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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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Zhi Y, Chuanjiang Z, Xinfang Y, Mengyi D, Zhenlei W, Fenfen Y, Cuiyun W, Jiurui W, Mengjun L, Minjuan L. Genetic analysis of mixed models of fruit sugar-acid fractions in a cross between jujube ( Ziziphus jujuba Mill.) and wild jujube ( Z. acido jujuba). FRONTIERS IN PLANT SCIENCE 2023; 14:1181903. [PMID: 37251778 PMCID: PMC10213531 DOI: 10.3389/fpls.2023.1181903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill.), an economically significant species in the Rhamnaceae family, is a popular fruit tree in Asia. The sugar and acid concentrations in jujube are considerably higher than those in other plants. Due to the low kernel rate, it is extremely difficult to establish hybrid populations. Little is known about jujube evolution and domestication, particularly with regard to the role of the sugar and acid components of jujube. Therefore, we used cover net control as a hybridization technique for the cross-breeding of Ziziphus jujuba Mill and 'JMS2' and (Z. acido jujuba) 'Xing16' to obtain an F1 population (179 hybrid progeny). The sugar and acid levels in the F1 and parent fruit were determined by HPLC. The coefficient of variation ranged from 28.4 to 93.9%. The sucrose and quinic acid levels in the progeny were higher than those in the parents. The population showed continuous distributions with transgressive segregation on both sides. Analysis by the mixed major gene and polygene inheritance model was performed. It was found that glucose is controlled by one additive-dominant major gene and polygenes, malic acid is controlled by two additive-dominant major genes and polygenes, and oxalic acid and quinic acid are controlled by two additive-dominant-epistatic major genes and polygenes. The results of this study provide insights into the genetic predisposition and molecular mechanisms underlying the role of sugar acids in jujube fruit.
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Affiliation(s)
- Yang Zhi
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Zhang Chuanjiang
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Yang Xinfang
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Dong Mengyi
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wang Zhenlei
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Yan Fenfen
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wu Cuiyun
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wang Jiurui
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, China
| | - Liu Mengjun
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, China
| | - Lin Minjuan
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
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Dias KOG, Dos Santos JPR, Krause MD, Piepho HP, Guimarães LJM, Pastina MM, Garcia AAF. Leveraging probability concepts for cultivar recommendation in multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1385-1399. [PMID: 35192008 DOI: 10.1007/s00122-022-04041-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
We propose using probability concepts from Bayesian models to leverage a more informed decision-making process toward cultivar recommendation in multi-environment trials. Statistical models that capture the phenotypic plasticity of a genotype across environments are crucial in plant breeding programs to potentially identify parents, generate offspring, and obtain highly productive genotypes for target environments. In this study, our aim is to leverage concepts of Bayesian models and probability methods of stability analysis to untangle genotype-by-environment interaction (GEI). The proposed method employs the posterior distribution obtained with the No-U-Turn sampler algorithm to get Hamiltonian Monte Carlo estimates of adaptation and stability probabilities. We applied the proposed models in two empirical tropical datasets. Our findings provide a basis to enhance our ability to consider the uncertainty of cultivar recommendation for global or specific adaptation. We further demonstrate that probability methods of stability analysis in a Bayesian framework are a powerful tool for unraveling GEI given a defined intensity of selection that results in a more informed decision-making process toward cultivar recommendation in multi-environment trials.
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Affiliation(s)
- Kaio O G Dias
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - Jhonathan P R Dos Santos
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Antonio A F Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
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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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Calderan-Rodrigues MJ, de Barros Dantas LL, Cheavegatti Gianotto A, Caldana C. Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential. FRONTIERS IN PLANT SCIENCE 2021; 12:637166. [PMID: 33679852 PMCID: PMC7935522 DOI: 10.3389/fpls.2021.637166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/27/2021] [Indexed: 05/21/2023]
Abstract
Sugarcane (Saccharum spp.), a C4 grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.
