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Abstract
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
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Affiliation(s)
- Atul Grover
- a Biotechnology Division , Defence Institute of Bio Energy Research , Goraparao, P.O. Arjunpur , Haldwani , Uttarakhand , India and
| | - P C Sharma
- b University School of Biotechnology, Guru Gobind Singh Indraprastha University , Dwarka Sec. 16C , New Delhi , India
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Grover A, Kumari M, Singh S, Rathode SS, Gupta SM, Pandey P, Gilotra S, Kumar D, Arif M, Ahmed Z. Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:139-42. [PMID: 24554848 PMCID: PMC3925477 DOI: 10.1007/s12298-013-0204-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 05/09/2023]
Abstract
Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in 'nr' database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms "Fatty acid metabolic process" and "Fatty acid biosynthetic process" were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.
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Affiliation(s)
- Atul Grover
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Maya Kumari
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sadhana Singh
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Shivender Singh Rathode
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sanjay Mohan Gupta
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Pankaj Pandey
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sween Gilotra
- />Department of Biotechnology, Indian Institute of Technology, Guwahati, India
| | - Devender Kumar
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Mohommad Arif
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Zakwan Ahmed
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
- />Directorate of Management Services, Defence Research and Development Organization, DRDO Bhawan, New Delhi, 110011 India
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Kumari M, Grover A, Yadav PV, Arif M, Ahmed Z. Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0118-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:970920. [PMID: 23008801 PMCID: PMC3449130 DOI: 10.1155/2012/970920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/11/2012] [Accepted: 07/05/2012] [Indexed: 12/26/2022]
Abstract
Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.
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Roorkiwal M, Sharma PC. Mining functional microsatellites in legume unigenes. Bioinformation 2011; 7:264-70. [PMID: 22125396 PMCID: PMC3218422 DOI: 10.6026/97320630007264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 10/21/2011] [Indexed: 11/23/2022] Open
Abstract
Highly polymorphic and transferable microsatellites (SSRs) are important for comparative genomics, genome analysis and phylogenetic studies. Development of novel species-specific microsatellite markers remains a costly and labor-intensive project. Therefore, interest has been shifted from genomic to genic markers owing to their high inter-species transferability as they are developed from conserved coding regions of the genome. This study concentrates on comparative analysis of genic microsatellites in nine important legume (Arachis hypogaea, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus, Medicago truncatula, Phaseolus vulgaris, Pisum sativum and Vigna unguiculata) and two model plant species (Oryza sativa and Arabidopsis thaliana). Screening of a total of 228090 putative unique sequences spanning 219610522 bp using a microsatellite search tool, MISA, identified 12.18% of the unigenes containing 36248 microsatellite motifs excluding mononucleotide repeats. Frequency of legume unigene-derived SSRs was one SSR in every 6.0 kb of analyzed sequences. The trinucleotide repeats were predominant in all the unigenes with the exception of C. cajan, which showed prevalence of dinucleotide repeats over trinucleotide repeats. Dinucleotide repeats along with trinucleotides counted for more than 90% of the total microsatellites. Among dinucleotide and trinucleotide repeats, AG and AAG motifs, respectively, were the most frequent. Microsatellite positive chickpea unigenes were assigned Gene Ontology (GO) terms to identify the possible role of unigenes in various molecular and biological functions. These unigene based microsatellite markers will prove valuable for recording allelic variance across germplasm collections, gene tagging and searching for putative candidate genes.
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Affiliation(s)
- Manish Roorkiwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi-110075, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru-502324, India
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi-110075, India
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