Total SSR Research Articles

Development of genomic SSR markers and genetic diversity of Sphaerulina musiva in China

AbstractSphaerulina musiva is an important poplar pathogenic fungus that causes leaf spot and stem canker. SSR markers serve as excellent molecular markers for assessing genetic diversity in fungi. To date, few SSR markers have been developed and applied in S. musiva. In this study, genomic‐SSR markers were developed from the S. musiva genome, and applied to analyse the genetic diversity of S. musiva isolates from Henan province in China. A total of 9923 SSR loci were identified with a relative abundance of 343.15 SSR loci per Mb. Tri‐nucleotide repeats were the most abundant in five types of SSRs, and accounted for 56.82% of the total SSR loci. Twelve genomic‐SSR markers were successfully developed from tri‐nucleotide SSR loci. The number of alleles per locus ranged from 3 to 8 with an average of 4.08 alleles. The polymorphism information content of these loci ranged from 0.428 to 0.770, with an average of 0.553. Based on the SSR markers, a total of 48 haplotypes were identified from 48 S. musiva isolates. Forty‐eight isolates were divided into four main genetic groups at a genetic distance of 0.21. Genetic relationships of the isolates had no obvious correlation with geographic origin. It is the first time to develop genomic SSR markers in S. musiva. The developed SSR markers will be a useful tool to evaluate genetic diversity and population structure of S. musiva.

Analysis on SSR Loci in Transcriptome and Development of EST-SSR Molecular Markers in <i>Lonicera macranthoides</i>

Huizhanmao-rendong ( Lonicera macranthoides ), as a species of original plant of wild honeysuckle flower ( Flos Lonicerae ), the traditional Chinese medicine, is widely distributed in South China and features high medicinal and economic value. In this study, the SSR loci of 74 057 unigenes in the transcriptome of L .  macranthoides  were analyzed by MISA. Among them, 15 587 unigenes contained 20 161 SSR loci, and the frequency of SSR was 21.05%. The types of SSR sites in the transcriptome of L .  macranthoides  were distributed from single nucleotide to six nucleotide repeats. The main repeats were dinucleotide (9 704) and trinucleotide (5 847), accounting for 48.13 % and 29.00 % of the total SSRs, respectively. The main repeat units were AG/CT (6 086), AT/AT (3 071) and A/T (2 826), accounting for 30.79%, 15.23%, and 14.02% of the total SSRs, respectively. There were 4 897 and 3 531 repeats (the numbers of repeats were the most) in 6 and 5 SSR loci, accounting for 24.29 % and 17.51 % of the total SSR number, respectively. By using primer 6.0 software, 17 611 pairs of SSR primers were designed, and 30 pairs of primers were randomly selected for amplification verification. Among them, 14 pairs of amplified bands showed polymorphism, and then the genetic diversity of 6 varieties of L .  macranthoides  was analyzed by using these 14 pairs of primers. The results will provide a scientific basis for species identification, genetic diversity analysis, and molecular marker-assisted breeding of  L .  macranthoides .

Characterization of Sri Lankan maize accessions using SSR markers associated with insect-resistant traits

Maize genetic diversity is utmost to develop new varieties conferred with favorable agronomic traits. Landraces are priceless resources that can serve to strengthen crop breeding programs. Hence, this study aimed to characterize 19 Sri Lankan maize landraces and one elite commercial variety Bhadra using SSR markers linked with insect-resistant traits. Using established procedures, genomic DNA extraction was done from immature maize leaves and PCR was performed utilizing bnlg1017, bnlg339, umc1021, umc1187, bnlg1346, bnlg1588, bnlg1556, umc1178, nc134, umc1688 and umc1045 primers. GenAlex and DARwin software were used for the data analysis. According to the results, a sum of 77 alleles was amplified with the maximum number of observed (13) and effective (11.28) alleles for bnlg1588. The highest gene diversity and PIC values were recorded in bnlg1588 (0.911 and 0.904 respectively), while the lowest was in umc1045 (0.640 and 0.581 respectively). Out of the total SSR primers used, bnlg1588, bnlg339, bnlg1346, and bnlg1017 linked with FAW-resistant traits were found to be more informative based on their genetic diversity parameters. The accessions SEU7, SEU11, SEU16, and SEU20 showed more genetic diversity compared to Bhadra, whereas SEU17 showed the lowest diversity. The dendrogram divided the 20 maize accessions into two main clusters with the mean similarity of 0.752. Similarly, the principle coordinate analysis explained 40.63 % of the genetic variation and grouped the maize accessions into two. Considering the genetic diversity parameters, the accessions SEU6 and SEU7 from cluster I and SEU9, SEU11, SEU16, and SEU20 from cluster II could be utilized for strategic maize breeding programs in Sri Lanka.

Analysis of SSR Information of Flower Transcriptome in Loquat

In order to provide scientific basis for studying the genetic diversity and molecular marker-assisted breeding of loquat, new molecular markers of loquat were developed by analyzing flower transcriptome data. In this study, MIcroSAtellite (MISA) and Blast2GO were used for SSR searching, screening, identification, and analysis of non-redundant Unigenes, and Primer 3 was used for SSR primer design. A search found that 28 617 Unigenes contained 44 622 SSR loci, and the frequency of occurrence of SSR loci was 47.51%, and the total average distribution distance was 4.87 kb. Mononucleotide and dinucleotide repeats were the main repeat types of SSR in the loquat flower transcriptome that the SSR of mononucleotide and dinucleotide repeats accounted for 52.09% and 32.83% of the total SSR, respectively. The dominant repeat motifs were A/T and AG/CT, which accounted for 50.94% and 26.70% of the mononucleotide repeats and dinucleotide respectively, and the 65.79% length of motif was concentrated in 12~20 bp. Gene Ontology (GO) functional classification showed that 28 617 loquat flower transcriptome Unigenes containing SSR loci were enriched in 51 GO terms of the 3 GO categories, and the biological process category involved the most GO terms (21). Primers for 34 301 SSR sequences were successfully designed, with a success rate of 76.87%. It is shown by the analysis that the flower transcriptome SSR loci had high frequency, high distribution density, and high polymorphism potential and could provide abundant repeat types. These could provide scientific basis for studying quantitative trait loci mapping, molecular marker-assisted breeding, genome evolution, genetic diversity analysis.

Development and characterization analysis of potato SSR primers and the amplification research in colored potato materials

<p id="C3">Compared with commonly cultivated potato, colored potato is rich in nutrition, especially in anthocyanins, which is the focus of breeding research in recent years. To date, the number of potato SSR primers developed is limited, especially those related to colored potato. In this study, SSR loci were analyzed using MISA software based on the whole genome. The results were as follows: a total of 218,997 SSR loci were obtained from potato genome with an average of 3.39 kb. Mononucleotide was the main repeat type, accounting for 62.05% of the total SSR, followed by dinucleotide and trinucleotide, accounting for 22.39% and 13.11%, respectively. The repeats of the six nucleotide types ranged from 5 to 746, mainly from 5 to 10, accounting for 60.9% of the total SSRs. A total of 215 motif types were obtained in all detected SSRs. The dominant motifs of the other five nucleotide repeat types were mainly A/T-containing motifs, except for hexanucleotide repeat type. The length of SSR motifs ranged from 12 bp to 20 bp, accounting for 43.19% of all SSRs. A total of 100 SSR primers were designed by Primer 5 software, among which 48 primers were preliminarily screened using parents’ genomic DNA of the colored potato, with an effective amplification rate of 48%. Then, six F₂ individuals were randomly selected for PCR amplification, and 26 primers with clear and stable bands and high polymorphism were finely screened, with the average polymorphism rate of 72.52%. In summary, the number and types of SSR loci in potato genome was abundant and diverse, and the polymorphism was moderate. The developed primers were highly polymorphic, which can be used in the development of SSR markers, genetic diversity analysis, and SSR fingerprint of colored potato, providing a scientific basis for further mining genes related to anthocyanin content.

Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel).

Simple SummaryIn this study, a full-length transcriptome was analyzed with single-molecule real-time (SMRT) sequencing, which was first used to discover simple sequence repeat (SSR) genetic markers from B. dorsalis. Moreover, SSR markers from isoforms were screened for the identification of species diversity. These results could provide molecular biology methods for further population research.Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.

Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae

Background: Comparative study of the complete chloroplast genomes of some species in the Subtribe Asclepiadeae was conducted to evaluate the variations and similarities between the species and to resolve the phylogenetic relationship within the subtribe. P. tomentosa has been used for medicinal uses in Saudi Arabia, Middle East, Africa and Brazil. It is used often in cosmetics and tanning industries, although it’s very well utilized as a traditional medicine in many civilizations.Methods: The genomes were compared using Mvista Bioinformatics tools to evaluate the inverted repeats (IR), large single copy (LSC) and small single copy (SSC) regions and also the border junctions were visualized with IR scope to express the expansion and contraction of the circular genome structure. While SSR markers were determined using the Reputer program, the genome map was done using OGDRAW (OrganellarGenomeDRAW).Result: Observed variations of the Mvista alignments is mainly at the coding regions of the sequences, while IR borders were varied at the SSC region of A. nivea genome; with ycf1 and rps19 due to evolutionary events. The genome sizes of C. procera are 166,010 bp, P. tomentosa 164,213bp, A. nivea 161,592 bp and C. wilfordii 161,180 bp. GC contents of A. nivea, C. wilfordii and P. tomentosa are 38% respectively; while C. procera is the least with 37%.; total SSR markers as well as the circular genome map were presented in this study.

Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane

Sugarcane generates the vast majority of sugar consumed worldwide. The large-scale development of EST-SSR markers are crucial for the analysis of genetic mechanisms important in agronomic traits of sugarcane. In this study, based on published 107,598 full-length expressed sequence tags (ESTs) from 22 sugarcane cultivars, we identified a total of 46,043 loci of simple repeat sequences. The SSRs with di-nucleotide (8175 loci) and tri-nucleotide (10,709 loci) repeat motifs account for 40.96% (18,884) of the total SSR loci, with (AT/TA)n and (ACA/TGT)n being found to be the major repeat motifs. A total of 1070 pairs of primers were randomly selected to verify using 12 accessions including S. officinarum, S. robustum, S. spontaneum and cultivars. The results showed that 847 (79.1%) were successfully amplified, of which 349 (32.60%) were polymorphic in the analyzed samples. The polymorphic rates of EST-SSR markers with di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide and hexa-nucleotide repeat motifs were 36.82% (81), 49.40% (165), 43.04% (34), 30.19% (32) and 34.26% (37), respectively. Among them, the EST-SSRs comprising five types of repeat motifs (CA)n, (CCG)n, (CCGC)n, (CGGCG)n and (GCCGGC)n presented high degrees of polymorphism. Finally, 20 EST-SSR markers with polymorphisms were selected to perform a cluster analysis of 48 accessions from Saccharum and Erianthus genera. These results demonstrated that Chinese sugarcane cultivars from group IV (25/39) had a lower genetic divergence than cultivars from other countries and EST-SSR markers can also be used in determining the genetic diversity of Erianthus genus. This set of EST-SSR markers is an important molecular resource for analyzing genetic diversity, molecular fingerprinting and genetic mapping.

Development and application of SSR loci in monoploid reference genome of sugarcane cultivar

<p indent="0mm">Sugarcane is one of the most important sugar crops in the world. However, it is difficult to develop SSR on a large scale since the genome of cultivar has not been sequenced, which limits the genetic improvement of sugarcane. In this study, a template of monoploid sugarcane genome was assembled using a set of 4660 BAC library sequences (with a cumulative length of 382 Mb, predicting 25,316 genes) from cultivar ‘R570’. SSR loci were identified by using MISA (Microsatellite identification tool) software. The distribution characteristics of the monoploid genome ‘R570’ was comprehensively analyzed by comparing with the SSR loci of four Gramineae plants (<italic>Sorghum bicolor</italic>,<italic> Zea mays</italic>,<italic> Oyrza sativa</italic>, and <italic>Brachypodium distachyon</italic>). Fifty pairs of primers with TG and AG repeat motifs were designed to verify the amplification efficiency and polymorphism by PCR amplification in four <italic>Saccharum</italic> clones (R570, ROC1, LA purple, and SES208) and twenty four core parents of sugarcane. A total of 27,241 SSR loci were identified, with an average of 6.29 SSR loci per BAC clone and an average density of 71.33 SSR Mb^–1 which was much lower than that of sorghum (350.00 SSR Mb^–1). The mono-nucleotide (11,079) and tri-nucleotide repeat motifs (6447) accounted for 64.33% of the total SSR loci. The number and proportion of tri-nucleotide repeat motifs were the largest in the four Gramineae plants. In addition, A/T (accounting for 84.8%) motif had the highest proportion and C/G (accounting for 15.2%) motif the lowest proportion in the mono-nucleotide repeat motifs and TGT/ACA (accounting for 16.04%) motif had the highest proportion in the trinucleotide repeat motifs. In general, the genomes in Gramineae plants are rich in A/T repeat motifs. In the polymorphism validation of 50 pairs of primers (41 pairs of TG motif and 9 pairs of AG motif), 45 pairs of primers (90%) were found to be able to amplify successfully, of which 35 (70%) were polymorphic in 4 sugarcane clones. Furthermore, 20 pairs of polymorphic SSR primers were used to detect 24 core parents of sugarcane, a total of 95 alleles were amplified with an average of 4.75 alleles per primer, verifying the application feasibility of these primers for the genetic diversity analysis in sugarcane. The development of SSR markers from the monoploid genome of cultivars ‘R570’ not only enriches the number of SSR markers available in sugarcane genetic analysis, but also facilitates the genetic diversity analysis of sugarcane population and the genetic mechanism dissection of important agronomic traits, which provides a foundation for the in-depth research of molecular breeding in sugarcane.

