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Perera MF, Ostengo S, Malavera ANP, Balsalobre TWA, Onorato GD, Noguera AS, Hoffmann HP, Carneiro MS. Genetic diversity and population structure of Saccharum hybrids. PLoS One 2023; 18:e0289504. [PMID: 37582090 PMCID: PMC10426985 DOI: 10.1371/journal.pone.0289504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
Sugarcane breeding programs incorporate foreign material to broaden the genetic base, expanding the gene pool. In South America, the Inter-university Network for the Development of the Sugarcane Industry (RIDESA) and Estación Experimental Agroindustrial Obispo Colombres (EEAOC) sugarcane breeding programs from Brazil and Argentina, respectively, have never exchanged materials. In that sense, the knowledge of the genetic diversity and population structure among sugarcane genotypes of both germplasm banks, determined in a reliable way through their molecular profiles, will provide valuable information to select the best parental accessions for crossing aimed at the efficient introgression of desirable alleles. For that, the aim was to determine the genetic diversity and population structure of 96 Saccharum commercial hybrids from RIDESA and EEAOC sugarcane breeding programs by using TRAP, SSR and markers related to disease resistance (e.g. Bru1 and G1). Genetic structure was determined through genetic similarity analysis, analysis of molecular variance (AMOVA), Multidimensional scaling (MDS), and a Bayesian method. Average PIC values were 0.25 and 0.26, Ho values were 0.24 and 0.28, and He values were 0.25 and 0.28, for TRAP and SSR primers, respectively. Genetic similarity, MDS, and analysis of structure revealed that Brazilian and Argentinean genotypes clustered in two groups clearly differentiated, whereas AMOVA suggested that there is more variability within programs than between them. Regarding Bru1 markers, Brazilian genotypes showed high frequency of haplotype 1 (71.4%) whereas Argentinean genotypes showed high frequency of haplotype 4 (80.8%); haplotypes 1 and 4 are indicated for the presence and absence of the brown rust resistance gene (Bru1), respectively. Respecting the G1 marker, most of the evaluated genotypes (60.4%) showed the presence of the fragment, in a similar proportion for genotypes of both programs. In conclusion, the exchange of materials, at least the most diverse genotypes, between RIDESA and EEAOC breeding programs will allow extending the genetic base of their germplasm banks, and the knowledge of genetic diversity will help breeders to better manage crosses, increasing the probability of obtaining more productive varieties.
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Affiliation(s)
- María Francisca Perera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Santiago Ostengo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Andrea Natalia Peña Malavera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | | | | | - Aldo Sergio Noguera
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Las Talitas, Tucumán, Argentina
| | - Hermann Paulo Hoffmann
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, São Paulo, Brazil
- Departamento de Biotecnologia e Producão Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), Araras, São Paulo, Brazil
| | - Monalisa Sampaio Carneiro
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, São Paulo, Brazil
- Departamento de Biotecnologia e Producão Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), Araras, São Paulo, Brazil
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Xiong H, Chen Y, Pan YB, Shi A. A Genome-Wide Association Study and Genomic Prediction for Fiber and Sucrose Contents in a Mapping Population of LCP 85-384 Sugarcane. PLANTS (BASEL, SWITZERLAND) 2023; 12:1041. [PMID: 36903902 PMCID: PMC10005238 DOI: 10.3390/plants12051041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the time and cost of developing new sugarcane varieties. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify DNA markers associated with fiber and sucrose contents and to perform genomic prediction (GP) for the two traits. Fiber and sucrose data were collected from 237 self-pollinated progenies of LCP 85-384, the most popular Louisiana sugarcane cultivar from 1999 to 2007. The GWAS was performed using 1310 polymorphic DNA marker alleles with three models of TASSEL 5, single marker regression (SMR), general linear model (GLM) and mixed linear model (MLM), and the fixed and random model circulating probability unification (FarmCPU) of R package. The results showed that 13 and 9 markers were associated with fiber and sucrose contents, respectively. The GP was performed by cross-prediction with five models, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB) and Bayesian least absolute shrinkage and selection operator (BL). The accuracy of GP varied from 55.8% to 58.9% for fiber content and 54.6% to 57.2% for sucrose content. Upon validation, these markers can be applied in MAS and genomic selection (GS) to select superior sugarcane with good fiber and high sucrose contents.
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Affiliation(s)
- Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
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Gao Y, Zhou S, Huang Y, Zhang B, Xu Y, Zhang G, Lakshmanan P, Yang R, Zhou H, Huang D, Liu J, Tan H, He W, Yang C, Duan W. Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 12:796189. [PMID: 35069651 PMCID: PMC8766830 DOI: 10.3389/fpls.2021.796189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/13/2021] [Indexed: 06/02/2023]
Abstract
Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.
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Affiliation(s)
- Yijing Gao
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Shan Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuxin Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Baoqing Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Gemin Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Prakash Lakshmanan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Rongzhong Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hui Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Dongliang Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Junxian Liu
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hongwei Tan
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weizhong He
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Cuifang Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Weixing Duan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
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A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of Panama. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02421-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractPolyploidy may contribute to invasive ability as it can lead to high survival and fitness during establishment and enhance the processes of adaptation to novel environments by increasing genetic diversity in invading propagules. Many grasses are polyploid and many are aggressive invaders, making them persistent problems in disturbed environments worldwide. Today, vast areas of central Panama are dominated by Saccharum spontaneum, a perennial grass that originates from Asia. While widely regarded as invasive, it is not known when or how it arrived in Panama. We explore hypotheses regarding the timing and origins of this invasion through literature review and comparisons of genetic diversity in Panama with accessions from available sugarcane germplasm collections, highlighting historical accessions that were likely brought to Panama in 1939 as part of a USDA sugarcane germplasm collection. Samples were haplotyped at two chloroplast loci and genotyped using eight microsatellite markers. All sequenced individuals from Panama belong to a single chloroplast lineage which is common worldwide and was common in the Historic germplasm collection. Although genotypic diversity was extremely high in all samples due to high ploidy, samples from Panama had reduced diversity and clustered with several accessions in the Historic collection which had the same haplotype and high ploidy levels. Our results suggest that accidental escape from the historical sugarcane germplasm collection is the likely origin of the S. spontaneum invasion in Panama. Intraspecific hybridization among several historical accessions and pre-adaptation to local conditions may have facilitated its rapid spread and persistence. We discuss the implications of our findings for biosecurity of germplasm collections.
