Development and characterisation of EST-SSR markers by transcriptome sequencing in taro (Colocasia esculenta (L.) Schoot)

You, Yongning; DuChen, Liu; Liu, Huabo; Zheng, Xianwei; Diao, Youxiang; Huang, Xinfang; Hu, Zhongli

doi:10.1007/s11032-015-0307-4

Cited by 29 publications

(38 citation statements)

References 44 publications

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“…Furthermore, the distribution density of EST-SSRs was one SSR in every 6.98 kb. This value was higher than the frequency reported in the tree peony (1/9.24 kb) and Pinus dabeshanensis (1/23.08 kb) (Xiang et al, 2015), but lower than that in N. sericea (1/ 3.8 kb) (Chen et al, 2015) and taro (1/5.90 kb) (You et al, 2015). Chrysanthemum may have a higher frequency of EST-SSRs, but alternative explanations, such as the size of the data set, SSR search criteria, and database-mining tools also should be considered (Varshney et al, 2005).…”

Section: Discussioncontrasting

confidence: 64%

“…In contrast, CCG/CGG (0.6%) motifs were very rare (see Fig. 1), found mostly in monocots such as maize, barley, and taro (Morgante et al, 2002;Toth et al, 2000;You et al, 2015). The observed rarity of CCG/CGG repeat units has been reported in some dicots, such as the common bean, D. versipellis, S. guianensis, N. sericea, P. dabeshanensis, and the tree peony (Chen et al, 2014(Chen et al, , 2015Ding et al, 2015;Guo et al, 2014;Wu et al, 2014;Xiang et al, 2015).…”

Section: Discussionmentioning

confidence: 89%

“…The most prevalent trinucleotide motif type often differs among species. In chrysanthemum, TCA (10.2%) predominated, unlike those in Dysosma versipellis, S. guianensis, and N. sericea (AAG) (Chen et al, 2015;Ding et al, 2015;Guo et al, 2014); taro (CCG) (You et al, 2015); P. dabeshanensis (AGC) (Xiang et al, 2015); and tree peony (CCA) . In contrast, CCG/CGG (0.6%) motifs were very rare (see Fig.…”

Section: Discussionmentioning

confidence: 99%

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Characterization and Development of EST-SSR Markers from Transcriptome Sequences of Chrysanthemum (Chrysanthemum ×morifolium Ramat.)

Fan¹,

Gao²,

Gao³

et al. 2019

horts

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Simple sequence repeat (SSR) markers are valuable for genetic and breeding applications, but SSR resources for the ornamental genus chrysanthemum (Chrysanthemum ×morifolium Ramat.) are still limited. Expressed sequence tags (ESTs) are sources of SSRs that represent an opportunity to develop SSRs to accelerate molecular breeding in chrysanthemum. In total, 4661 SSR loci were identified from 3823 SSR-containing unigenes in the chrysanthemum transcriptome with an average of one SSR per 6.98 kb. Of these SSR sequences, trinucleotide repeats (30.0%) predominated, followed by dinucleotide repeats (17.9%). In total, 1584 primer pairs were subsequently synthesized. By screening the parents and six individuals of the F1 progeny, 831 (52.5%) valid EST-SSR markers were identified, of which 361 (43.4%) were polymorphic. The annotation of unigenes containing polymorphic SSRs indicated that 330 (93.5%) demonstrated significant homology to other plant protein sequences. Twenty-five polymorphic EST-SSR markers were further selected for transferability analysis and exhibited 93% amplification in six Ajania species and six other Chrysanthemum species. Based on genotyping of the 59 samples, neighbor-joining analysis revealed six phylogenetic groupings, which was confirmed by population structure analysis and principal component analysis (PCA). Phylogenetic relationships among the 59 samples revealed by SSRs were highly consistent with the traditional taxonomic classification of Chrysanthemum and Ajania. The polymorphism information content (PIC) values ranged from 0.29 to 0.86, with a mean of 0.67, indicating high levels of informativeness. This research reveals the SSR distribution characteristics of chrysanthemum and provides a large number of new EST-SSR markers for further genetic diversity studies, genetic mapping, and molecular marker-assisted selection breeding for chrysanthemum.

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Section: Discussioncontrasting

confidence: 64%

Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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Characterization and Development of EST-SSR Markers from Transcriptome Sequences of Chrysanthemum (Chrysanthemum ×morifolium Ramat.)