Identification, distribution and comparative analysis of microsatellites in the chloroplast genome of Oryza species

Chloroplast genome is important because of its maternally inherited, conserved within species and stable in structure. This allows elucidation of inter-specific comparison, identification and establishment of evolutionary relationship among different species. Different classes of DNA elements were present in chloroplast genome of Oryza species, among them chloroplast microsatellites were supposed to be highly variable. In this study, a total of 102 sequences of chloroplast genome of 23 species of Oryza genus belonging to ten different genome types were downloaded from NCBI nucleotide database. The chloroplast DNA length varied from 134,401bp to 136,133bp. Microsatellite analysis revealed that total SSR number varied from 268 in O. coarctata to 281 in O. granulata. Comparative analysis of repeat type revealed that mononucleotide and trinucleotide were least present, while penta and hexa nucleotide motif were the most common type among all the Oryza species. Frequency analysis of the repeat revealed that T repeat among mono, AT among di, AAT among tri, AATA among tetra, AATTC among penta and AAAGAA among hexa nucleotide repeat was found to be common among most of the Oryza species. Total of five set of SSR markers flanking to penta and hexa nucleotide repeat types were developed which uniquely present among species, namely, O. barthi, O. sativa Japonica, O. cocarctata, O. rhizomatis and O. ridley. Phylogeny based on SSR markers indicate separate evolution of different SSR markers among individual species.

Genetic Stability of Banana Plant Regenerated from Floral Axis Organogenesis Assessed by Newly Developed SSR Markers

Molecular marker is robust to precisely monitor the genetic stability of in vitro -banana plants. This study examined the genetic stability of 8 monthold banana plants of Soka variety derived from floral axis organogenesis using newly developed SSR markers. The results showed that the same qualitative and similar quantitative morphological characters of pseudostem, leaf and fruit were identified between mother plants and culture plants from floral axis regeneration. Both plants types were quite similar in number of tillers, brix percentage, fruit peel/mesocarp thickness and fruit length. Eleven out of 211 good quality of SSR loci showing high homology with important genes were selected for suitable PCR primers and produced unambiguous bands.The number of total bands was 323 for total SSR primers, in range of 20-60 per primer for total individual plants. Most culture plants showed identical with their mother plants, with very minor variation as reflected by genetic similarity coefficient range of 0.9-1.0. A high similar pattern on SSR to support morphological characters of mother plants and culture plants indicated a successful micropropagation using floral axis to encounter off-type clones.The floral axis organogenesis in this study is able to provide sufficient genetic materials of Soka for varietal registration and other applications.

Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers

Common bean (Phaseolus vulgaris L.), besides being an agricultural product that can be consumed as fresh vegetable, is a significant legume widely being planted in both Turkey and world. Because of having different usage areas, it is being considered as a valuable plant for human nutrition, trade and in many respects. In this study, we aimed at genetically characterization of the local and registered common bean genotypes and population structure of genotype groups belong to these common bean genotypes in Turkey. For this purpose, total 102 common bean genotypes including 93 local genotypes from 8 provinces, 7 cultivars and 2 reference cultivars were analyzed by 13 fluorescent SSR markers. As the result of the study, it was determined that the total SSR allele number was 192 and the average allele number was 14.8. While it was found that there were no synonymous genotypes, the highest heterozygosity rate was determined in three loci. Factorial correspondence analysis partially demonstrated substructure among common bean genotype groups. Structure analysis showed the same results as the Nm values and the Fst values. In the study, it was observed that SSR markers could be easily used in the molecular studies of common bean germplasm. The obtained results will be able to be used at the conservation, utilization of local common bean genetic resources and at the marker assisted selection studyings.

Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem artichoke (Helianthus tuberosus L.)

In recent years, Jerusalem artichoke has received widespread attention as a novel source of sugar, biofuel, and animal feed. Currently, only few gDNA-SSRs derived from sunflower were verified in the Jerusalem artichoke; therefore, it is particularly important to develop SSR primer markers that belonged to Jerusalem artichoke resources. Using EST data to develop EST-SSR markers is simple and effective. In order to understand the general characteristics of SSR markers in Jerusalem artichoke EST sequences and accelerate the use of SSR markers in Jerusalem artichoke research. This study used 40,370 sequenced unigene fragments and MISA software to identify SSR loci. The 48 pairs of EST-SSR primers assessed for the identification of 45 varieties of Jerusalem artichoke. Cluster, genetic diversity parameters and AMOVA analysis was conducted using the genetic similarity coefficient, revealing genetic differences between 48 genetic material. A total of 1204 SSR loci were identified with 13 different types of repeats, distributed among 1020 EST sequences, of which trinucleotide repeats were the most common, accounting for 38.21% of the total SSR loci. Among the 44 repeat motifs, AG/CT, AAG/CTT, and ATC/ATG motifs had the highest frequencies, accounting for 22.45, 14.71, and 7.84% of all motifs, respectively. From these sequences, 48 pairs of EST-SSR primers were designed, and 22 primer pairs for loci with high polymorphism were selected to analyze the genetic diversity of 45 Jerusalem artichoke germplasm sources. The results indicated that the variation range of the effective number of alleles for 22 primers ranged between 1.7502 and 4.5660. The Shannon's information index ranged between 0.6200 and 1.6423. The variation range of PIC ranged between 0.3121 and 0.6662 with an average of 0.5184. Cluster analysis was conducted using the genetic similarity coefficient, revealing significant genetic differences between Asian and European genetic material. Cluster analysis revealed a relationship between the genotypes and geographic origins of the Jerusalem artichoke. The results of AMOVA as well as the genetic identity and genetic distance in the Jerusalem artichoke population showed that there presented certain genetic heterogeneity in Jerusalem artichoke genetic structure of 45 samples from seven different geographic populations. The Jerusalem artichoke EST-SSR marker system established in this study provides an effective molecular marker system for future research focused on Jerusalem artichoke genetic diversity and the breeding of new varieties.

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

BackgroundMicrosatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections.ResultsA total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations.ConclusionThe large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2870-4) contains supplementary material, which is available to authorized users.

Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.).

The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars.

Study on quality evaluation of sequence and SSR information in transcriptome of Astragalus membranacus

In this study, 454/Roche GS FLX sequencing technology was used to obtain the data of the Astragalus membranaceus. Four hundred and fifty-four Sequencing System Software was applied to carry out the transcription of the group from scratch. Using MISA tools, 9 893 unigenes were selected for the sequence of the genome of A. membranaceus, and the information of SSR locus was analyzed. According to the result, the average length of reads was 413 bp, about 86% of the reads was involved in the splicing, the length of the N50 was 1 205 bp, the number of unigenes was measured by the whole transcript. 1 729 SSR loci in the A. membranaceus transcriptome were searched, the occurrence frequency of SSR was 9.24%, the frequency of SSR in the whole transcriptome was 13.42%, the average length of SSR was 7.97 kb. One hundred and twenty-seven kinds of core repeat sequences were found, the dominant type was TG/AC type of dinucleotide, it appeared to account for 4.25% of the total SSR locus. The results of the sequence of the transcription of the A. membranaceus transcriptome revealed the overall expression, and a large number of unigenessequence was obtained, and the SSR locus in the genome of the A. membranaceus is high, and the type is diverse, and the polymorphism of the gene is high.