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Moura YA, Alves-Pereira A, da Silva CC, Souza LM, de Souza AP, Koehler S. Secondary origin, hybridization and sexual reproduction in a diploid-tetraploid contact zone of the facultatively apomictic orchid Zygopetalum mackayi. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:939-948. [PMID: 32558140 DOI: 10.1111/plb.13148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/26/2020] [Indexed: 05/26/2023]
Abstract
The production of triploids and apomictic reproduction are important processes for polyploid establishment and cytotype coexistence, but we know little about the interaction between triploids and facultatively apomictic plants. To bridge this gap, we studied the pollen-dependent, facultatively apomictic orchid Zygopetalum mackayi from high-elevation outcrops of southeast Brazil. We described the nature of the contact between Z. mackayi cytotypes and patterns of genetic diversity and structure based on eight microsatellite markers and 155 individuals of pure tetraploid, pure diploid and mixed cytotype populations. Our results revealed high values of genetic and genotypic diversity within all populations of Z. mackayi. Each cytotype emerged as a genetic distinct cluster, combining individuals from different populations. Triploids clustered in an intermediate position between diploids and tetraploids. Most genetic variance is associated with individuals within populations and genetic differentiation is high among populations. Mixed cytotype populations of Z. mackayi originate from secondary contact. Triploids are hybrids between diploids and tetraploids and likely act as a bridge. Our results point to the predominance of sexual reproduction in all populations but do not corroborate previous basic chromosome number for this species. Polyploidy rather than facultative apomixis may explain the larger geographic distribution of tetraploids of Z. mackayi.
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Affiliation(s)
- Y A Moura
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
| | - A Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
| | - C C da Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
| | - L M Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
| | - A P de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
| | - S Koehler
- Departamento de Biologia Vegetal, Instituto de Biologia, CP 6109, Universidade Estadual de Campinas - UNICAMP, 13083-970, Campinas, SP, Brazil
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An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane. Sci Rep 2020; 10:13390. [PMID: 32770152 PMCID: PMC7414218 DOI: 10.1038/s41598-020-70292-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/27/2020] [Indexed: 11/23/2022] Open
Abstract
Sugarcane crop is important for both sugar and biofuels. A world collection of sugarcane and related grasses (WCSRG) maintained at Miami, FL contains > 1,200 non-redundant clones of different species and genera within the Saccharum complex. However, linkage of undesirable alleles with useful genes in wild species has hindered its efficient utilization in sugarcane breeding. A core collection developed previously with smaller number of clones representing WCSRG did not take into account > 120 wild/exotic clones maintained at the USDA-ARS Sugarcane Research Unit in Houma, Louisiana. Moreover, the genome complexity and sub-tropical to temperate growing climate of Louisiana warrant a region-specific core collection that can be used for base-broadening breeding aimed at efficient introgression of desirable alleles. Genetic diversity of 1,485 clones within WCSRG and Louisiana (commercials, wild/exotic) using 423 SSR alleles showed an average gene diversity (h) at 0.208 among all species groups where Erianthus-like Saccharum species (ELSS), Miscanthus spp., and S. spontaneum each formed a distinct cluster, Saccharum robustum, S. officinarum, hybrid cultivars, and S. edule grouped together in a major cluster, and Saccharum sinense and S. barberi formed distinct grouping. A 309-clone diversity panel (SDP1) was developed that captured the genetic diversity based on the combination of maximum length subtree and manual selection to maximize representation of Louisiana clones and minimize import of clones from Miami. SDP1 shared 324 alleles out of the 423 alleles in the entire population of 1,485 clones and captured the genetic diversity of the entire collection with an average gene diversity (h) at 0.163. The variation within (11–17%) and among (83–89%) the populations in SDP1 were comparable with the entire population of 1,485 clones (9–15% and 85–91%, respectively). The breadth of the genetic variation of SDP1 was exemplified by the intra- and inter-specific diversity of a 190-clone mini-core collection with markers derived from known cold-responsive genes. SDP1 will facilitate genome-wide association studies for identification of trait-specific markers for use in marker-assisted breeding in Louisiana and elsewhere.
