurai CP, Philip M, Viswanathan R. Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen. PLANT CELL REPORTS 2021; 40:851-870. [PMID: 33818644 DOI: 10.1007/s00299-021-02682-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
KEY MESSAGE Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - A R Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - C P Rajadurai
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - Manuel Philip
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
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Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Varietal Breakdown to Red Rot in Sugarcane Revealed by Comparing Two Colletotrichum falcatum Inoculation Methods. SUGAR TECH 2020. [DOI: 10.1007/s12355-020-00855-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Kumar VG, Viswanathan R, Malathi P, Sundar AR, Prasanth CN, Nandakumar M. Identification of differential expressed proteins and establishing a defense proteome of sugarcane in response to Colletotrichum falcatum infection. JOURNAL OF PLANT PATHOLOGY 2020. [DOI: 10.1007/s42161-020-00577-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Ali A, Khan M, Sharif R, Mujtaba M, Gao SJ. Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E344. [PMID: 31547331 PMCID: PMC6784093 DOI: 10.3390/plants8090344] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022]
Abstract
Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world's sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.
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Affiliation(s)
- Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Muhammad Mujtaba
- Institute of Biotechnology, Ankara University, Ankara 06110, Turkey
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Singh P, Singh SN, Tiwari AK, Pathak SK, Singh AK, Srivastava S, Mohan N. Integration of sugarcane production technologies for enhanced cane and sugar productivity targeting to increase farmers' income: strategies and prospects. 3 Biotech 2019; 9:48. [PMID: 30729072 DOI: 10.1007/s13205-019-1568-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
The idea of doubling the farmers' income in next 5 years has been slated by the Government of India. The specific target of increasing sugarcane farmers' income could be achieved by developing cost-effective technologies, transferring them from laboratory to land, educating the farmers and creating a linkage between all stakeholders. Consistent efforts shall be required to harness all possible sources for increasing farmer's income in and outside the agriculture sector with respect to improvement in sugarcane and sugar productivity, enhancement in resource use efficiency and adopting various other ways and means including intercropping, management of pests and diseases, use of biotechnological tools and minimizing post-harvest deterioration. The advances in sugarcane biotechnology could become remarkable in the coming years, both in terms of improving productivity as well as increasing the value and utility of this crop substantially. In future, genetically modified sugarcane varieties with increased resistance to different biotic and abiotic stresses would serve more towards sugarcane crop improvement. Any possibility of enhancement in the income of sugarcane farmers shall also be dependent upon the profitability and sustainability of the sugar industry. Integration of sugarcane production technologies for improvement in farm productivity, diversified sugarcane production system, reduced cost of cultivation along with increased processing plant efficiency and diversification to produce value added products shall ensure smooth and higher payment to the farmers. Development of low-cost technologies to convert "waste to resource" on a smaller scale shall also help the farmers to increase their income further. This paper focuses on possible measures to be taken up in each aspects of sugarcane cultivation including biotechnological approaches to achieve the goal of enhancing the income of sugarcane farmers substantially, particularly in the sub-tropical region of India.
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Ferreira CADS, Santana MV, Santos JBD, Santos TTMD, Lôbo LM, Fernandes PM. Yield and technological quality of sugarcane cultivars under infestation of Diatraea saccharalis (Fabr., 1794). ARQUIVOS DO INSTITUTO BIOLÓGICO 2018. [DOI: 10.1590/1808-1657000042017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT: The sugarcane borer, Diatraea saccharalis (Fabr., 1794) (Lepidoptera: Crambidae), is one of the main pests of sugarcane. This pest can reduce the quality and yield of the crop. Information on the quality and yield of cultivars in relation to the attack of sugarcane borer are necessary, since they guide the choice of the best materials for use in joint with other management tactics. Two field experiments were conducted in 2011 and 2012 to compare the quality and yield of 16 commercial sugarcane cultivars (IACSP93-3046, IACSP94-2094, IACSP94-2101, IAC91-1099, IACSP95-5000, IAC87-3396, RB92579, RB867515, RB966928, CTC2, CTC4, CTC9, CTC11, CTC15, CTC18 and SP86-0042) relative to the natural infestation of D. saccharalis. The experimental design was a randomized complete block with four replications. There was no difference between treatments for infestation index, with averages of 1.2 to 8.7% of bored internodes. Higher percentages of internodes with red rot were observed for CTC9, CTC2 and RB966928. The cultivars CTC4 and RB92579 infested with D. saccharalis resulted in lower technological quality, due the reduction in the contents of brix, apparent sucrose content (POL) and purity; and increase of the reducing sugars and, consequently, lower theoretically recoverable sugar (TRS). On the other hand, the lowest yields (t of cane ha-1) were observed for CTC18, IACSP94-2094, IACSP94-2101 and RB966928. Therefore, according to the hierarchical cluster analysis (UPGMA), the cultivars RB867515, CTC11, IAC91-1099, CTC15, SP86-0042, CTC2 and IACSP94-3046 were resistant to D. saccharalis.
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Comparative analysis of constitutive proteome between resistant and susceptible tomato genotypes regarding to late blight. Funct Integr Genomics 2017; 18:11-21. [DOI: 10.1007/s10142-017-0570-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/18/2017] [Accepted: 08/23/2017] [Indexed: 01/07/2023]
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Souza TP, Dias RO, Silva-Filho MC. Defense-related proteins involved in sugarcane responses to biotic stress. Genet Mol Biol 2017; 40:360-372. [PMID: 28222203 PMCID: PMC5452140 DOI: 10.1590/1678-4685-gmb-2016-0057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/27/2016] [Indexed: 11/22/2022] Open
Abstract
Sugarcane is one of the most important agricultural crops in the world. However, pathogen infection and herbivore attack cause constant losses in yield. Plants respond to pathogen infection by inducing the expression of several protein types, such as glucanases, chitinases, thaumatins, peptidase inhibitors, defensins, catalases and glycoproteins. Proteins induced by pathogenesis are directly or indirectly involved in plant defense, leading to pathogen death or inducing other plant defense responses. Several of these proteins are induced in sugarcane by different pathogens or insects and have antifungal or insecticidal activity. In this review, defense-related proteins in sugarcane are described, with their putative mechanisms of action, pathogen targets and biotechnological perspectives.
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Affiliation(s)
- Thais P Souza
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Renata O Dias
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
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