In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4–5 years) made in plant genetics using SSR markers.

Microsatellite markers: an overview of the recent progress in plants

Plant responses to atmospheric CO2 enrichment with emphasis on roots and the rhizosphere.

The pophelper r package and web app are software tools to aid in population structure analyses. They can be used for the analyses and visualization of output generated from population assignment programs such as admixture, structure and tess. Some of the functions include parsing output run files to tabulate data, estimating K using the Evanno method, generating files for clumpp and functionality to create barplots. These functions can be streamlined into standard r analysis workflows. The latest version of the package is available on github (https://github.com/royfrancis/pophelper). An interactive web version of the pophelper package is available which covers the same functionalities as the r package version with features such as interactive plots, cluster alignment during plotting, sorting individuals and ordering of population groups. The interactive version is available at http://pophelper.com/.

pophelper: an R package and web app to analyse and visualize population structure.

Each perennial woody plant is a highly integrated system of competing carbohydrate sinks (utilization sites). Internal competition for carbohydrates is shown by changes in rates of carbohydrate movement from sources to sinks and reversals in direction of carbohydrate transport as the relative sink strengths of various organs change. Most carbohydrates are produced in foliage leaves but some are synthesized in cotyledons, hypocotyls, buds, twigs, stems, flowers, fruits, and strobili. Although the bulk of the carbohydrate pool moves to sinks through the phloem, some carbohydrates are obtained by sinks from the xylem sap. Sugars are actively accumulated in the phloem and move passively to sinks along a concentration gradient. The dry weight of a mature woody plant represents only a small proportion of the photosynthate it produced. This discrepancy results not only from consumption of plant tissues by herbivores and shedding of plant parts, but also from depletion of carbohydrates by respiration, leaching, exudation, secretion, translocation to other plants through root grafts and mycorrhizae and losses to parasites. Large spatial and temporal variations occur in the use of reserve- and currently produced carbohydrates in metabolism and growth of shoots, stems, roots, and reproductive structures. A portion of the carbohydrate pool is diverted for production of chemicals involved in defense against fungi, herbivores, and competing plants. Woody plants accumulate carbohydrates during periods of excess production and deplete carbohydrates when the rate of utilization exceeds the rate of production. Stored carbohydrates play an important role in metabolism, growth, defense, cold hardiness, and postponement or prevention of plant mortality.

Carbohydrate sources and sinks in woody plants

http://www.bio-nica.info/Biblioteca/Meudt2007AFLPApplicationAnalysis.pdf

Almost forgotten or latest practice? AFLP applications, analyses and advances.

RAPDs, AFLPs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among 32 olive cultivars cultivated in Italy and Spain. SSRs presented a higher level of polymorphism and a greater information content, as assessed by the expected heterozygosity, than AFLPs and RAPDs. The lowest values of expected heterozygosity were obtained for AFLPs, which, nevertheless were the most efficient marker system due to their capacity to reveal the highest number of bands per reaction and because of the high values achieved for a considerable number of indexes. All three techniques discriminated the genotypes very effectively, but only SSRs were able to discriminate the cultivars Frantoio and Cellina. The correlation coefficients of similarity were statistically significant for all three marker systems used but were lower for the SSR data than for RAPDs and AFLPs. For all markers a high similarity in dendrogram topologies was obtained although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect some relationships for most of the cultivars according to their geographic diffusion. AMOVA analysis detected greater genetic differentiation among cultivars within each country than it did between the two countries.

Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive

El cultivo del olivo

Cultivar identification is a primary concern for olive growers, breeders, and scientists. This study was aimed at examining the SSR markers retrieved from the literature and currently used in olive study, in order to select those most effective in characterizing the olive accessions and to make possible the comparison of data obtained by different laboratories. Olive microsatellite profiles were assessed by four independent laboratories, which analyzed 37 pre-selected SSR loci on a set of 21 cultivars. These SSR markers were initially tested for their reproducibility, power of discrimination and number of amplified loci/alleles. Independent segregation was tested for each pair of SSRs in a controlled cross and the allelic error rate was quantified. Some of them were finally selected as the most informative and reliable. Most of the alleles were sequenced and their sizes were determined. Profiles of the reference cultivars and a list of alleles with their sizes obtained by sequencing are reported. Several genetic parameters have been analysed on a larger set of cultivars allowing for a deeper characterization of the selected loci. Results of this study provide a list of recommended markers and protocols for olive genotyping as well as the allelic profile of a set of reference cultivars that would be useful for the establishment of a universal database of olive accessions.

A consensus list of microsatellite markers for olive genotyping

Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigacion y Formacion Agraria "Alameda del Obispo" in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar- specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.

/pdf/polymorphism-and-discrimination-capacity-of-randomly-4uyedec1uh.pdf

Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

Summary
Olive (Olea europaea ssp. europaea) is the most important oil fruit crop in temperate areas, but the origin of the cultivated olive remains unclear. The existence of one or several domestication events in the Mediterranean Basin (MB) is still debated.
We analyzed a dataset of 387 cultivated and wild accessions that were genotyped at 25 simple-sequence repeat (SSR) loci. The sample represented genetic diversity at the geographic extremes of the MB. We inferred relationships among samples and also applied approximate Bayesian computation to estimate the most probable demographic model of our samples.
Cultivated olives clustered into three different gene pools (Q1, Q2 and Q3), corresponding loosely to the west, central and eastern MB, respectively. Q1 consisted primarily of accessions from southern Spain, retained the fingerprint of a genetic bottleneck, and was closely related to accessions from the eastern MB. Q2 showed signs of recent admixture with wild olives and may derive from a local domestication event in the central MB.
Overall our results suggest that admixture shaped olive germplasm and perhaps also local domestication events.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13181

Luis Rallo

Papers

Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive

El cultivo del olivo

A consensus list of microsatellite markers for olive genotyping

Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

Olive domestication and diversification in the Mediterranean Basin