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Osei MK, Danquah E, Danquah A, Blay E, Adu-Dapaah H. Hybridity testing of tomato F1 progenies derived from parents with varying fruit quality and shelf life using single nucleotide polymorphism (SNPs). SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Abstract
Sugarcane (Saccharum hybrids spp.) is a wind-pollinated species that bears very small yet complete flowers. During crossing, a lack of pollen control (trimming off dehisced florets and hot water treatment) may result in both self-pollination (selfs) and unintentional pollination from stray pollen (off-types). Due to this uncertainty, it is important to estimate the percentage of intentional paternal hybridizations to better understand and possibly improve the crossing process. In this study, six pairs of simple sequence repeats (SSR) primers were used to assess the fidelity of 343 bi-parental crosses made at three U.S. breeding stations in 2002, 2003, 2004, 2005, and 2006. By comparing the SSR fingerprints between the two parents and 20 random progenies, three types of progenies were identified, namely, hybrids, selfs, and off-types. Hybrids had only SSR fingerprints found in either parent; selfs had only SSR fingerprints of the maternal parent; and off-types had SSR fingerprints that were not found in either parent. The fidelity of the 343 crosses fluctuated from 100% hybrids to 100% off-types. Multinomial analysis indicated that the ratio of hybrids from intentional hybridization to selfs and off-types fluctuated by year and location. Selfing rates (−30.5%) and off-type rates (−9.2%) were lower in crosses from which superior progenies were selected and advanced through 10-year field evaluation and testing, but off-type rates were not significant indicating that selfing may reduce advancement rates more than the off-types. Hot water treatment reduced off-types by 27% and selfing by 20%. This research demonstrates the utility of SSR markers for measuring hybridization rates and highlights the importance of pollen control measures through trimming and hot water treatment of sugarcane flowers.
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Crispim BDA, Déo TG, Fernandes JDS, de Vasconcelos AA, Vieira MDC, Carnevali TDO, Bajay MM, Zucchi MI, Barufatti A. Development and characterization of microsatellite markers in Campomanesia adamantium, a native plant of the Cerrado ecoregions of South America. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11287. [PMID: 31572628 PMCID: PMC6764490 DOI: 10.1002/aps3.11287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/28/2019] [Indexed: 05/23/2023]
Abstract
PREMISE A novel set of nuclear microsatellite markers was developed and characterized for Campomanesia adamantium (Myrtaceae) and tested for cross-amplification in the related species C. sessiliflora. METHODS AND RESULTS Forty-one primer pairs were designed for simple sequence repeat loci, of which 36 successfully amplified and were polymorphic. The number of alleles ranged from two to 14, with an average of 8.14 alleles per locus. Additionally, cross-amplification was tested in C. sessiliflora; more than 55.5% of the microsatellite loci amplified, confirming the use of these microsatellite markers in a related species. CONCLUSIONS We developed a set of microsatellite markers that will be useful for future studies of genetic diversity and population structure of C. adamantium and a closely related species, which will aid in future conservation efforts.
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Affiliation(s)
- Bruno do Amaral Crispim
- Faculdade de Ciências Exatas e TecnologiaUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Thamiris Gatti Déo
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Juliana dos Santos Fernandes
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Adrielle Ayumi de Vasconcelos
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Maria do Carmo Vieira
- Faculdade de Ciências AgráriasUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Thiago de Oliveira Carnevali
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
| | - Miklos Maximiliano Bajay
- Universidade Estadual de Santa CatarinaLagunaRua Cel. Fernandes Martins, 270 ‐ Progresso– LagunaSanta Catarina88.790‐000Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos AgronegóciosPólo Centro‐Sul (APTA)PiracicabaSão PauloBrazil
| | - Alexeia Barufatti
- Faculdade de Ciências Exatas e TecnologiaUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosMato Grosso do Sul79804‐970Brazil
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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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Ali A, Pan YB, Wang QN, Wang JD, Chen JL, Gao SJ. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Sci Rep 2019; 9:395. [PMID: 30674931 PMCID: PMC6344583 DOI: 10.1038/s41598-018-36630-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 11/26/2018] [Indexed: 11/09/2022] Open
Abstract
In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.
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Affiliation(s)
- Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA, 70360, USA
| | - Qin-Nan Wang
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, Guangdong, 510316, China
| | - Jin-Da Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jun-Lü Chen
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, Guangdong, 510316, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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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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Parthiban S, Govindaraj P, Senthilkumar S. Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane. 3 Biotech 2018; 8:144. [PMID: 29484283 DOI: 10.1007/s13205-018-1172-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 02/14/2018] [Indexed: 01/09/2023] Open
Abstract
Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to morphological/agronomical traits.
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Affiliation(s)
- S Parthiban
- Division of Crop Improvement, ICAR- Sugarcane, Breeding Institute, Coimbatore, 641 007 Tamil Nadu India
| | - P Govindaraj
- Division of Crop Improvement, ICAR- Sugarcane, Breeding Institute, Coimbatore, 641 007 Tamil Nadu India
| | - S Senthilkumar
- Division of Crop Improvement, ICAR- Sugarcane, Breeding Institute, Coimbatore, 641 007 Tamil Nadu India
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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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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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17
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Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M. Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis). BMC PLANT BIOLOGY 2014; 14:384. [PMID: 25522814 PMCID: PMC4279980 DOI: 10.1186/s12870-014-0384-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis. RESULTS In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers. CONCLUSIONS In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis. Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.
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Affiliation(s)
- Yong Xiao
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Lixia Zhou
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Wei Xia
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Annaliese S Mason
- />School of Agriculture and Food Sciences and Centre for Integrative Legume Research, the University of Queensland, 4072 Brisbane, Australia
| | - Yaodong Yang
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Zilong Ma
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
| | - Ming Peng
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
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High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production. Appl Biochem Biotechnol 2014; 175:965-73. [PMID: 25351629 DOI: 10.1007/s12010-014-1340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
Abstract
High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations.
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Nayak SN, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X, Todd J, Glynn NC, Kuhn DN, Glaz B, Gilbert RA, Comstock JC, Wang J. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS One 2014; 9:e110856. [PMID: 25333358 PMCID: PMC4205016 DOI: 10.1371/journal.pone.0110856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022] Open
Abstract
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.
