Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6

Abstract

Simple sequence repeat motifs are abundant in plant genomes and are commonly used molecular markers in plant breeding. In tomato, currently available genetic maps possess a limited number of simple sequence repeat (SSR) markers that are not evenly distributed in the genome. This situation warrants the need for more SSRs in genomic regions lacking adequate markers. The objective of the study was to develop SSR markers pertaining to chromosome 6 from bacterial artificial chromosome (BAC) sequences available at Solanaceae Genomics Network. A total of 54 SSR primer pairs from 17 BAC clones on chromosome 6 were designed and validated. Polymorphism of these loci was evaluated in a panel of 16 genotypes comprising of Solanum lycopersicum and its wild relatives. Genetic diversity analysis based on these markers could distinguish genotypes at species level. Twenty-one SSR markers derived from 13 BAC clones were polymorphic between two closely related tomato accessions, West Virginia 700 and Hawaii 7996 and were mapped using a recombinant inbred line population derived from a cross between these two accessions. The markers were distributed throughout the chromosome spanning a total length of 117.6 cM following the order of the original BAC clones. A major QTL associated with resistance to bacterial wilt was mapped on chromosome 6 at similar location of the reported Bwr-6 locus. These chromosome 6-specific SSR markers developed in this study are useful tools for cultivar identification, genetic diversity analysis and genetic mapping in tomato.

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

“…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.…”

“…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).…”

“…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).…”

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

“…These genotypes represented diverse origins and possessed useful traits such as resistance to biotic and abiotic stresses. More details of the accessions are available in Geethanjali et al (2010). The seeds of these genotypes were obtained from Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center (AVRDC), Taiwan.…”

“…Recently, Ohyama et al (2009) and Shirasawa et al (2010) developed a large number of SSR markers using bacterial artificial chromosome (BAC)-ends, cDNA and EST sequences from genome databases. Geethanjali et al (2010) developed a total of 54 SSR markers from 17 complete BAC clone sequences on chromosome 6 and mapped 21 of them. Currently, a total of 1707 tomato SSR markers have been mapped; 1686 of them in high density linkage map derived from S. lycopersicum 9 S. pennellii cross and 21 of them in the linkage map derived from West Virginia 700 (S. pimpinellifolium) and Hawaii 7996 (S. lycopersicum) cross.…”