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Divakar S, Jha RK, Kamat DN, Singh A. Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane. FRONTIERS IN PLANT SCIENCE 2023; 14:1273740. [PMID: 37965001 PMCID: PMC10641762 DOI: 10.3389/fpls.2023.1273740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.
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Affiliation(s)
- S. Divakar
- Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - Ratnesh Kumar Jha
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - D. N. Kamat
- Sugarcane Research Institute, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
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Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
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Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
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Mapping of QTLs and Screening Candidate Genes Associated with the Ability of Sugarcane Tillering and Ratooning. Int J Mol Sci 2023; 24:ijms24032793. [PMID: 36769121 PMCID: PMC9917849 DOI: 10.3390/ijms24032793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
The processes of sugarcane tillering and ratooning, which directly affect the yield of plant cane and ratoon, are of vital importance to the population establishment and the effective stalk number per unit area. In the present study, the phenotypic data of 285 F1 progenies from a cross of sugarcane varieties YT93-159 × ROC22 were collected in eight environments, which consisted of plant cane and ratoon cultivated in three different ecological sites. The broad sense heritability (H2) of the tillering and the ratoon sprouting was 0.64 and 0.63, respectively, indicating that they were middle to middle-high heritable traits, and there is a significantly positive correlation between the two traits. Furthermore, a total of 26 quantitative trait loci (QTLs) related to the tillering ability and 11 QTLs associated with the ratooning ability were mapped on two high-quality genetic maps derived from a 100K SNP chip, and their phenotypic variance explained (PVE) ranged from 4.27-25.70% and 6.20-13.54%, respectively. Among them, four consistent QTLs of qPCTR-R9, qPCTR-Y28, qPCTR-Y60/qRSR-Y60 and PCTR-Y8-1/qRSR-Y8 were mapped in two environments, of which, qPCTR-Y8-1/qRSR-Y8 had the PVEs of 11.90% in the plant cane and 7.88% in the ratoon. Furthermore, a total of 25 candidate genes were identified in the interval of the above four consistent QTLs and four major QTLs of qPCTR-Y8-1, qPCTR-Y8-2, qRSR-R51 and qRSR-Y43-2, with the PVEs from 11.73-25.70%. All these genes were associated with tillering, including eight transcription factors (TFs), while 15 of them were associated with ratooning, of which there were five TFs. These QTLs and genes can provide a scientific reference for genetic improvement of tillering and ratooning traits in sugarcane.
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Senthilkumar S, Vinod KK, Parthiban S, Thirugnanasambandam P, Lakshmi Pathy T, Banerjee N, Sarath Padmanabhan TS, Govindaraj P. Identification of potential MTAs and candidate genes for juice quality- and yield-related traits in Saccharum clones: a genome-wide association and comparative genomic study. Mol Genet Genomics 2022; 297:635-654. [PMID: 35257240 DOI: 10.1007/s00438-022-01870-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/06/2022] [Indexed: 11/30/2022]
Abstract
Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop.
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Affiliation(s)
- Shanmugavel Senthilkumar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Selvaraj Parthiban
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | | | - Thalambedu Lakshmi Pathy
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - Nandita Banerjee
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh, 226002, India
| | | | - P Govindaraj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 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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Farsangi FJ, Thorat AS, Devarumath RM. Assessment of the Utility of TRAP and EST-SSRs Markers for Genetic Diversity Analysis of Sugarcane Genotypes. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718060026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gutierrez AF, Hoy JW, Kimbeng CA, Baisakh N. Identification of Genomic Regions Controlling Leaf Scald Resistance in Sugarcane Using a Bi-parental Mapping Population and Selective Genotyping by Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:877. [PMID: 29997640 PMCID: PMC6028728 DOI: 10.3389/fpls.2018.00877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/05/2018] [Indexed: 05/23/2023]
Abstract
Leaf scald, caused by Xanthomonas albilineans, is a major sugarcane disease worldwide. The disease is managed primarily with resistant cultivars obtained through classical breeding. However, erratic symptom expression hinders the reliability and reproducibility of selection for resistance. The development and use of molecular markers associated with incompatible/compatible reactions could overcome this limitation. The aim of the present work was to find leaf scald resistance-associated molecular markers in sugarcane to facilitate marker-assisted breeding. A genetic linkage map was constructed by selective genotyping of 89 pseudo F2 progenies of a cross between LCP 85-384 (resistant) and L 99-226 (susceptible) using 1,948 single dose (SD) markers generated from SSR, eSSR, and SNPs. Of these, 1,437 SD markers were mapped onto 294 linkage groups, which covered 19,464 cM with 120 and 138 LGs assigned to the resistant and susceptible parent, respectively. Composite interval mapping identified 8 QTLs associated with the disease response with LOD scores ranging from 3.0 to 7.6 and explained 5.23 to 16.93% of the phenotypic variance. Comparative genomics analysis with Sorghum bicolor allowed us to pinpoint three SNP markers that explained 16% phenotypic variance. In addition, representative stress-responsive genes close to the major effect QTLs showed upregulation in their expression in response to the bacterial infection in leaf/meristem tissue.
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Affiliation(s)
- Andres F. Gutierrez
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Jeffrey W. Hoy
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Collins A. Kimbeng
- Sugar Research Station, Louisiana State University Agricultural Center, St. Gabriel, LA, United States
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Ukoskit K, Posudsavang G, Pongsiripat N, Chatwachirawong P, Klomsa-Ard P, Poomipant P, Tragoonrung S. Detection and validation of EST-SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping. Genomics 2018; 111:1-9. [PMID: 29608956 DOI: 10.1016/j.ygeno.2018.03.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 01/17/2023]
Abstract
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis. Association analysis was performed on a set of 200 accessions, based on the mixed linear model. Validation of the EST-SSR markers using association mapping within the target QTL genomic regions identified two EST-SSR markers showing a putative relationship with uridine diphosphate (UDP) glycosyltransferase, and beta-amylase, which are associated with pol and sugar yield. These functional markers can be used for marker-assisted selection of sugarcane.
