A set of EST‐SSRs isolated from peach fruit transcriptome and their transportability across <i>Prunus</i> species

Vendramin, Elisa; Dettori, Maria Teresa; Giovinazzi, J.; Micali, Simona; Quarta, R.; Verde, Ignazio

doi:10.1111/j.1471-8286.2006.01590.x

Cited by 59 publications

(40 citation statements)

References 7 publications

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“…duranensis, A. batizocoi, and A. hypogaea (Huang et al, 2016), as well in Picea abies and Pinus taeda (Ranade et al, 2015). SSR developments in Prunus have continued since 2000 (Yamamoto et al, 2002;Xu et al, 2004;Xie et al, 2006;Vendramin et al, 2007;Chen et al, 2014;Dettor et al, 2015;. The novel 72 EST-SSR loci will be useful in apricot breeding and especially in mapping and anchoring parental maps.…”

Section: Discussionmentioning

confidence: 99%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions ('Stark Early Orange' (SEO), 'Hacıhaliloğlu' (HH), 'Perfection' , 'Iğdır' , 'Roxana' , 'Esen1' , and 'Esen2'), which yielded a total number of transcripts ranging from 30,363 for 'SEO' to 59,751 for 'Iğdır' . The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in the transcript pool and 14,722 di-, tri-tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions, including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri-and tetranucleotide repeats.

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Section: Discussionmentioning

confidence: 99%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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“…The first is that large introns exist within the amplification region, which may make the product much bigger than expected; the second is that the SSR loci and the markers are within transposons or repetitive DNA, resulting in multiple products deviating from the expected bands. Regarding no amplification in any of the 38 accessions for some primers, the reason may be that the forward primer or reverse primer covers the editing site of mRNA or that large introns exist in the genomic DNA (Vendramin et al, 2007).…”

Section: Development Amplification and Characteristics Of The Salt-mentioning

confidence: 99%

Development of EST-SSR markers related to salt tolerance and their application in genetic diversity and evolution analysis in Gossypium

Wang¹,

Zhu²,

Yuán³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Salt stress is becoming one of the major problems in global agriculture with the onset of global warming, an increasing scarcity of fresh water, and improper land irrigation and fertilization practices, which leads to reduction of crop output and even causes crop death. To speed up the exploitation of saline land, it is a good choice to grow plants with a high level of salt tolerance and economic benefits. As the leading fiber crop grown commercially worldwide, cotton is placed in the moderately salt-tolerant group of plant species, and there is promising potential to improve salt tolerance in cultivated cotton. To facilitate the mapping of salt-tolerant quantitative trait loci in cotton so as to serve the aims of salt-tolerant molecular breeding in cotton, it is necessary to develop salt-tolerant molecular markers. The objective of this research was to develop simple sequence repeat (SSR) markers based on cotton salt-tolerant expressed sequence tags. To test the efficacy of these SSR markers, their polymorphism and cross-species transferability were evaluated, and their value was further investigated on the basis of genetic diversity and evolution analysis.

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“…Microsatellites were found in approximately 1 % of olive ESTs. Considerably higher frequencies were reported for other fruit species, including 20 % in citrus fruits , 18 % in peaches (Vendramin et al, 2007) and 11 % in pomegranates (Jian et al, 2012). These differences in frequency and distribution of ESTSSRs can be attributed to the different criteria used to identify SSRs in the database mining, dataset size and database-mining tools (Varshney et al, 2005).…”

Section: Discussionmentioning

confidence: 97%

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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A set of EST‐SSRs isolated from peach fruit transcriptome and their transportability across Prunus species

Cited by 59 publications

References 7 publications

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Development of EST-SSR markers related to salt tolerance and their application in genetic diversity and evolution analysis in Gossypium

Identification and validation of novel EST-SSR markers in olives

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