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Affiliation(s)
- Spurthi N. Nayak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jian Song
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- College of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Andrea Villa
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Bhuvan Pathak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Tomas Ayala-Silva
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - James Todd
- Everglades Research and Education Center, University of Florida, Belle Glade, Florida, United States of America
| | - Neil C. Glynn
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - David N. Kuhn
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Barry Glaz
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Robert A. Gilbert
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jack C. Comstock
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, Florida, United States of America
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Chandra A, Grisham MP, Pan YB. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane. Genome 2014; 57:363-72. [PMID: 25247737 DOI: 10.1139/gen-2014-0072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneupolyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible through capillary electrophoresis (CE) using fluorescence-labeled SSR markers. Twenty-four sugarcane cultivars, 12 each from India and the USA, were genetically assessed using 21 fluorescence-labeled polymorphic SSR markers. These markers primed the amplification of 213 alleles. Of these alleles, 161 were common to both Indian and US cultivars, 25 were specific to the Indian cultivars, and 27 were observed only in the US cultivars. Only 10 alleles were monomorphic. A high level of heterozygosity was observed in both Indian (82.4%) and US (91.1%) cultivars resulting in average polymorphism information content (PIC) values of 0.66 and 0.77 and marker index (MI) values of 5.07 and 5.58, respectively. Pearson correlation between PIC and MI was significant in both sets of cultivars (r = 0.58 and 0.69). UPGMA clustering separated cultivars into three distinct clusters at 59% homology level. These results propose the potential utility of six Indian cultivar-specific SSR alleles (mSSCIR3_182, SMC486CG_229, SMC36BUQ_125, mSSCIR74_216, SMC334BS_154, and mSSCIR43_238) in sugarcane breeding, vis a vis transporting CE-based evaluation in clone or variety identity testing, cross fidelity assessments, and genetic relatedness among species of the genus Saccharum and related genera.
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Affiliation(s)
- Amaresh Chandra
- a USDA-ARS, MSA, Sugarcane Research Laboratory, Houma, LA 70360, USA
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21
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Saxena S, Singh A, Archak S, Behera TK, John JK, Meshram SU, Gaikwad AB. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability. Appl Biochem Biotechnol 2014; 175:93-118. [PMID: 25240849 DOI: 10.1007/s12010-014-1249-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022]
Abstract
Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.
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Affiliation(s)
- Swati Saxena
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
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22
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Kalwade SB, Devarumath RM. Single strand conformation polymorphism of genomic and EST-SSRs marker and its utility in genetic evaluation of sugarcane. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:313-21. [PMID: 25049458 PMCID: PMC4101139 DOI: 10.1007/s12298-014-0231-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/07/2014] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
Sugarcane is an important crop producing around 75 % of sugar in world and used as first generation biofuel. In present study, the genomic and gene based microsatellite markers were analyzed by low cost Single Strand Confirmation Polymorphism technique for genetic evaluation of 22 selected sugarcane genotypes. Total 16 genomic and 12 Expression Sequence Tag derived markers were able to amplify the selected sugarcane genotypes. Total 138 alleles were amplified of which 99 alleles (72 %) found polymorphic with an average of 4.9 alleles per locus. Microsatellite marker, VCSSR7 and VCSSR 12 showed monomorphic alleles with frequency 7.1 % over the average of 3.5 obtained for polymorphic locus. The level of Polymorphic Information Content (PIC) varied from 0.09 in VCSSR 6 to 0.88 in VCSSR 11 marker respectively with a mean of 0.49. Genomic SSRs showed more polymorphism than EST-SSRs markers on selected sugarcane genotypes whereas, the genetic similarity indices calculated by Jaccard's similarity coefficient varied from 0.55 to 0.81 indicate a high level of genetic similarity among the genotypes that was mainly attributed to intra specific diversity. Hence, the SSR-SSCP technique helped to identify the genetically diverse clones which could be used in crossing program for introgression of sugar and stress related traits in hybrid sugarcane.
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Affiliation(s)
- Sachin B. Kalwade
- />Molecular Biology and Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk.), Tal. Haveli, Pune, 412307 India
- />Department of Biotechnology, Shivaji University, Vidyanagari, Kolhapur, 416004 India
| | - Rachayya M. Devarumath
- />Molecular Biology and Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk.), Tal. Haveli, Pune, 412307 India
- />Department of Biotechnology, Shivaji University, Vidyanagari, Kolhapur, 416004 India
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23
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Verma P, Sharma TR, Srivastava PS, Abdin MZ, Bhatia S. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers. Mol Biol Rep 2014; 41:5607-25. [PMID: 24893599 DOI: 10.1007/s11033-014-3431-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/21/2014] [Indexed: 12/01/2022]
Abstract
Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement.
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Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India
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24
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Moyle RL, Birch RG. Diversity of sequences and expression patterns among alleles of a sugarcane loading stem gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1775-82. [PMID: 23546592 DOI: 10.1007/s00122-013-2091-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/21/2013] [Indexed: 05/13/2023]
Abstract
Modern sugarcane cultivars are highly polyploid and aneuploid hybrids, which are propagated as clones. Their complex genome structure comprises 100-130 chromosomes and 10-13 hom(e)ologous copies of most loci. There is preliminary evidence of very high heterozygosity, with implications for genetic improvement approaches ranging from marker-assisted selection to transgenics. Here, we report that sugarcane cultivar Q200 has at least nine alleles at the Loading Stem Gene (ScLSG) locus. Exon-intron structure is identical and the predicted protein products show at least 92 % identity, across sugarcane alleles and the Sorghum homologue Sb07g027880. There is substantial variation in the 5' UTR and promoter regions including numerous allele-specific nucleotide polymorphisms, insertions and deletions. We developed an allele-specific qRT-PCR method to undertake the first compelling test of allele-specific expression in polyploid sugarcane. Seven alleles distinguished by this method all showed peak expression in the sucrose-loading zone of the stem, but there was apparent variability in expression patterns across other tissues. The ScLSG2 and ScLSG5 alleles appear promising for specificity of expression in stems, relative to leaf, meristem, emerging shoot and root tissues. Within the stem, there was activity in parenchyma, vascular and rind tissues. This expression pattern is of interest in basic research and biotechnology aimed at enhanced sucrose content, engineering value-added products, and manipulation of stem biomass composition.
