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

Kumari, Maya; Grover, Atul; Yadav, Patade Vikas; Arif, Mohammad; Ahmed, Zakwan

doi:10.1007/s13258-013-0118-0

Cited by 10 publications

(5 citation statements)

References 32 publications

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“…The highest proportion of mononucleotide repeat sequences in Taxodium 'zhongshansa' is in accordance with the results from J. curcas L. (Kumari et al 2013) and wheat (Asadi and Monfared 2014), but in contrast to those from citrus (Chen et al 2006), lily (Du et al 2014), pineapple (Ong et al 2012), and arabidopsis (Cardle et al 2000), in which trinucleotides were identified as the most numerous repeats. A potential explanation for the high ratio of mononucleotide SSR loci in this study was that mononucleotide SSRs would be amplified rapidly after interspecific hybridization (Gao et al 2011).…”

Section: Discussionsupporting

confidence: 79%

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

et al. 2015

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Taxodium 'zhongshansa', an extremely floodtolerant tree species, has been widely planted in eastern China due to its environmental attributes. Although much progress has been made in understanding its physiological response to flooding stress, as well as its rapid propagation and variety selection, little is known regarding its molecular genetics due primarily to a lack of reliable molecular markers. In this paper, 108,692 expressed sequence tags (ESTs) with a total size of 69.3 Mb derived from T. 'zhongshansa' were analyzed. And 10,038 simple sequence repeat (SSR) loci were identified from 8137 SSR-containing EST sequences. The average SSR frequency in the transcriptome was one in 6.90 kb of EST sequences. The most abundant repeat type was mononucleotide (6581, 65.56 %), followed by trinucleotide (2246, 22.37 %) and dinucleotide (1080, 10.76 %). After filtering unqualified SSR loci, loci with mononucleotide repeats and compound SSRs, 1958 EST-SSR loci were selected to design SSR makers. To validate this set of SSR markers, 503 primer pairs were randomly selected to amplify across 12 genomic DNA templates from three Taxodium species. Two hundred fifty-seven (51.09 %) out of 503 primer pairs amplified the expected products, of which 81 and 176 could amplify polymorphic and monomorphic bands, respectively. The functional categorization of EST sequences containing randomly selected markers revealed that 264 (52.49 %) had homology with known proteins. This set of EST-SSR markers will provide a valuable genetic and genomic tool for further genetic research in Taxodium, such as genetic map construction, quantitative trait loci mapping, and marker assisted selection.

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Section: Discussionsupporting

confidence: 79%

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

et al. 2015

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“…In silico identification of SSRs from various sequence resources like genomic sequences, ESTs or unigenes is a low cost and easy method for development of microsatellite markers. The present work itself has been a source of development of twenty four EST SSR markers for Jatropha (Kumari et al 2013), with PIC values 0.024-0.495, demonstrated on a panel of 41 accessions, collected from all over India. Importantly, the designated primers targeting EST SSRs amplified at more than one locus, leading to multiple bands in the 4 % agarose gel analysis.…”

Section: Resultsmentioning

confidence: 99%

“…Another equally important area is to use them as functional molecular markers. A representative set of microsatellite sequences, preferably with length > 30 bp have already been developed into molecular markers for their abilities to discriminate different accessions of Jatropha curcas collected from all over India (Kumari et al 2013). We further aim to use this information alongwith the gene ontology information towards development of trait-specific markers for rapid identification of high yielding genotypes in near future.…”

Section: Future Linesmentioning

confidence: 99%

Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers

Grover

Kumari

Singh

et al. 2013

Physiol Mol Biol Plants

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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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“…Up to now, EST-SSRs have been successfully identified and developed in various plant species, and used for multiple applications including genetic diversity analysis, cultivar identification, construction of high-density genetic linkage maps, markerassisted selection, identification of quantitative trait loci (QTLs), association mapping and molecular breeding (Kumari et al 2013). EST-SSRs, which located in coding region of the genome, demonstrated some valuable advantages such as they can be rapidly found by electronic sorting and have greater transferability between species than genomic SSR, since genic regions are more conserved among related species (Shirasawa et al 2011;Chen et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Development of Est-SSR Markers to Assess Genetic Diversity of Broccoli and Its Related Species

Izzah¹,

Reflinur²,

Yang³

2017

Indones. J. Agric. Sci.

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Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.[Keywords: Broccoli, cauliflower, kohlrabi, EST-SSR markers, genetic diversity] ABSTRAK

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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

Cited by 10 publications

References 32 publications

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers

Development of Est-SSR Markers to Assess Genetic Diversity of Broccoli and Its Related Species

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