Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD‐Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next‐generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost‐efficient markers.

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Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross‐amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost‐efficient markers. The loci presented here are a valuable resource for researchers.

Background. Soil salinity is a major menace to plants. Salt tolerant plants have developed different morphological, structural and physiological characteristics, which enable them to survive and reproduce under high salt concentrations. Hypothesis. It was hypothesized that differently adapted ecotypes of T. domingensis may have different structural and biochemical response to various levels of salt stress. Studied species/Data description. Six ecotypes of Typha domingensis Pers. were evaluated for anatomical and biochemical response and to find out the mechanism of adaptation under salt stress. Methods. All the ecotypes of Typha domingensis were acclimatized for a period of six months. Four levels of salinity viz. 0, 100, 200 and 300 mM NaCl were maintained. The plants were carefully collected from the medium to study various anatomical and biochemical characteristics. Results. The most promising anatomical modifications were; reduced leaf thickness in Sheikhupura, Gatwala and Treemu ecotype, increased cell vacuolar volume in Sahianwala and Knotti ecotype, larger metaxylem vessel in Sheikhupura and Gatwala ecotype, aerenchyma formation in all ecotypes and high sclerification in Sahianwala and Knotti ecotype. Accumulation of osmolytes mainly proline and glycinebetaine in Treemu, Sahianwala, Jahlar and Knotti ecotype under different levels of salt stress may be defense mechanism of T. domingensis to prevent severe loss in turgor. Conclusions. The results demonstrate that genetic potential of T. domingensis to grow under salt stress could be used for the purpose of phytoremediation and reclamation of soil salinity.

In Ecuador, there is a progressive loss of the native forest. To mitigate these problems, several reforestation plans have been carried out in the country. To recover the Andean forest, Polylepis racemosa was introduced from Peru, due to its similarity to native species like Polylepis incana. This genus fulfills important ecological functions that help mitigate the effects of local climate change. However, reforestation of introduced species close to natural populations threatens the genetic diversity of Polylepis native forests. In the long term, it can trigger hybridization processes and create problems for ecosystem conservation. This study used geometry morphometric (GM), to differentiate species quickly and economically, using the form of leaves, stomata, flowers, and pollen of P. incana and P. racemosa in three populations: Illinizas Ecological Reserve, Mojanda Lagoons and Cayambe-Coca National Park. To obtain the data, the composite leaves were scanned, the stomata and pollen were photographed with an increase of 400× and on flowers with 100×. 15, 10, 12, and 9 landmarks (LM) were digitized for leaves, stomata, flowers, and pollen, respectively, using ImageJ software. Then, the shape variables and statistical analysis were performed in MorphoJ software. As a result, it was obtained that the discriminant function analysis (DFA) shows that leaves and flowers can be used as indicators to differentiate species from this genus, discarding stomata and pollen. After that, Canonical Variate Analysis (CVA) of leaves and flowers showed that reforested species jointly are separated into two different species; except for the flowers of the population of Mojanda, where there is an intersection of few individuals, which share similar phenotypic characteristics so they can be considered as potentially hybrid individuals. This study generates information on the location of species introduced inside and outside the National System of Protected Areas that threaten the Andean highlands. Finally, GM is an accessible tool for monitoring biodiversity through morphological characteristics and discriminating against species with complex taxonomic problems.

Situación taxonómica de las especies del género Polylepis. Implicancias para los estudios ecológicos, la conservación y la restauración de sus bosques