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Affiliation(s)
| | | | | | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Camila Caldana,
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Tolhurst DJ, Mathews KL, Smith AB, Cullis BR. Genomic selection in multi-environment plant breeding trials using a factor analytic linear mixed model. J Anim Breed Genet 2019; 136:279-300. [PMID: 31247682 DOI: 10.1111/jbg.12404] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
Genomic selection (GS) is a statistical and breeding methodology designed to improve genetic gain. It has proven to be successful in animal breeding; however, key points of difference have not been fully considered in the transfer of GS from animal to plant breeding. In plant breeding, individuals (varieties) are typically evaluated across a number of locations in multiple years (environments) in formally designed comparative experiments, called multi-environment trials (METs). The design structure of individual trials can be complex and needs to be modelled appropriately. Another key feature of MET data sets is the presence of variety by environment interaction (VEI), that is the differential response of varieties to a change in environment. In this paper, a single-step factor analytic linear mixed model is developed for plant breeding MET data sets that incorporates molecular marker data, appropriately accommodates non-genetic sources of variation within trials and models VEI. A recently developed set of selection tools, which are natural derivatives of factor analytic models, are used to facilitate GS for a motivating data set from an Australian plant breeding company. The power and versatility of these tools is demonstrated for the variety by environment and marker by environment effects.
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Affiliation(s)
- Daniel J Tolhurst
- National Institute for Applied Statistics Research Australia, Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Ky L Mathews
- National Institute for Applied Statistics Research Australia, Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Alison B Smith
- National Institute for Applied Statistics Research Australia, Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Brian R Cullis
- National Institute for Applied Statistics Research Australia, Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, New South Wales, Australia
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You Q, Yang X, Peng Z, Islam MS, Sood S, Luo Z, Comstock J, Xu L, Wang J. Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2829-2845. [PMID: 31321474 DOI: 10.1007/s00122-019-03391-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/05/2019] [Indexed: 05/13/2023]
Abstract
An Axiom Sugarcane100K SNP array has been designed and successfully utilized to construct the sugarcane genetic map and to identify the QTLs associated with SCYLV resistance. To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single-nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single-dose (SD) SNPs and 68,648 low-dosage (33,277 SD and 35,371 double dose) SNPs from two datasets, respectively, were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This array was used to genotype 469 sugarcane clones, including one F1 population derived from the cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3482 SD SNP markers spanning 3336 cM, a map for IND81-146 with 1513 SD SNP markers spanning 2615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3651 cM. Quantitative trait loci (QTL) analysis identified 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease-resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high-throughput genotyping in highly polyploid sugarcane.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | | | - Sushma Sood
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jack Comstock
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350001, Fujian, China.
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A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.). PLoS One 2019; 14:e0219843. [PMID: 31318931 PMCID: PMC6638961 DOI: 10.1371/journal.pone.0219843] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection.