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Affiliation(s)
- Richard L Moyle
- Hines Plant Science Building, University of Queensland, Brisbane 4072, Australia
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Ortiz-Morea FA, Vicentini R, Silva GF, Silva EM, Carrer H, Rodrigues AP, Nogueira FT. Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2307-20. [PMID: 23564956 PMCID: PMC3654421 DOI: 10.1093/jxb/ert089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth.
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Affiliation(s)
- Fausto A. Ortiz-Morea
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- These authors contributed equally to this work
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
- These authors contributed equally to this work
| | - Geraldo F.F. Silva
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Eder M. Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Helaine Carrer
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
| | - Ana P. Rodrigues
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Fabio T.S. Nogueira
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- To whom correspondence should be addressed.
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Singh RK, Jena SN, Khan S, Yadav S, Banarjee N, Raghuvanshi S, Bhardwaj V, Dattamajumder SK, Kapur R, Solomon S, Swapna M, Srivastava S, Tyagi AK. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene 2013; 524:309-29. [PMID: 23587912 DOI: 10.1016/j.gene.2013.03.125] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 03/20/2013] [Accepted: 03/27/2013] [Indexed: 12/01/2022]
Abstract
Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5'UTR and in the ORF (about 27%) and a low frequency was observed in the 3'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane.
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Affiliation(s)
- Ram K Singh
- Indian Institute of Sugarcane Research (ICAR), Rai Bareli Road, Lucknow-226002, U.P., India.
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Chandra A, Jain R, Solomon S, Shrivastava S, Roy AK. Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses. BMC Res Notes 2013; 6:47. [PMID: 23379891 PMCID: PMC3598963 DOI: 10.1186/1756-0500-6-47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
Background Sugarcane is an important cash crop, providing 70% of the global raw sugar as well as raw material for biofuel production. Genetic analysis is hindered in sugarcane because of its large and complex polyploid genome and lack of sufficiently informative gene-tagged markers. Modern genomics has produced large amount of ESTs, which can be exploited to develop molecular markers based on comparative analysis with EST datasets of related crops and whole rice genome sequence, and accentuate their cross-technical functionality in orphan crops like tropical grasses. Findings Utilising 246,180 Saccharum officinarum EST sequences vis-à-vis its comparative analysis with ESTs of sorghum and barley and the whole rice genome sequence, we have developed 3425 novel gene-tagged markers — namely, conserved-intron scanning primers (CISP) — using the web program GeMprospector. Rice orthologue annotation results indicated homology of 1096 sequences with expressed proteins, 491 with hypothetical proteins. The remaining 1838 were miscellaneous in nature. A total of 367 primer-pairs were tested in diverse panel of samples. The data indicate amplification of 41% polymorphic bands leading to 0.52 PIC and 3.50 MI with a set of sugarcane varieties and Saccharum species. In addition, a moderate technical functionality of a set of such markers with orphan tropical grasses (22%) and fodder cum cereal oat (33%) is observed. Conclusions Developed gene-tagged CISP markers exhibited considerable technical functionality with varieties of sugarcane and unexplored species of tropical grasses. These markers would thus be particularly useful in identifying the economical traits in sugarcane and developing conservation strategies for orphan tropical grasses.
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Affiliation(s)
- Amaresh Chandra
- Division of Plant Physiology and Biochemistry, Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, Uttar Pradesh 226002, India.
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Bressan EDA, Scotton DC, Ferreira RR, Jorge EC, Sebbenn AM, Gerald LTS, Figueira A. Development of microsatellite primers for Jatropha curcas (Euphorbiaceae) and transferability to congeners. AMERICAN JOURNAL OF BOTANY 2012; 99:e237-9. [PMID: 22575369 DOI: 10.3732/ajb.1100532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed for Jatropha curcas (Euphorbiaceae), a tree species with large potential for biofuel production, to investigate its natural genetic diversity and mating system to facilitate the establishment of tree improvement and conservation programs. METHODS AND RESULTS Using a protocol for genomic library enrichment, 104 clones containing 195 repeat motifs were identified. Primer pairs were developed for 40 microsatellite loci and validated in 41 accessions of J. curcas from six provenances. Nine loci were polymorphic revealing from two to eight alleles per locus, and six primers were able to amplify alleles in the congeners J. podagrica, J. pohliana, and J. gossypifolia, but not in other Euphorbiaceae species, such as Hevea brasiliensis, Manihot esculenta, or Ricinus communis. CONCLUSIONS The primers developed here revealed polymorphic loci that are suitable for genetic diversity and structure, mating system, and gene flow studies in J. curcas, and some congeners.
