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Oliveira GK, Barreto FZ, Balsalobre TWA, Chapola RG, Hoffmann HP, Carneiro MS. Molecular evaluation and phenotypic screening of brown and orange rust in Saccharum germplasm. PLoS One 2024; 19:e0307935. [PMID: 39078834 PMCID: PMC11288420 DOI: 10.1371/journal.pone.0307935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Brazil is the largest global producer of sugarcane and plays a significant role-supplier of sugar and bioethanol. However, diseases such as brown and orange rust cause substantial yield reductions and economic losses, due decrease photosynthesis and biomass in susceptible cultivars. Molecular markers associated with resistance genes, such as Bru1 (brown rust) and G1 (orange rust), could aid in predicting resistant genotypes. In this study, we sought to associate the phenotypic response of 300 sugarcane accessions with the genotypic response of Bru1 and G1 markers. The field trials were conducted in a randomized block design, and five six-month-old plants per plot were evaluated under natural disease conditions. Genotypic information about the presence or absence of Bru1 (haplotype 1) and G1 gene was obtained after extraction of genomic DNA and conventional PCR. Of the total accessions evaluated, 60.3% (181) showed resistance to brown rust in the field, and of these, 70.7% (128) had the Bru1 gene present. Considering the field-resistant accessions obtained from Brazilian breeding programs (116), the Bru1 was present in 77,6% of these accessions. While alternative resistance sources may exist, Bru1 likely confers enduring genetic resistance in current Brazilian cultivars. Regarding the phenotypic reaction to orange rust, the majority of accessions, 96.3% (288), were field resistant, and of these, 52.7% (152) carried the G1 marker. Although less efficient for predicting resistance when compared to Bru1, the G1 marker could be part of a quantitative approach when new orange rust resistance genes are described. Therefore, these findings showed the importance of Bru1 molecular markers for the early selection of resistant genotypes to brown rust by genetic breeding programs.
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Affiliation(s)
- Gleicy Kelly Oliveira
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
| | - Fernanda Zatti Barreto
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
| | | | | | - Hermann Paulo Hoffmann
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, SP, Brazil
| | - Monalisa Sampaio Carneiro
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, SP, Brazil
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Perera MF, Ostengo S, Malavera ANP, Balsalobre TWA, Onorato GD, Noguera AS, Hoffmann HP, Carneiro MS. Genetic diversity and population structure of Saccharum hybrids. PLoS One 2023; 18:e0289504. [PMID: 37582090 PMCID: PMC10426985 DOI: 10.1371/journal.pone.0289504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
Sugarcane breeding programs incorporate foreign material to broaden the genetic base, expanding the gene pool. In South America, the Inter-university Network for the Development of the Sugarcane Industry (RIDESA) and Estación Experimental Agroindustrial Obispo Colombres (EEAOC) sugarcane breeding programs from Brazil and Argentina, respectively, have never exchanged materials. In that sense, the knowledge of the genetic diversity and population structure among sugarcane genotypes of both germplasm banks, determined in a reliable way through their molecular profiles, will provide valuable information to select the best parental accessions for crossing aimed at the efficient introgression of desirable alleles. For that, the aim was to determine the genetic diversity and population structure of 96 Saccharum commercial hybrids from RIDESA and EEAOC sugarcane breeding programs by using TRAP, SSR and markers related to disease resistance (e.g. Bru1 and G1). Genetic structure was determined through genetic similarity analysis, analysis of molecular variance (AMOVA), Multidimensional scaling (MDS), and a Bayesian method. Average PIC values were 0.25 and 0.26, Ho values were 0.24 and 0.28, and He values were 0.25 and 0.28, for TRAP and SSR primers, respectively. Genetic similarity, MDS, and analysis of structure revealed that Brazilian and Argentinean genotypes clustered in two groups clearly differentiated, whereas AMOVA suggested that there is more variability within programs than between them. Regarding Bru1 markers, Brazilian genotypes showed high frequency of haplotype 1 (71.4%) whereas Argentinean genotypes showed high frequency of haplotype 4 (80.8%); haplotypes 1 and 4 are indicated for the presence and absence of the brown rust resistance gene (Bru1), respectively. Respecting the G1 marker, most of the evaluated genotypes (60.4%) showed the presence of the fragment, in a similar proportion for genotypes of both programs. In conclusion, the exchange of materials, at least the most diverse genotypes, between RIDESA and EEAOC breeding programs will allow extending the genetic base of their germplasm banks, and the knowledge of genetic diversity will help breeders to better manage crosses, increasing the probability of obtaining more productive varieties.