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Rosa JRBF, Mantello CC, Garcia D, de Souza LM, da Silva CC, Gazaffi R, da Silva CC, Toledo-Silva G, Cubry P, Garcia AAF, de Souza AP, Le Guen V. QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions. BMC PLANT BIOLOGY 2018; 18:223. [PMID: 30305095 PMCID: PMC6180592 DOI: 10.1186/s12870-018-1450-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 09/27/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rubber tree is cultivated in mainly Southeast Asia and is by far the most significant source of natural rubber production worldwide. However, the genetic architecture underlying the primary agronomic traits of this crop has not been widely characterized. This study aimed to identify quantitative trait loci (QTLs) associated with growth and latex production using a biparental population established in suboptimal growth conditions in Brazil. RESULTS A full-sib population composed of 251 individuals was developed from crossing two high-producing Asiatic rubber tree cultivars, PR 255 and PB 217. This mapping population was genotyped with microsatellite markers from enriched genomic libraries or transcriptome datasets and single-nucleotide polymorphism (SNP) markers, leading to construction of a saturated multipoint integrated genetic map containing 354 microsatellite and 151 SNP markers. Height and circumference measurements repeated over a six-year period and registration of cumulative latex production during six consecutive months on the same individuals allowed in-depth characterization of the genetic values of several growth traits and precocious latex production. Growth traits, circumference and height, were overall positively correlated, whereas latex production was not correlated or even negatively correlated with growth traits. A total of 86 distinct QTLs were identified, most of which were detected for only one trait. Among these QTLs, 15 were linked to more than one phenotypic trait (up to 4 traits simultaneously). Latex production and circumference increments during the last wintering period were associated with the highest numbers of identified QTLs (eleven and nine, respectively), jointly explaining the most significantly observed phenotypic variances (44.1% and 44.4%, respectively). The most important QTL for latex production, located on linkage group 16, had an additive effect of the male parent PB 217 and corresponded to a QTL at the same position detected in a previous study carried out in Thailand for the biparental population RRIM 600 x PB 217. CONCLUSIONS Our results identified a set of significant QTLs for rubber tree, showing that the performance of modern Asiatic cultivars can still be improved and paving the way for further marker-assisted selection, which could accelerate breeding programs.
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Affiliation(s)
- João Ricardo Bachega Feijó Rosa
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
- FTS Sementes S.A., Avenida Newton Slaviero, Ponta Grossa, PR 84043-560 Brazil
| | - Camila Campos Mantello
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0 LE UK
| | - Dominique Garcia
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Lívia Moura de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Rodrigo Gazaffi
- Center of Agronomic Sciences, Department of Biotechnology and Vegetal and Animal Production, Federal University of São Carlos (UFSCAR), Jardim Residencial Pedras Preciosas, Araras, SP 13604900 Brazil
| | - Cícero Casimiro da Silva
- Plantation E. Michelin, R&D Department, Rua João de Barro quadra 22 lote 16, Ouro Branco do Sul, Itiquira, MT 78790-000 Brazil
| | - Guilherme Toledo-Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University Santa Catarina, Florianópolis, Brazil
| | - Philippe Cubry
- IRD, UMR DiADE, 911 avenue Agropolis, BP 64501, 34394, Montpellier cedex 5, France
| | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Vincent Le Guen
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
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Resende RT, de Resende MDV, Azevedo CF, Fonseca E Silva F, Melo LC, Pereira HS, Souza TLPO, Valdisser PAMR, Brondani C, Vianello RP. Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris. G3 (BETHESDA, MD.) 2018; 8:2841-2854. [PMID: 29967054 PMCID: PMC6071601 DOI: 10.1534/g3.118.200493] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int ) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker-trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.
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Affiliation(s)
| | - Marcos Deon V de Resende
- Department of Forestry
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
- EMBRAPA Florestas, Colombo, PR 83411-000, Brazil
| | - Camila F Azevedo
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | | | | | | | | | | | - Claudio Brondani
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
| | - Rosana Pereira Vianello
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
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Adhikari L, Lindstrom OM, Markham J, Missaoui AM. Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:934. [PMID: 30022989 PMCID: PMC6039623 DOI: 10.3389/fpls.2018.00934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22-0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.
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Affiliation(s)
- Laxman Adhikari
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | | | - Jonathan Markham
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
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Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models. Heredity (Edinb) 2018; 122:261-275. [PMID: 29941997 DOI: 10.1038/s41437-018-0105-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022] Open
Abstract
Genomic selection has been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies describing how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending on how well these assumptions align with the true genetic architecture of the phenotype. To investigate this, we used data from two recurrent selection populations of Coffea canephora, evaluated in two locations, and single nucleotide polymorphisms identified by Genotyping-by-Sequencing. In particular, we evaluated the performance of 13 statistical approaches to predict three important traits in the coffee-production of coffee beans, leaf rust incidence and yield of green beans. Analyses were performed for predictions within-environment, across locations and across populations to assess the reliability of genomic selection. Overall, differences in the prediction accuracy of the competing models were small, although the Bayesian methods showed a modest improvement over other methods, at the cost of more computation time. As expected, predictive accuracy for within-environment analysis, on average, were higher than predictions across locations and across populations. Our results support the potential of genomic selection to reshape traditional plant breeding schemes. In practice, we expect to increase the genetic gain per unit of time by reducing the length cycle of recurrent selection in coffee.