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Affiliation(s)
- Eduardo de A Bressan
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, São Paulo 13400-970, Brazil
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Marulanda M, López AM, Uribe M. Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers. GENETICS AND MOLECULAR RESEARCH 2012; 11:322-31. [PMID: 22370934 DOI: 10.4238/2012.february.10.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The species Rubus glaucus, also known as the Andean or "Castilla" blackberry, is one of nine edible species of this genus that grow naturally in Central and South America. In Colombia, this species is the most important of all Rubus species for agricultural and commercial purposes. We used 20 SSRs developed for other Rubus species to characterize 44 Colombian R. glaucus genotypes, collected from eight different departments, and to look for molecular differences between thornless and thorny cultivated blackberries. Eighty-two bands were obtained from 28 loci. The genotypes were classified into eight populations, corresponding to collection sites. The mean number of polymorphic alleles per locus in all populations and genotypes ranged from 1.857 to 2.393. Samples collected from Valle del Cauca, Quindío, Caldas, and Risaralda departments had the highest heterozygosity values. The finding of exclusive bands from R. glaucus genotypes from Valle del Cauca, Quindío, and Caldas demonstrates genetic and molecular differentiation between thorny and thornless Andean blackberries.
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Affiliation(s)
- M Marulanda
- Laboratorio de Biotecnología Vegetal, Facultad de Ciencias Ambientales, Universidad Tecnológica de Pereira, Pereira, Colombia.
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Rahimmalek M, Sayed Tabatabaei BE, Arzani A, Khorrami M. Development and characterization of microsatellite markers for genomic analysis of yarrow (Achillea millefolium L.). Genes Genomics 2011. [DOI: 10.1007/s13258-011-0045-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Marconi TG, Costa EA, Miranda HR, Mancini MC, Cardoso-Silva CB, Oliveira KM, Pinto LR, Mollinari M, Garcia AA, Souza AP. Functional markers for gene mapping and genetic diversity studies in sugarcane. BMC Res Notes 2011; 4:264. [PMID: 21798036 PMCID: PMC3158763 DOI: 10.1186/1756-0500-4-264] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database). FINDINGS A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process. CONCLUSIONS These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.
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Affiliation(s)
- Thiago G Marconi
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-970, Campinas, SP, Brazil.
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Andru S, Pan YB, Thongthawee S, Burner DM, Kimbeng CA. Genetic analysis of the sugarcane (Saccharum spp.) cultivar 'LCP 85-384'. I. Linkage mapping using AFLP, SSR, and TRAP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:77-93. [PMID: 21472411 DOI: 10.1007/s00122-011-1568-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 03/11/2011] [Indexed: 05/07/2023]
Abstract
Sugarcane hybrids are complex aneu-polyploids (2n = 100-130) derived from inter-specific hybridization between ancestral polyploid species, namely S. officinarum L. and S. spontaneum L. Efforts to understand the sugarcane genome have recently been enhanced through the use of new molecular marker technologies. A framework genetic linkage map of Louisiana's popular cultivar LCP 85-384 was constructed using the selfed progeny and based on polymorphism derived from 64 AFLP, 19 SSR and 12 TRAP primer pairs. Of 1,111 polymorphic markers detected, 773 simplex (segregated in 3:1 ratio) and 182 duplex (segregate in 77:4 ratio) markers were used to construct the map using a LOD value of ≥ 4.0 and recombination threshold of 0.44. The genetic distances between pairs of markers linked in the coupling phase was computed using the Kosambi mapping function. Of the 955 markers, 718 simplex and 66 duplex markers were assigned to 108 co-segregation groups (CGs) with a cumulative map length of 5,617 cM and a density of 7.16 cM per marker. Fifty-five simplex and 116 duplex markers remained unlinked. With an estimated genome size of 12,313 cM for LCP 85-384, the map covered approximately 45.6% of the genome. Forty-four of the 108 CGs were assigned into 9 homo(eo)logous groups (HGs) based on information from locus-specific SSR and duplex markers, and repulsion phase linkages detected between CGs. Meiotic behavior of chromosomes in cytogenetic studies and repulsion phase linkage analysis between CGs in this study inferred the existence of strong preferential chromosome pairing behavior in LCP 85-384. This framework map marks an important beginning for future mapping of QTLs associated with important agronomic traits in the Louisiana sugarcane breeding programs.
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Affiliation(s)
- Suman Andru
- School of Plant Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Genetic diversity and structure of a Mediterranean endemic plant in Corsica (Mercurialis corsica, Euphorbiaceae). POPUL ECOL 2011. [DOI: 10.1007/s10144-011-0266-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Isolation and characterization of microsatellite markers for Cichla monoculus (Agassiz, 1831), an important freshwater fish in the Amazon. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9240-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Parida SK, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T. Functionally relevant microsatellites in sugarcane unigenes. BMC PLANT BIOLOGY 2010; 10:251. [PMID: 21083898 PMCID: PMC3017843 DOI: 10.1186/1471-2229-10-251] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 11/17/2010] [Indexed: 05/08/2023]
Abstract
BACKGROUND Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. RESULTS The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus) with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. CONCLUSION Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6%) of which functions were determined in silico. High level of allelic diversity in repeats including those present in the functional domains of proteins encoded by the unigenes demonstrated their use in assay of useful variation in the genic component of complex polyploid sugarcane genome.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
| | - Awadhesh Pandit
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
| | - Tilak R Sharma
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India
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Vieira ESN, Pinho EVDRV, Carvalho MGG, Esselink DG, Vosman B. Development of microsatellite markers for identifying Brazilian Coffea arabica varieties. Genet Mol Biol 2010; 33:507-14. [PMID: 21637425 PMCID: PMC3036114 DOI: 10.1590/s1415-47572010005000055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 02/19/2010] [Indexed: 11/22/2022] Open
Abstract
Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffealiberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity.
