Development and validation of genic-SSR markers in sesame by RNA-seq

Zhang, Haiyang; Wei, Libin; Miao, Hongmei; Zhang, Tide; Wang, Cuiying

doi:10.1186/1471-2164-13-316

Cited by 128 publications

(124 citation statements)

References 45 publications

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“…In this study, dinucleotide SSRs were the most abundant (36 %), which is in accordance with results reported for sesame (Zhang et al, 2012) and some Rosaceae species (Jung et al, 2005). However, in most other fruit species and crop plants, trinucleotide repeats have been observed at the highest frequency (Jian et al, 2012;Liu et al, 2013).…”

Section: Discussionsupporting

confidence: 91%

Identification and validation of novel EST-SSR markers in olives

Arbeiter

Hladnik

Jakše

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri-(33 %) and hexa-(21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation.

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Section: Discussionsupporting

confidence: 91%

Identification and validation of novel EST-SSR markers in olives

Arbeiter

Hladnik

Jakše

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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“…The weak correlation coefficient for the two clustering matrices by a Mantel test showed an insignificant correlation between phenotypic and molecular marker information. Zhang et al (2012) concluded that molecular measures of genetic diversity may not fully explain quantitative genetic variability. Therefore, the combination of phenotypic and molecular based analysis in genetic diversity assessment of the sesame appears to be momentous in developing any breeding program.…”

Section: Discussionmentioning

confidence: 99%

Morphological and genetic diversity assessment of sesame (Sesamum indicum L.) accessions differing in origin

Pandey

Das

Rai

et al. 2015

Physiol Mol Biol Plants

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Sesame is an important ancient oilseed crop of high medicinal value. In the present study, 37 characters including both quantitative and qualitative traits of sixty genotypes were characterized following IPGRI morphological descriptors for sesame. Multivariate analysis was computed to distinguish the varieties into different groups. Though thirty six microsatellite markers including genomic and Est-SSR markers were initially selected, but, finally, the accessions were genotyped by eight polymorphic primers. Altogether, 27 alleles were detected among the 60 genotypes, with an average of 3.37 alleles per locus. The number of alleles ranged from 2 to 6 alleles. From data of microsatellite markers, dissimilarity coefficients between varieties were computed following Jaccard's coefficient method. Principal co-ordinate analysis was used to represent the varieties in bi-directional space. Dendrogram was constructed using NJ method based on dissimilarity matrix. Cluster analysis based on morphological and molecular marker classified sesame genotypes into two major groups. Mantel test showed an insignificant correlation between phenotypic and molecular marker information. The genotypes belonging to the same geographical area did not always occupy the same cluster. The results confirmed that both genetic and phenotypic diversity in a combined way could efficiently evaluate the variation present in different sesame accessions in any breeding program.

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“…As a result, there is often discrepancy among SSR density estimates reported for the same species by different authors. For example, while analyzing the same sequence data, the density of SSRs identified in sesame genic sequences decreased from one SSR per 6.6 to 10.8 kb, when the minimum SSR length was increased from 15 to 18 bases (Zhang et al, 2012). The average SSR density of the Arabidopsis thaliana (L.) Heynh.…”

Section: Simple Sequence Repeat Development and Validationmentioning

confidence: 99%

“…The trend also applied for trinucleotide SSRs with a predominance of AT-rich repeats, similar to our findings. Whether or not mononucleotide repeats are included in SSR surveys, all reports on genic SSR development in sesame indicate dinucleotide repeats as the predominant SSR type in coding sequences (Wei et al, 2008;Wei et al, 2011;Zhang et al, 2012;Yepuri et al, 2013;Wu et al, 2014). In addition, AG/CT was consistently found as the predominant motif in sesame genic SSRs.…”

Section: Simple Sequence Repeat Development and Validationmentioning

confidence: 99%

“…Simple sequence repeats are widely used in plant molecular genetic studies because they are hypervariable, reproducible, relatively abundant, and provide extensive genome coverage (Powell et al, 1996). Reports on SSR marker development in sesame are limited and most work involved the development of genic SSRs, either from expressed sequence tag (EST) sequences in public databases (Wei et al, 2008;Yepuri et al, 2013) or transcriptome sequencing (Wei et al, 2011;Zhang et al, 2012;Wu et al, 2014). Fewer authors described genomic SSRs in sesame (Dixit et al, 2005;Spandana et al, 2012;Wei et al, 2014;Surapaneni et al, 2014).…”

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confidence: 99%

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Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame

et al. 2015

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Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is an orphan crop species with most molecular genetic research work done in the last decade. In this study, we used a pyrosequencing approach for the development of genomic simple-sequence repeat (SSR) markers in sesame. Our approach proved successful in identifying 19,816 nonredundant SSRs, 5727 of which were identified in a contig assembly that covers 19.29% of the sesame genome. Mononucleotide repeats were the most abundant SSR type identified in the sesame genome (48.5% of all SSRs), followed by dinucleotide SSRs (45.0%). Adenine-thymine-rich motifs were predominant, representing 81.7, 51.7, 66.5, and 22.1% of the mononucleotide, dinucleotide, trinucleotide, and tetranucleotide SSRs, respectively. As a result of this work, we introduce 933 experimentally validated sesame specific markers, 849 of which are also applicable in Sesamum mulayanum (syn. Sesamum orientale var. malabaricum Nar.), the wild progenitor of cultivated sesame. Using a subset of the newly identified SSR markers, we analyzed molecular genetic diversity and population structure of a collection of world accessions. Results of the two analyses almost overlapped and suggested correlation between genetic similarity and geographical proximity. Indeed, a pattern of gene flow among sesame diversity centers was apparent, with levels of variability in some regions similar to that seen in the domestication origin of the crop. Taken together with the high rate of genomic marker transferability detected between S. indicum and S. mulayanum, our results represent additional molecular genetic evidence for designating the two taxa as cultivated and wild forms of the same species.

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Development and validation of genic-SSR markers in sesame by RNA-seq

Cited by 128 publications

References 45 publications

Identification and validation of novel EST-SSR markers in olives

Identification and validation of novel EST-SSR markers in olives

Morphological and genetic diversity assessment of sesame (Sesamum indicum L.) accessions differing in origin

Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame

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