Fan¹,

Gao²,

Gao³

et al. 2019

horts

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“…Coordinates 1 and 2 represent the 21.58 and 15.02% of the total variance, respectively five of the selected EST-SSRs showed trinucleotide repeated motifs and only one was a tetranucleotide, likely reflecting the distribution of repeat regions among transcribed and repeated DNAs in many other plants (Morgante et al 2002;Varshney et al 2005). The absence of longer repeated patterns within the selected set probably depends on their low frequency (288 long repeats found in the EST collections versus 1450 trinucleotidic patterns) and their low polymorphism level, as already observed in other plant species (Boccacci et al 2015;Long et al 2015;You et al 2015).…”

Section: Discussionmentioning

confidence: 61%

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

Mariotti

Cultrera

Mousavi

et al. 2016

Tree Genetics & Genomes

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Rapid and effective genotyping is an important goal to discriminate among the numerous olive cultivars and their wild related forms. The largely used di-nucleotide simple sequence repeat (SSR) markers show a high level of polymorphism and have strongly contributed to solve many inconsistencies in varietal identity, but many problems related to difficult discrimination of neighboring alleles and low comparability of data among different labs severely reduce their applicability for large-scale screening. The availability of numerous transcriptome libraries, which were developed from different tissues of several olive varieties, has allowed their intensive screening to search for polynucleotide microsatellite regions with long core repeats, potentially polymorphic among varieties. An accurate screening of all these polymorphisms has allowed to select a set of 25 trinucleotide and one tetranucleotide SSRs, showing a good level of discrimination power with a high allele pattern resolution and repeatability. They were preliminarily tested on a group of cultivated varieties then validated on a wider group of cultivated and wild plants, and related species and subspecies, demonstrating a good transferability within the entire Olea taxon. Furthermore, an in silico functional prediction has allowed to assign each transcribed sequence to their gene functions and biological process categories, highlighting their potential application of these new EST-SSRs as functional markers.

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“…With the development of next-generation sequencing (NGS) technologies, we can obtain a large number of EST-SSRs from high-throughput transcriptome data cost-effectively. Recently, numerous EST-SSR markers were mined by transcriptome sequencing in various plants, which were proved to be effective and more conserved compared to non-coding sequences (Wu et al, 2014;Liu et al, 2015;You et al, 2015). Moreover, some important horticultural traits can be directly mapped using EST-SSRs due to their association with coding region (Bouck & Vision, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Supplemental Information 1: Supplemental Table S1 the Detailed Information of Lagerstroemia accessions used in Th

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Crape myrtle is an important ornamental woody plant, due to its long-lasting mid summer bloom and rich color. However, limited molecular markers on this species hinder the breeding and genetic studies. In this work, 8,652 EST-SSRs were identified from crape myrtle transcriptome data. Di-nucleotide repeats (57.1%) were the most abundant type followed by tri-, tetra-, penta-, hexa-nucleotide repeats, with the AG/CT motif occurring most frequently. Of the 1200 synthesized primer pairs, 761 EST-SSRs (63.4%) were successfully amplified and 245 EST-SSRs (20.4%) showed polymorphic. High cross-species transferabilities of these markers were observed except in L. speciosa (26.7%). The polymorphic information content (PIC) for each locus ranged from 0.210 to 0.813 with a mean of 0.589, suggesting a high level of informativeness. Using 30 polymorphic EST-SSRs, structure and cluster analyses roughly divided the 73 accessions into three major groups with some admixtures. Based on the SSR data and clustering analysis, a final core collection (20 accessions) was identified, which captured Na, Ne, I, and PIC value with a retention rate of 92.8%, 113.6%, 110.6% and 109.7%, respectively. Thus, this work contributes to the better understanding of the genetic diversity and germplasm resources conservation in Lagerstroemia species.

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Development and characterisation of EST-SSR markers by transcriptome sequencing in taro (Colocasia esculenta (L.) Schoot)

Cited by 29 publications

References 44 publications

Characterization and Development of EST-SSR Markers from Transcriptome Sequences of Chrysanthemum (Chrysanthemum ×morifolium Ramat.)

Characterization and Development of EST-SSR Markers from Transcriptome Sequences of Chrysanthemum (Chrysanthemum ×morifolium Ramat.)

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

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