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Affiliation(s)
- Elisa S N Vieira
- Cooperativa Central de Pesquisa Agrícola, Núcleo de Biotecnologia, Cascavel, PR Brazil
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Characterization of 12 microsatellite loci from an enriched genomic library in polyploid Tibouchina pulchra Cogn. (Melastomataceae). CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9224-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Vinayak V, Dhawan AK, Gupta VK. PCR Primers for identification of high sucrose Saccharum genotypes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2010; 16:107-111. [PMID: 23572960 PMCID: PMC3550629 DOI: 10.1007/s12298-010-0002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The progeny of a cross between high sucrose sugarcane clone S. officinarum 'Gungera' and a low sucrose clone S. spontaneum 'SES 603' resulted in interspecific hybrids that were named as ISH-1 to ISH-29 and graded on the basis of sucrose content. Hybrids ISH-1, ISH-5, ISH-17 and ISH-23 were selected as very high sucrose (65 to 100 mg/g tissue) genotypes, whereas ISH-10, ISH-11, ISH-12 and ISH-25 were very low sucrose (2 to 25 mg/g tissue) genotypes. DNA from leaves of both the parent clones, as also the progeny hybrids, was amplified using selected primers, in order to identify markers for sucrose content. Ten specific primers were examined: primers 'A' and 'B' that detect polymorphism in promoter region of sucrose synthase-2 gene; primers AI, SS and SPS that were designed on the basis of nucleotide sequences of genes for acid invertase, sucrose synthase and sucrose phosphate synthase enzymes, respectively and primers MSSCIR43, MSSCIRI, SMC226CG, SMC1039CG and SCB07 selected for relation to sucrose accumulation process. DNA products specific to low or high sucrose clones were identified. Primer 'A' and AI amplified DNA products of size 230 and 500 bp, respectively only in high sucrose genotypes ('Gungera', ISH-1, ISH-5, ISH-17 and ISH-23), while primer SMC226CG generated a DNA product of size 920 bp only in low sucrose genotypes ('SES 603', ISH-10, ISH-11, ISH-12 and ISH-25). Ten random decamer primers were also examined, but their products did not show relationship to sucrose content of genotypes.
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Affiliation(s)
- Vandana Vinayak
- />Regional Research Station, CCS Haryana Agricultural University, Uchani, Karnal India
- />SSO, Biology, FSL(H), Madhuban, Karnal India
| | - Ashok K. Dhawan
- />Regional Research Station, CCS Haryana Agricultural University, Uchani, Karnal India
| | - V. K. Gupta
- />Regional Research Station, CCS Haryana Agricultural University, Uchani, Karnal India
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Isolation and characterization of microsatellite loci in the stingless bee Melipona interrupta manaosensis (Apidae: Meliponini). CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9130-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Francini IB, Sforça DA, Sousa ACB, Campos T, Cidade FW, Zucchi MI, Souza AP, Nunes-Silva CG, Carvalho-Zilse GA. Microsatellite loci for an endemic stingless bee Melipona seminigra merrillae (Apidae, Meliponini) from Amazon. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9113-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Development and characterization of 14 microsatellite loci from an enriched genomic library of Eucalyptus camaldulensis Dehnh. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9107-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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42
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Sousa ACB, Carvalho MA, Boaventura LR, Sforça DA, Campos T, Jungmann L, Zucchi MI, Jank L, Souza AP. Microsatellite markers in tropical legume (Centrosema pubescens Benth): development, characterization, and cross-species amplification in Centrosema sp. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9080-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Isolation and characterization of microsatellite markers for Brachiaria brizantha (Hochst. ex A. Rich.) Stap. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9839-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Mudge SR, Osabe K, Casu RE, Bonnett GD, Manners JM, Birch RG. Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploid crop species. PLANTA 2009; 229:549-58. [PMID: 19011894 DOI: 10.1007/s00425-008-0852-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 10/24/2008] [Indexed: 05/25/2023]
Abstract
Sugarcane is a crop of great interest for engineering of sustainable biomaterials and biofuel production. Isolated sugarcane promoters have generally not maintained the expected patterns of reporter transgene expression. This could arise from defective promoters on redundant alleles in the highly polyploid genome, or from efficient transgene silencing. To resolve this question we undertook detailed analysis of a sugarcane gene that combines a simple pattern in genomic Southern hybridization analysis with potentially useful, sink-specific, expression. Sequence analysis indicates that this gene encodes a member of the SHAQYF subfamily of MYB transcription factors. At least eight alleles were revealed by PCR analysis in sugarcane cultivar Q117 and a similar level of heterozygosity was seen in BAC clones from cultivar Q200. Eight distinct promoter sequences were isolated from Q117, of which at least three are associated with expressed alleles. All of the isolated promoter variants were tested for ability to drive reporter gene expression in sugarcane. Most were functional soon after transfer, but none drove reporter activity in mature stems of regenerated plants. These results show that the ineffectiveness of previously tested sugarcane promoters is not simply due to the isolation of non-functional promoter copies from the polyploid genome. If the unpredictable onset of silencing observed in most other plant species is associated with developmental polyploidy, approaches that avoid efficient transgene silencing in polyploid sugarcane are likely to have much wider utility in molecular improvement.
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Affiliation(s)
- Stephen R Mudge
- Botany Department, School of Integrative Biology, The University of Queensland, Brisbane, 4072, Australia.
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45
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Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AA, Souza AP. Characterization of new polymorphic functional markers for sugarcane. Genome 2009; 52:191-209. [DOI: 10.1139/g08-105] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarcane ( Saccharum spp.) varieties. A high proportion (65.5%) of the above EST–SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST–SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST–SSRs were found to be functional, showing homology to known genes. As the EST–SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST–SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.