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Affiliation(s)
- María Francisca Perera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Santiago Ostengo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Andrea Natalia Peña Malavera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | | | | | - Aldo Sergio Noguera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Hermann Paulo Hoffmann
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, São Paulo, Brazil
- Departamento de Biotecnologia e Producão Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), Araras, São Paulo, Brazil
| | - Monalisa Sampaio Carneiro
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, São Paulo, Brazil
- Departamento de Biotecnologia e Producão Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), Araras, São Paulo, Brazil
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Molina C, Aguirre NC, Vera PA, Filippi CV, Puebla AF, Poltri SNM, Paniego NB, Acevedo A. ddRADseq-mediated detection of genetic variants in sugarcane. PLANT MOLECULAR BIOLOGY 2023; 111:205-219. [PMID: 36367622 DOI: 10.1007/s11103-022-01322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
KEY MESSAGE The article presents an optimization of the key parameters for the identification of SNPs in sugarcane using a GBS protocol based on two Illumina NextSeq and NovaSeq platforms. Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fibre biotype for the detection of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), different sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored different variant calling strategies (with and without reference genome) and filtering schemes [combining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-effective approach, and filter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fibre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half affected coding, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confirming the protocol robustness.
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Affiliation(s)
- Catalina Molina
- Instituto de Suelos, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Cristina Aguirre
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Pablo Alfredo Vera
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Andrea Fabiana Puebla
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Susana Noemí Marcucci Poltri
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Alberto Acevedo
- Instituto de Suelos, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.
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Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane. Genes (Basel) 2022; 13:genes13081477. [PMID: 36011388 PMCID: PMC9408448 DOI: 10.3390/genes13081477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding
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Correr FH, Furtado A, Franco Garcia AA, Henry RJ, Rodrigues Alves Margarido G. Allele expression biases in mixed-ploid sugarcane accessions. Sci Rep 2022; 12:8778. [PMID: 35610293 PMCID: PMC9130122 DOI: 10.1038/s41598-022-12725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Antonio Augusto Franco Garcia
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
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Hosaka GK, Correr FH, da Silva CC, Sforça DA, Barreto FZ, Balsalobre TWA, Pasha A, de Souza AP, Provart NJ, Carneiro MS, Margarido GRA. Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:736797. [PMID: 34966397 PMCID: PMC8710541 DOI: 10.3389/fpls.2021.736797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.
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Affiliation(s)
- Guilherme Kenichi Hosaka
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Zatti Barreto
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
| | | | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Nicholas James Provart
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Monalisa Sampaio Carneiro
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
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Filho JDAD, Calsa Júnior T, Simões Neto DE, Souto LS, Souza ADS, de Luna RG, Gomes-Silva F, Moreira GR, Cunha-Filho M, Pinto dos Santos AL, Ramos de Brito CC, Cavalcante Silva FA, Fiuza Porto AC, da Costa MLL. Genetic divergence for adaptability and stability in sugarcane: Proposal for a more accurate evaluation. PLoS One 2021; 16:e0254413. [PMID: 34264990 PMCID: PMC8282048 DOI: 10.1371/journal.pone.0254413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
The best agro-industrial performance presented by a crop genotype in one environment may not be reproduced in another owing to complex edaphoclimatic variations. Therefore, breeding programs are constantly attempting to obtain, through artificial hybridization, novel genotypes with high adaptability and stability potential. The objective of this study was to analyze genetic divergence in sugarcane based on the genotypic values of adaptability and stability. A total of 11 sugarcane genotypes were analyzed for eight agro-industrial traits. The genotypic values of the traits were determined using mixed model methodology, and the genetic divergence based on phenotypic and genotypic values was measured using the Mahalanobis distance. The distance matrices were correlated using the Mantel test, and the genotypes were grouped using the Tocher method. Genetic divergence is more accurate when based on genotypic values free of genotype-environment interactions and will differ from genetic divergence based on phenotypic data, changing the genotype allocations in the groups. The above methodology can be applied to assess genetic divergence to obtain novel sugarcane genotypes with higher productivity that are adapted to intensive agricultural systems using diverse technologies. This methodology can also be tested in other crops to increase accuracy in selecting the parents to be crossed.
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Affiliation(s)
| | | | - Djalma Euzébio Simões Neto
- Carpina Sugarcane Experimental Station, Federal Rural University of Pernambuco, Carpina, Pernambuco, Brazil
| | - Lauter Silva Souto
- Agrarian Sciences Academic Unit, Federal University of Campina Grande, Pombal, Paraíba, Brazil
| | | | - Rômulo Gil de Luna
- Environmental Technology Sciences Academic Unit, Federal University of Campina Grande, Pombal, Paraíba, Brazil
| | - Frank Gomes-Silva
- Statistics and Informatics Department, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - Guilherme Rocha Moreira
- Statistics and Informatics Department, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - Moacyr Cunha-Filho
- Statistics and Informatics Department, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | | | | | | | - Andréa Chaves Fiuza Porto
- Agricultural College Dom Agostinho Ikas, Federal Rural University of Pernambuco, Carpina, Pernambuco, Brazil
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