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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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You Q, Yang X, Peng Z, Xu L, Wang J. Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array. FRONTIERS IN PLANT SCIENCE 2018; 9:104. [PMID: 29467780 PMCID: PMC5808122 DOI: 10.3389/fpls.2018.00104] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/19/2018] [Indexed: 05/18/2023]
Abstract
Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Liping Xu
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, United States
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Jianping Wang
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15
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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: 68] [Impact Index Per Article: 9.7] [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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16
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Vigna BBZ, Santos JCS, Jungmann L, do Valle CB, Mollinari M, Pastina MM, Pagliarini MS, Garcia AAF, Souza AP. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping. PLoS One 2016; 11:e0153764. [PMID: 27104622 PMCID: PMC4841517 DOI: 10.1371/journal.pone.0153764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/04/2016] [Indexed: 01/30/2023] Open
Abstract
The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.
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Affiliation(s)
- Bianca B. Z. Vigna
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- Embrapa Pecuária Sudeste, CP 399, CEP 13560–970, São Carlos, SP, Brazil
| | - Jean C. S. Santos
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
| | - Leticia Jungmann
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Cacilda B. do Valle
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Marcelo Mollinari
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Maria M. Pastina
- Embrapa Milho e Sorgo, Rod. MG 424, Km 65, CEP 35701–970, Sete Lagoas, MG, Brazil
| | - Maria Suely Pagliarini
- University of Maringá (UEM), Department of Genetics and Cell Biology, Av. Colombo, 5790, Zona 7, CEP 87020–900, Maringá, PR, Brazil
| | - Antonio A. F. Garcia
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Anete P. Souza
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- University of Campinas (UNICAMP), Biology Institute, Department of Plant Biology, CP6109, CEP 13083–970, Campinas, SP, Brazil
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17
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Singh RK, Banerjee N, Khan MS, Yadav S, Kumar S, Duttamajumder SK, Lal RJ, Patel JD, Guo H, Zhang D, Paterson AH. Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping. Mol Genet Genomics 2016; 291:1363-77. [DOI: 10.1007/s00438-016-1190-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
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18
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Bilal M, Saeed M, Nasir IA, Tabassum B, Zameer M, Khan A, Tariq M, Javed MA, Husnain T. Association mapping of cane weight and tillers per plant in sugarcane. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1008203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Gentile A, Dias LI, Mattos RS, Ferreira TH, Menossi M. MicroRNAs and drought responses in sugarcane. FRONTIERS IN PLANT SCIENCE 2015; 6:58. [PMID: 25755657 PMCID: PMC4337329 DOI: 10.3389/fpls.2015.00058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 01/22/2015] [Indexed: 05/03/2023]
Abstract
There is a growing demand for renewable energy, and sugarcane is a promising bioenergy crop. In Brazil, the largest sugarcane producer in the world, sugarcane plantations are expanding into areas where severe droughts are common. Recent evidence has highlighted the role of miRNAs in regulating drought responses in several species, including sugarcane. This review summarizes the data from miRNA expression profiles observed in a wide array of experimental conditions using different sugarcane cultivars that differ in their tolerance to drought. We uncovered a complex regulation of sugarcane miRNAs in response to drought and discussed these data with the miRNA profiles observed in other plant species. The predicted miRNA targets revealed different transcription factors, proteins involved in tolerance to oxidative stress, cell modification, as well as hormone signaling. Some of these proteins might regulate sugarcane responses to drought, such as reduction of internode growth and shoot branching and increased leaf senescence. A better understanding on the regulatory network from miRNAs and their targets under drought stress has a great potential to contribute to sugarcane improvement, either as molecular markers as well as by using biotechnological approaches.