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Affiliation(s)
- K. M. Oliveira
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - L. R. Pinto
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - T. G. Marconi
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - M. Mollinari
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - E. C. Ulian
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - S. M. Chabregas
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - M. C. Falco
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - W. Burnquist
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - A. A.F. Garcia
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
| | - A. P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) – Universidade Estadual de Campinas (UNICAMP), Departamento de Genética e Evolução, Instituto de Biologia, Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas-SP, Brasil
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana – IAC/Apta, Anel Viário Contorno Sul, Km 321, CP 206, CEP 14.001-970, Ribeirão Preto-SP, Brasil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, CEP 13400-970, Piracicaba-SP, Brasil
- Centro de Tecnologia Canavieira – CTC, Caixa Postal 162, 13400-970, Piracicaba, São Paulo, Brasil
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Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:327-38. [PMID: 18946655 DOI: 10.1007/s00122-008-0902-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Accepted: 09/20/2008] [Indexed: 05/24/2023]
Abstract
Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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47
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Angelici CM, Hoshino AA, Nóbile PM, Palmieri DA, Valls JFM, Gimenes MA, Lopes CR. Genetic diversity in section Rhizomatosae of the genus Arachis (Fabaceae) based on microsatellite markers. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000100016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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McIntyre CL, Casu RE, Drenth J, Knight D, Whan VA, Croft BJ, Jordan DR, Manners JM. Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance. Genome 2007; 48:391-400. [PMID: 16121236 DOI: 10.1139/g05-006] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.
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Affiliation(s)
- C L McIntyre
- CSIRO Plant Industry, Queensland Bioscience Precinct, Brisbane, Australia.
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49
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Bai SL, Zhong X, Ma L, Zheng W, Fan LM, Wei N, Deng XW. A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:354-66. [PMID: 17156412 DOI: 10.1111/j.1365-313x.2006.02951.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here we report the adaptation and optimization of an efficient, accurate and inexpensive assay that employs custom-designed silicon-based optical thin-film biosensor chips to detect unique transgenes in genetically modified (GM) crops and SNP markers in model plant genomes. Briefly, aldehyde-attached sequence-specific single-stranded oligonucleotide probes are arrayed and covalently attached to a hydrazine-derivatized biosensor chip surface. Unique DNA sequences (or genes) are detected by hybridizing biotinylated PCR amplicons of the DNA sequences to probes on the chip surface. In the SNP assay, target sequences (PCR amplicons) are hybridized in the presence of a mixture of biotinylated detector probes and a thermostable DNA ligase. Only perfect matches between the probe and target sequences, but not those with even a single nucleotide mismatch, can be covalently fixed on the chip surface. In both cases, the presence of specific target sequences is signified by a color change on the chip surface (gold to blue/purple) after brief incubation with an anti-biotin IgG horseradish peroxidase (HRP) to generate a precipitable product from an HRP substrate. Highly sensitive and accurate identification of PCR targets can be completed within 30 min. This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low to high throughput and very economical. This technology can be customized for any nucleotide sequence-based identification assay and widely applied in crop breeding, trait mapping, and other work requiring positive detection of specific nucleotide sequences.
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Affiliation(s)
- Su-Lan Bai
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, and The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Hokanson K, Smith M, Connor A, Luby J, Hancock JF. Relationships among subspecies of New World octoploid strawberry species, Fragaria virginiana and Fragaria chiloensis, based on simple sequence repeat marker analysis. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Simple sequence repeat (SSR) markers, developed from Fragaria ×ananassa Duchesne ex Rozier ‘Earliglow’, were used to assess diversity among all of the proposed taxa of Fragaria virginiana Mill. and Fragaria chiloensis (L.) Mill. to facilitate strawberry germplasm utilization and conservation and to help resolve taxonomic relationships. DNA was obtained from 111 individuals representing F. chiloensis subsp. pacifica Staudt, F. chiloensis subsp. lucida (E. Vilm. ex Gray) Staudt, F. virginiana subsp. virginiana Mill., F. virginiana subsp. glauca (S. Watson) Staudt, F. virginiana subsp. grayana (Vilm. ex J. Gay) Staudt, and F. virginiana subsp. platypetala (Rydb.) Staudt from North America, F. chiloensis subsp. chiloensis f. chiloensis and F. chiloensis subsp. chiloensis f. patagonica from South America, F. chiloensis subsp. s andwicensis (Decne.) Staudt from Hawaii, as well as F. ×ananassa subsp. cuneifolia (Nutt ex Howell), and F. ×ananassa subsp. ananassa . A total of 108 bands were scored among all accessions using the five SSR primer pairs, for a mean of 21.6 bands per primer pair with 3–8 bands in individual accessions. Cluster analysis and principal coordinate analysis using Jaccard similarity coefficients based on presence or absence of bands supported the separation of F. virginiana and F. chiloensis as distinct species. The various F. virginiana subspecies were not distinguishable. The two South American forms of F. chiloensis subsp. chiloensis are very similar to each other and distinct from the North American subspecies. The F. chiloensis subsp. sandwicensis accessions were distinct from other taxonomic classes. The F. ×ananassa cultivars clustered most closely with the South American F. chiloensis supporting the origin of F. ×ananassa primarily from South American rather than North American F. chiloensis. While the North and South American F. chiloensis subspecies should remain separated based on their molecular distinction, consideration should be given to classifying F. chiloensis subsp. pacifica and subsp. lucida as different forma of a single North American F. chiloensis subspecies, rather than as separate subspecies. This is similar to the current classification of the two South American forma of F. chiloensis subsp. chiloensis (L.) Mill. Similarly, the F. virginiana subspecies should be reclassified as forms of a single subspecies, F. virginiana subsp. virginiana, rather than separate subspecies.
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Affiliation(s)
- K.E. Hokanson
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - M.J. Smith
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - A.M. Connor
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - J.J. Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - James F. Hancock
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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