Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium

Araki, Naoyuki; Masuzaki, Shin-ichi; Tsukazaki, Hikaru; Yaguchi, Shigenori; Wako, Tadayuki; Tashiro, Yosuke; Yamauchi, Naoki; Shigyo, Masayoshi

doi:10.1007/s10681-009-0087-1

Cited by 23 publications

(10 citation statements)

References 25 publications

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“…Genomic SSRs require optimization of PCR conditions and amplify rarely in onion and allied Alliums McCallum et al 2008;Santos et al 2010). In contrast, Araki et al (2010) reported their amplification but it was in bulb onion and closely related species of section Cepa and Phyllodon only. EST-SSR primer set revealed an average of 3.2 amplicons (range, 1-7 alleles) and is equal to the average (3.6) reported by McCallum et al (2008).…”

Section: Discussionmentioning

confidence: 99%

“…Fischer and Bachmann (2000) were the first to develop and use genomic microsatellite primers in onion and allied species followed by development of expressed sequence tag (EST) derived microsatellites (Kuhl et al 2004;Martin et al 2005) and their utilisation for mapping (McCallum et al 2006) and cultivar discrimination McCallum et al 2008). Microsatellites have also been identified and characterised in Allium fistulosum L. (Song et al 2004;Tsukazaki et al 2007), garlic (Kim et al 2009) and tested for their applicability in onion and related wild species (Araki et al 2010). Despite so many reports, molecular marker application and diversity assessment in Indian bulb onions is still in its nascent stage.…”

Section: Introductionmentioning

confidence: 99%

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Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.

Khar

Lawande

Negi

2010

Genet Resour Crop Evol

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This paper deals with the diversity assessment of tropical Indian onion and cross amplification of genomic and EST-SSR markers in distantly related native wild species. Out of 60 SSRs, 10% genomic SSRs were able to amplify as compared to EST-SSR where 53.3% primers were able to reveal amplicons. Clustering revealed five groups and indigenous short day onion formed separate cluster from the exotic short day and long day onions. A. roylei accessions exhibited a dissimilarity index of 35.5% between themselves whereas 'Pran' and A. 9 proliferum grouped together at a genetic distance of 0.4. A. fistulosum accessions formed a tight cluster and distantly related wild species A. carolinianum, A. chinense and A. hookeri formed neutral nodes. Present results are important to aid in analyzing the diversity present in short day onion and its utilization in breeding programs. Further, this is the first time that three accessions of A. roylei Stearn were used and rare alleles amplified in wild species will aid in detecting population structure and molecular marker aided selection for interspecific hybrid development.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.

Khar

Lawande

Negi

2010

Genet Resour Crop Evol

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“…Lee et al (2011) tested the transferability of 50 SSR markers of A. sativum in five Allium species, obtaining the highest transferability (73%) in A. ampeloprasum L. var porrum and the lowest (47.6%) in A. altaicum. Araki et al (2010) using 29 SSRs, derived from bulb onions, found a transferability rate ranging from 73.3% to 93.3% in six Allium species. Tsukazaki et al (2008) cross-amplified bulb onion EST-SSRs in bunching onions (A. fistulosum L.) with a value of 75.1% and Khar et al (2011) reported that the transferability of EST-SSR markers developed from A. cepa in the five Allium species achieved a ratio of 53.5%.…”

Section: Microsatellite Analysismentioning

confidence: 99%

Assessing the genetic diversity of Spanish Allium cepa landraces for onion breeding using microsatellite markers

Giménez

Arnedo-Andrés

Garcés-Claver

2014

Scientia Horticulturae

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“…The high level of transferability of SSR markers among three Rubus species means that they have a close genetic relationship with each other (Ipek et al 2009;Lee et al 2015). Similarly, high rates of transferability of SSR markers were reported in pine (94.2% between Pinus taeda and Pinus radiata), buckwheat (97.1% between Fagopyrum esculentum and Fagopyrum homotropicum), and onion (93.5% between Allium fistulosum and Allium altaicum) (Araki et al 2010;Chagné et al 2004;Ma et al 2009). …”

Section: Discussionmentioning

confidence: 96%

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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Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium

Cited by 23 publications

References 25 publications

Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.

Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.

Assessing the genetic diversity of Spanish Allium cepa landraces for onion breeding using microsatellite markers

Study of Transferability of Rubus Microsatellite Markers to Hybrid Boysenberry

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