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Affiliation(s)
| | | | | | | | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, São Paulo, Brazil
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20
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Boden SA, Cavanagh C, Cullis BR, Ramm K, Greenwood J, Jean Finnegan E, Trevaskis B, Swain SM. Ppd-1 is a key regulator of inflorescence architecture and paired spikelet development in wheat. NATURE PLANTS 2015; 1:14016. [PMID: 27246757 DOI: 10.1038/nplants.2014.16] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
The domestication of cereal crops such as wheat, maize, rice and barley has included the modification of inflorescence architecture to improve grain yield and ease harvesting(1). Yield increases have often been achieved through modifying the number and arrangement of spikelets, which are specialized reproductive branches that form part of the inflorescence. Multiple genes that control spikelet development have been identified in maize, rice and barley(2-5). However, little is known about the genetic underpinnings of this process in wheat. Here, we describe a modified spikelet arrangement in wheat, termed paired spikelets. Combining comprehensive QTL and mutant analyses, we show that Photoperiod-1 (Ppd-1), a pseudo-response regulator gene that controls photoperiod-dependent floral induction, has a major inhibitory effect on paired spikelet formation by regulating the expression of FLOWERING LOCUS T (FT)(6,7). These findings show that modulated expression of the two important flowering genes, Ppd-1 and FT, can be used to form a wheat inflorescence with a more elaborate arrangement and increased number of grain producing spikelets.
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Affiliation(s)
- Scott A Boden
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Colin Cavanagh
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Brian R Cullis
- National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics &Applied Statistics, University of Wollongong, New South Wales, 2522, Australia
- CSIRO Digital Productivity Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Kerrie Ramm
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Julian Greenwood
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - E Jean Finnegan
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Ben Trevaskis
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Steve M Swain
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
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21
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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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22
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Heo JY, Feng D, Niu X, Mitchell-Olds T, van Tienderen PH, Tomes D, Schranz ME. Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta. PLANT, CELL & ENVIRONMENT 2014; 37:2459-69. [PMID: 24811132 PMCID: PMC4416058 DOI: 10.1111/pce.12365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/21/2014] [Accepted: 04/22/2014] [Indexed: 05/29/2023]
Abstract
Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of Boechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day (LD), short-day (SD) and in an outdoor environment (OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single- and multi-trait analyses, three main-effect quantitative trait loci (QTL) were identified. QTL on linkage group (LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co-localization of photosynthetic performance and freezing tolerance effects supports these traits being co-regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C-repeat binding factor locus, known regulators of chilling and freezing responses in Arabidopsis thaliana and other species.
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Affiliation(s)
- Jae-Yun Heo
- Biosystematics Group, Wageningen University & Research Center, Wageningen, the Netherlands
| | - Dongsheng Feng
- Pioneer Hi-Bred International, Inc., a DuPont Business, Johnston, USA
| | - Xiaomu Niu
- Pioneer Hi-Bred International, Inc., a DuPont Business, Johnston, USA
| | | | - Peter H. van Tienderen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Dwight Tomes
- Pioneer Hi-Bred International, Inc., a DuPont Business, Johnston, USA
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University & Research Center, Wageningen, the Netherlands
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23
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Nishiyama MY, Ferreira SS, Tang PZ, Becker S, Pörtner-Taliana A, Souza GM. Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PLoS One 2014; 9:e107351. [PMID: 25222706 PMCID: PMC4164538 DOI: 10.1371/journal.pone.0107351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
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Affiliation(s)
| | | | - Pei-Zhong Tang
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | - Scott Becker
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | | | - Glaucia Mendes Souza
- Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
- * E-mail:
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24
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Nelson MN, Rajasekaran R, Smith A, Chen S, Beeck CP, Siddique KHM, Cowling WA. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L. PLoS One 2014; 9:e102611. [PMID: 25061822 PMCID: PMC4111298 DOI: 10.1371/journal.pone.0102611] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/20/2014] [Indexed: 11/18/2022] Open
Abstract
Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85–0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.
