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

Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature.

/pdf/extensive-simple-sequence-repeat-genotyping-of-potato-4rvtuctr7k.pdf

Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification

The fingerprinting of 742 potato landraces with 51 simple sequence repeat (SSR, or microsatellite) markers resulted in improving a previously constructed potato genetic identity kit. All SSR marker loci were assayed with a collection of highly diverse landraces of all species of cultivated potato with ploidies ranging from diploid to pentaploid. Loci number, amplification reproducibility, and polymorphic information content were recorded. Out of 148 SSR markers of which 30 are new, we identified 58 new SSR marker locations on at least one of three potato genetic linkage maps. These results permitted the selection of a new potato genetic identity kit based on 24 SSR markers with two per chromosome separated by at least 10 cM, single locus, high polymorphic information content, and high quality of amplicons as determined by clarity and reproducibility. The comparison of a similarity matrix of 742 landraces obtained with the 24 SSR markers of the new kit and with the entire dataset of 51 SSR markers showed a high correlation (r = 0.94) by a Mantel test and even higher correlations (r = 0.99) regarding topological comparisons of major branches of a neighbor joining tree. This new potato genetic identity kit is able to discriminate 93.5% of the 742 landraces compared to 98.8% with 51 SSR markers. In addition, we made a marker-specific set of allele size standards that conveniently and unambiguously provide accurate sizing of all alleles of the 24 SSR markers across laboratories and platforms. The new potato genetic identity kit will be of particular utility to standardize the choice and allele sizing of microsatellites in potato and aid in collaborative projects by allowing cumulative analysis of independently generated data.

/pdf/robust-and-highly-informative-microsatellite-based-genetic-t79xv0ctvk.pdf

Robust and highly informative microsatellite-based genetic identity kit for potato.

Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP(®) and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)-reported for the first time for tetraploid potato-was observed up to approximately 5 cM using r (2) higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities.

https://link.springer.com/content/pdf/10.1007%2Fs00122-010-1379-5.pdf

Population structure and linkage disequilibrium unravelled in tetraploid potato.

Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis × Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of ~13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.

/pdf/analysis-of-13000-unique-citrus-clusters-associated-with-52ibi2rrj5.pdf

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance

Microsatellites, or simple sequence repeats (SSRs) are very useful molecular markers for a number of plant species. They are commonly used in cultivar identification, plant variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Early development of SSRs was hampered by the high cost of library screening and clone sequencing. Currently, large public SSR datasets exist for many crop species, but the number of publicly available, mapped SSRs for potato is relatively low (~100). We have utilized a database mining approach to identify SSR-containing sequences in The Institute For Genomic Research Potato Gene Index database (http://www.tigr.org), focusing on sequences with size polymorphisms present in this dataset. Ninety-four primer pairs flanking SSR sequences were synthesized and used to amplify potato DNA. This study rendered 61 useful SSRs that were located in pre-existing genetic maps, fingerprinted in a set of 30 cultivars from South America, North America, and Europe or a combination thereof. The high proportion of success (65%) of expressed sequence tag-derived SSRs obtained in this work validates the use of transcribed sequences as a source of markers. These markers will be useful for genetic mapping, taxonomic studies, marker-assisted selection, and cultivar identification.

Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.)

Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.

/pdf/genome-wide-analyses-of-aspartic-proteases-on-potato-genome-2yp6phor.pdf

Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress

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Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.)

Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress