Development of tomato SSR markers from anchored BAC clones of chromosome 12 and their application for genetic diversity analysis and linkage mapping

Geethanjali, S.; Kadirvel, P.; Pena, Rodica; Rao, Eguru Sreenivasa; Wang, Jaw‐Fen

doi:10.1007/s10681-010-0331-8

Cited by 18 publications

(15 citation statements)

References 48 publications

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“…GD analysis is important for collections, conservation, and sustainable utilization of Genbank accessions (Suresh et al 2014). Various types of DNA markers studies have been carried out to estimate the GD and phylogenetic relationship among tomato genotypes (Klein-Lankhorst et al 1991;Kwon et al 2009;Geethanjali et al 2011). Various methods have been used for surveying population structures.…”

Section: Discussionmentioning

confidence: 99%

“…He et al (2003) have identified 2.7 alleles per locus on average among 17 varieties and 2 parental lines of tomatoes. We used diverse tomato genetic resources preserved in the National Agrobiodiversity Center (RDA, Republic of Korea) and applied the 18 SSR markers which revealed high alleles and polymorphism based on the previous studies (Kwon et al 2009;Geethanjali et al 2010;Geethanjali et al 2011). These factors might cause relatively high average NA per locus in this study.…”

Section: Discussionmentioning

confidence: 99%

“…The final concentration of each DNA sample was adjusted to 20 ng/l. For SSR assays, a total of 18 polymorphic SSR markers were selected from SOL Genomics Network (https://solgenomics.net) and those reported previously (Kwon et al 2009;Geethanjali et al 2010;Geethanjali et al 2011). SSR alleles were amplified with fluorescent labelled primers, resolved on ABI Prism 3100 DNA sequencer (Applied Biosystems, Foster City, CA, USA) using GeneScan 3.7 software (Applied Biosystems), and sized precisely using GeneScan 500 ROX (6-carbon-X-rhodamine) molecular size standards (35-500 bp) and Genotyper 3.7 software (Applied Biosystems).…”

Section: Ssr Genotypingmentioning

confidence: 99%

“…Simplesequence repeats (SSRs) are the most frequently used markers for genotyping (Tautz 1989). Several studies have described the use of SSRs to reveal polymorphisms in tomato (He et al 2003;Ohyama et al 2009;Geethanjali et al 2010;Geethanjali et al 2011).…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

Raveendar¹,

Chung²,

Lee³

et al. 2016

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. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The objective of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall FST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Ssr Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

Raveendar¹,

Chung²,

Lee³

et al. 2016

Plant Breed. Biotech.

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show abstract

“…Though the markers were minimum but are highly potential in distinguishing closely related cultivars of tomato [11]. Reported marker density based on in vivo method is relatively less on every chromosome, for example 12 th chromosome has just 37 [12]. For plant variety identification along with degree of admixture, STR is always preferred if they are in multiplex mode (for example, Basmati and non-Basmati rice can be differentiated by 8 plex/ single cocktail based PCR) [13].…”

Section: Introductionmentioning

confidence: 99%

First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification

et al. 2013

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BackgroundThe cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market.DescriptionWe present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor).ConclusionBesides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading to increased tomato productivity in India as well as other parts of the world. In era of IPR the new variety can be identified based on allelic variation among varieties supplementing DUS test and product traceability.

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Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis

et al. 2018

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Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease. In total, 5259 non-synonymous SNPs were found between the two groups. Among them, only 265 SNPs were located in the coding DNA sequences, and the majority of these SNPs were located on chromosomes 6 and 12. The genes that both carry SNP(s) and are near Bwr-6 and Bwr-12 were selected. In particular, four genes in chromosome 12 encode putative leucine-rich repeat (LRR) receptor-like proteins. SNPs within these four genes were used to develop SNP markers, and each SNP marker was validated by a high-resolution melting method. Consequently, one SNP marker, including a functional SNP in a gene, Solyc12g009690.1, could efficiently distinguish tomato varieties resistant to bacterial wilt from susceptible varieties. These results indicate that Solyc12g009690.1, the gene encoding a putative LRR receptor-like protein, might be tightly linked to Bwr-12, and the SNP marker developed in this study will be useful for selection of tomato cultivars resistant to bacterial wilt.

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Development of tomato SSR markers from anchored BAC clones of chromosome 12 and their application for genetic diversity analysis and linkage mapping

Abstract: In this study, we developed a total of 37 simple sequence repeat (

Cited by 18 publications

References 48 publications

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification

Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis

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