Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Woodhead, M.; McCallum, Susan; Smith, Kay; Cardle, Linda; Mazzitelli, Luca; Graham, Julie

doi:10.1007/s11032-008-9198-y

Cited by 47 publications

(46 citation statements)

References 15 publications

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“…In recent years, in silico approaches have been effectively utilized to detect SSR amplifying genic regions (Igarashi et al, 2008;Woodhead et al, 2008). The development of SSR markers following the conventional approach of genomic library construction is time consuming (Zane et al, 2002) and resource intensive (Squirrell et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

Kaur¹,

Sharma²,

Raina³

2015

Turk J Agric For

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Section: Discussionmentioning

confidence: 99%

Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

Kaur¹,

Sharma²,

Raina³

2015

Turk J Agric For

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“…Rubus transcriptome (454) database (Woodhead M, Cardle L, Hedley P, Bayer M and Graham J, personal communication) and the existing Rubus EST database (Woodhead et al 2008) were mined for genes of interest. Primers were designed to these genes using Primer 3 (Rozen and Skaletsky 2000) (Table 5).…”

Section: Candidate Gene Identification and Genotypingmentioning

confidence: 99%

“…Size polymorphisms were amplified using the Qiagen Multiplex PCR plus kit according to the manufacturer's instructions or as described previously Woodhead et al 2010), and analysed on the ABI 3730 capillary sequencer (Applied Biosystems, Foster City, CA, USA) using ROX500 (Applied Biosystems) as an internal size standard. Single nucleotide polymorphisms (SNPs) were identified and mapped either by Sanger sequencing or by Pyrosequencing as previously described Woodhead et al 2008Woodhead et al , 2010.…”

Section: Candidate Gene Identification and Genotypingmentioning

confidence: 99%

Environmental and seasonal influences on red raspberry flavour volatiles and identification of quantitative trait loci (QTL) and candidate genes

et al. 2012

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Raspberry volatiles are important for perceptions of sensory quality, mould resistance and some have nutraceutical activities. Twelve raspberry character volatiles were quantified, 11 of them in fruit from two seasons, from plants from the Glen Moy 9 Latham mapping population growing in both open field and under cover (polytunnels). Effects of season and environment were examined for their impact on the content of a-ionone, a-ionol, b-ionone, b-damascenone, linalool, geraniol, benzyl alcohol, (Z)-3-hexenol, acetoin, acetic and hexanoic acids, whilst raspberry ketone was measured in one season. A significant variation was observed in fruit volatiles in all progeny between seasons and method of cultivation. Quantitative trait loci were determined and mapped to six of the seven linkage groups, as were candidate genes in the volatiles pathways.

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“…These SSR markers were selected from previous works. Among those, 53 SSR markers were developed from a blackberry and red raspberry genomic library, and 50 SSR markers were derived from a blackberry and red raspberry EST library (Graham et al 2004;Lewers et al 2008;Castillo et al 2010;Castro et al 2013;Woodhead et al 2008). All primer pairs amplified a product in each of the 10 boysenberry genotypes that showed 100% transferability in boysenberry.…”

Section: Ssr Marker Selectionmentioning

confidence: 99%

“…DNA markers could be a useful tool for cultivar identification and for the assessment of genetic diversity in breeding programs. In red raspberry, highly polymorphic and co-dominant simple sequence repeat (SSR) markers have been developed from genomic and cDNA libraries (Graham et al 2002;Graham et al 2004;Woodhead et al 2008). Castillo et al (2010) also developed SSR markers from genomic libraries of red raspberry and blackberry.…”

Section: Introductionmentioning

confidence: 99%

Study of Transferability of Rubus Microsatellite Markers to Hybrid Boysenberry

Ryu

Kim

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Boysenberry, a Rubus hybrid between loganberry and a trailing blackberry, possesses distinctive polyphenol compounds, which have demonstrated positive biological effects on human health. Several new boysenberry genotypes have recently been developed from mutation breeding technology. In this study, a total of 103 SSR markers developed from expressed sequence tag (EST) and genomic libraries in blackberry and red raspberry were tested for cross-amplifications in 10 boysenberry genotypes. All primer pairs successfully produced amplification products, ranging from 1 to 4 loci per primer. Eleven polymorphic SSR markers (RH_MEa0007aB01, RH_MEa12cE03, RH_MEa14bF07, RH_MEa15aD04, RH_MEa13cF08, ERubLR_SQ01_N03, ERubLR_ SQ053_H01, ERubLR_SQ191_A05, RubfruitG7, Rubusr43a, and RiM019) were detected among boysenberry genotypes, while polymorphic loci were not detected in 92 markers. Polymorphism information content (PIC) and genetic diversity (GD) values ranged from 0.160 to 0.580 and from 180 to 0.640, with average values of 0.359 and 0.407, respectively, in the 11 polymorphic markers. According to a cluster analysis, all the mutant boysenberry genotypes can be classified into one category. Although the level of genetic diversity revealed by SSR markers in 10 boysenberry genotypes was low, these SSR markers will be useful for future genetic diversity, cultivar identification, QTL mapping, and gene cloning studies in boysenberry.

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Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Cited by 47 publications

References 15 publications

Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

Environmental and seasonal influences on red raspberry flavour volatiles and identification of quantitative trait loci (QTL) and candidate genes

Study of Transferability of Rubus Microsatellite Markers to Hybrid Boysenberry

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