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Affiliation(s)
- Matthew N. Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- * E-mail:
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Alison Smith
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia
| | - Sheng Chen
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Cameron P. Beeck
- School of Plant Biology, The University of Western Australia, Crawley, Australia
| | | | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
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25
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Nelson MN, Rajasekaran R, Smith A, Chen S, Beeck CP, Siddique KHM, Cowling WA. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L. PLoS One 2014. [PMID: 25061822 DOI: 10.1371/journalpone.0102611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85-0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.
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Affiliation(s)
- Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia; The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Alison Smith
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia
| | - Sheng Chen
- School of Plant Biology, The University of Western Australia, Crawley, Australia; The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Cameron P Beeck
- School of Plant Biology, The University of Western Australia, Crawley, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
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26
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de Siqueira Ferreira S, Nishiyama MY, Paterson AH, Souza GM. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. Genome Biol 2013; 14:210. [PMID: 23805917 PMCID: PMC3707038 DOI: 10.1186/gb-2013-14-6-210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
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Affiliation(s)
- Savio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Glaucia Mendes Souza
- 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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27
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Singh RK, Singh SP, Tiwari DK, Srivastava S, Singh SB, Sharma ML, Singh R, Mohapatra T, Singh NK. Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane. EUPHYTICA 2013. [PMID: 0 DOI: 10.1007/s10681-012-0841-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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28
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Malosetti M, Ribaut JM, van Eeuwijk FA. The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis. Front Physiol 2013; 4:44. [PMID: 23487515 PMCID: PMC3594989 DOI: 10.3389/fphys.2013.00044] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/25/2013] [Indexed: 12/04/2022] Open
Abstract
Genotype-by-environment interaction (GEI) is an important phenomenon in plant breeding. This paper presents a series of models for describing, exploring, understanding, and predicting GEI. All models depart from a two-way table of genotype by environment means. First, a series of descriptive and explorative models/approaches are presented: Finlay–Wilkinson model, AMMI model, GGE biplot. All of these approaches have in common that they merely try to group genotypes and environments and do not use other information than the two-way table of means. Next, factorial regression is introduced as an approach to explicitly introduce genotypic and environmental covariates for describing and explaining GEI. Finally, QTL modeling is presented as a natural extension of factorial regression, where marker information is translated into genetic predictors. Tests for regression coefficients corresponding to these genetic predictors are tests for main effect QTL expression and QTL by environment interaction (QEI). QTL models for which QEI depends on environmental covariables form an interesting model class for predicting GEI for new genotypes and new environments. For realistic modeling of genotypic differences across multiple environments, sophisticated mixed models are necessary to allow for heterogeneity of genetic variances and correlations across environments. The use and interpretation of all models is illustrated by an example data set from the CIMMYT maize breeding program, containing environments differing in drought and nitrogen stress. To help readers to carry out the statistical analyses, GenStat® programs, 15th Edition and Discovery® version, are presented as “Appendix.”
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Affiliation(s)
- Marcos Malosetti
- Biometris - Applied Statistics, Department of Plant Science, Wageningen University Wageningen, Netherlands
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29
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Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W, Jordão H, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AAF, Vieira MLC. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 2012; 13:51. [PMID: 22742069 PMCID: PMC3443450 DOI: 10.1186/1471-2156-13-51] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/13/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. RESULTS The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. CONCLUSIONS Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
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Affiliation(s)
- Alessandra C Palhares
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Taislene B Rodrigues-Morais
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Douglas S Domingues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Present address: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, 86047-902, Londrina, Brazil
| | - Walter Maccheroni
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Hamilton Jordão
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Thiago G Marconi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Marcelo Mollinari
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Rodrigo Gazaffi
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Antonio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
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