A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology

Abstract

Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995–2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

“…The findings were in agreement with those in Sesame (Yi and Kim, 2012) and olive species (Mariotti et al, 2010). Majority of the microsatellites in the chloroplast genome are mononucleotide A/T repeats (Wheeler et al, 2014). Likewise, mononucleotides A/T were predominant in both pigeonpea genotypes which is in agreement with results from previous studies in Oryza sativa, V. radiata, Camellia species and Sesame indicum (Rajendrakumar et al, 2007; Tangphatsornruang et al, 2010; Yi and Kim, 2012; Huang et al, 2014).…”

Genetic diversity and structure of wild populations ofCarica papayain Northern Mesoamerica inferred by nuclear microsatellites and chloroplast markers

“…fewer mutations producing homoplasy, could explain the differences in variation between the two cpDNA markers. Discordant patterns may arise from hybridization/introgression between different species (or even between highly differentiated populations in time and space), by homoplasy or even heteroplasmy (reviewed by Wheeler et al, 2014). Yet for papaya, little is known about these processes.…”

Complete Chloroplast Genome Sequence of Musa balbisiana Corroborates Structural Heterogeneity of Inverted Repeats in Wild Progenitors of Cultivated Bananas and Plantains

“…Chloroplast DNA microsatellite markers, either alone or in conjunction with nuclear microsatellites, have been extensively used to investigate the population genetic structure and phylogeography of plants (Ebert and Peakall, 2009). A targeted approach using the species-specific primers has proven to be more productive than the universal primers in identifying polymorphic loci in chloroplast genomes (Wheeler et al, 2014).…”