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Affiliation(s)
- Kittipat Ukoskit
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand.
| | - Ganlayarat Posudsavang
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand
| | - Nattapat Pongsiripat
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand
| | - Prasert Chatwachirawong
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, (Kamphaengsean Campus), Nakhon Pathom, 73140, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Patthinun Poomipant
- Institute of Food Research and Product Development, Kasetsart University, P.O. Box 1043, Kasetsart, Chatuchak, Bangkok 10903, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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Zhang J, Yuan H, Yang Q, Li M, Wang Y, Li Y, Ma X, Tan F, Wu R. The genetic architecture of growth traits in Salix matsudana under salt stress. HORTICULTURE RESEARCH 2017; 4:17024. [PMID: 28638623 PMCID: PMC5469942 DOI: 10.1038/hortres.2017.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 05/24/2023]
Abstract
Willow (Salix) is one of the most important ornamental tree species in landscape plants. One species, Salix matsudana, is widely used as a shade tree and border tree because of its soft branches and plump crown. Some varieties of S. matsudana were salt tolerant and could grow normally in coastal regions. However, the molecular mechanisms of salt tolerance for S. matsudana have been less clear. Here, we addressed this issue by performing a mapping experiment containing 195 intraspecific F1 progeny of S. matsudana, derived from salt-sensitive 'yanjiang' and salt-tolerant '9901', grown by cuttings in a 100 mM NaCl solution. Growth performance of these progeny under salt stress was investigated, displaying marked genotypic variability with the coefficients of variance of 28.64-86.11% in shoot and root growth traits. We further mapped specific QTLs contributing to these differences to the Salix genome. Of the 204 QTLs identified, a few were detected to explain a remarkably larger portion of the phenotypic variation than many others. Many detected QTLs were found to reside in the region of candidate genes of known biological function. The discovery of growth QTLs expressed under salt stress provides important information for marker-assisted breeding of salt tolerant Salix varieties and founds the basis for the application of S. matsudana in coastal afforestation.
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Affiliation(s)
- Jian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China
- Center for Cultivation of Subtropical Forest Resources (CCSFR), School of Forestry & Bio-technology, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China
| | - Qingshan Yang
- Shandong Academy of Forestry, Jinan, Shandong 250014, China
| | - Min Li
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Ying Wang
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Yujuan Li
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Xiangjian Ma
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Feng Tan
- Jiangsu Riverine Institute of Agricultural Sciences, Nantong, Jiangsu 226541, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
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Balsalobre TWA, da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP, Garcia AAF, Carneiro MS. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 2017; 18:72. [PMID: 28077090 PMCID: PMC5225503 DOI: 10.1186/s12864-016-3383-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. RESULTS We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. CONCLUSIONS This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.
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Affiliation(s)
- Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Guilherme da Silva Pereira
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Rodrigo Gazaffi
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Fernanda Zatti Barreto
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Carina Oliveira Anoni
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Cláudio Benício Cardoso-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Estela Araújo Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Melina Cristina Mancini
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Hermann Paulo Hoffmann
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
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Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T. Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. PLANT CELL REPORTS 2016; 35:1629-1653. [PMID: 27289592 DOI: 10.1007/s00299-016-1978-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/21/2016] [Indexed: 06/06/2023]
Abstract
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjay Kalia
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India
| | - Awadhesh Pandit
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India
| | - Preetam Nayak
- Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India
| | - Ram Kushal Singh
- U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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Margarido GRA, Pastina MM, Souza AP, Garcia AAF. Multi-trait multi-environment quantitative trait loci mapping for a sugarcane commercial cross provides insights on the inheritance of important traits. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:175. [PMID: 26273212 PMCID: PMC4529881 DOI: 10.1007/s11032-015-0366-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 07/29/2015] [Indexed: 05/13/2023]
Abstract
Breeding trials typically consist of phenotypic observations for various traits evaluated in multiple environments. For sugarcane in particular, repeated measures are obtained for plant crop and one or more ratoons, such that joint analysis through mixed models for modeling heterogeneous genetic (co)variances between traits, locations and harvests is appropriate. This modeling approach also enables us to include molecular marker information, aiding in understanding the genetic architecture of quantitative traits. Our work aims at detecting QTL and QTL by environment interactions by fitting mixed models with multiple QTLs, with appropriate modeling of multi-trait multi-environment data for outcrossing species. We evaluated 100 individuals from a biparental cross at two locations and three years for fiber content, sugar content (POL) and tonnes of cane per hectare (TCH). We detected 13 QTLs exhibiting QTL by location, QTL by harvest or the three-way interaction. Overall, 11 of the 13 effects presented some degree of pleiotropy, affecting at least two traits. Furthermore, these QTLs always affected fiber and TCH in the same direction, whereas POL was affected in the opposite way. There was no evidence in favor of the linked QTL over the pleiotropic QTL hypothesis for any detected genome position. These results provide valuable insights into the genetic basis of quantitative variation in sugarcane and the genetic relation between traits.
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Affiliation(s)
- G. R. A. Margarido
- />Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), CP 83, Piracicaba, SP 13418-900 Brazil
| | - M. M. Pastina
- />Embrapa Milho e Sorgo, CP 285, Sete Lagoas, MG 35701-970 Brazil
| | - A. P. Souza
- />Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP6010, Campinas, SP 13083-875 Brazil
| | - A. A. F. Garcia
- />Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), CP 83, Piracicaba, SP 13418-900 Brazil
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