Patterns of SSR variation in bread wheat (Triticum aestivum L.) seeds under ex situ genebank storage and accelerated ageing

Maintaining seed viability and germplasm integrity is a challenging task in conservation of plant genetic resources, as seeds under storage will lose viability and genetic changes will occur. Attempt was made to analyze the patterns of genetic changes in wheat germplasm under ex situ genebank storage and accelerated ageing treatments. A set of 16 naturally aged wheat accessions under ex situ genebank storage since 1994 were sampled. Four recently regenerated wheat accessions were selected, four random seed samples were chosen from each accession, and three of them were exposed to three different accelerated ageing treatments. These 32 seed samples in two germplasm sets displayed a range of germination rates from 4 to 98 %. Thirty-seven microsatellite markers representing 21 wheat chromosomes were applied to screen 12 seeds of each sample and 449 SSR alleles were scored. Large SSR variation was found in each germplasm set. There was 73.1 % of the total SSR variation present among the naturally aged samples and 78.2 % present among the accelerated ageing samples. Several analyses for genetic association consistently revealed no clear genetic separations among samples of high or low germination rates in both germplasm sets. Samples under different accelerated ageing treatments did not show much genetic differentiations from the original sample of each accession. Mantel tests revealed non-significant associations between SSR variability and sample germination rates for both germplasm sets. These findings are useful for understanding seed deterioration under different ageing conditions and suggest that genome-wide SSR variability may not provide sensitive markers for the monitoring of wheat seed viability.

Relationship Between Financial Crisis, Suicide and Social Parameters in Greece

Introduction Suicide constitutes one of the major public health problems worldwide. The aim of this study is to examine the possible correlation of suicide rates in Greece with some social indices during the financial crisis. Material and Methods Our study includes all suicide rates recorded in Greece during the time period 2001-2011 (EL.STAT). We assessed the standardized suicide rates (number of suicide cases per 100.000 inhabitants, SSR). We obtained data from EL.STAT. regarding the following social indices: unemployment, population at-risk-of poverty or social exclusion and material deprivation. Results During the period 2001-2011 a total number of 4.133 cases of suicide were recorded. Male suicides were 3.424 (82.8%) and female suicides were 710 (17.2%). The mean SSR for the period study (2001–2011) was 3.37±0.37/100.000 inhabitants. The mean male SSR was 5.64±0.64/100.000 and the mean female SSR was 1.15±0.22/100.000. Our analysis has clearly demonstrated a positive correlation between unemployment and total SSR (r=0.64, p=0.03), as well as between unemployment and male SSR (r=0.68, p=0.02) for the period 2001-2011. During the period of economic crisis (2008-2011) an even positive correlation between unemployment and male SSR was observed (r=0.96, p=0.03). Yet, during the period of economic crisis a positive correlation between population at risk of poverty or social exclusion and total SSR (r=0.96, p=0.03) as well as between material deprivation and male SSR (r=0.99, p=0.01) was revealed. Conclusions The results of this study show that the effect of economic crisis and recession in Greece on social parameters is evident.

Prediction of F1 progeny variation in tomato (Solanum Lycopersicum L.) from parental divergence assessed by SSR markers

Background: Although the use of heterosis is one of the most significant achievements of agriculture, the genetic mechanisms of this phenomenon still remain unclear. Development of numerous molecular tools stimulated efforts to determine the prognostic criteria for selection of best parental combinations. In result of studying the relationship between heterosis in F1 and genetic divergence of the parents, the prospects of utilizing DNA markers have not been persuasively established due to inconsistent findings. Materials and methods: Molecular-genetic data have been used to predict heterosis in F1 hybrids of tomato. Estimates of the genetic dissimilarity of parents for all pair-wise combinations of testcross (4 × 6) were performed based on patterns of 11 SSR informative markers (PIC 0.28-0.85). The general (GCA) and specific (SCA) combining ability of line, mid-parent heterosis (MPH) and high-parent heterosis (HPH) of F1 were assessed. Relationship between GD, MPH and HPH were calculated by correlation analysis. Result: The level of total SSR divergence of the parental lines was significantly associated with heterosis and SCA (sij) for fruit weight and fruit number per plant. Notably, the highest values of MPH and HPH were obtained in the most divergent pair-wise combinations. Lowest negative values of heterosis were observed in the F1 progeny from the least divergent lines. But the main group of F1 progeny demonstrates wide variation of heterosis due to SSR GD have low prognostic potential. Conclusion: Estimation of GDs may be useful for predicting promising combinations, but has limitations, since only a part of F1 heterotic advantage may be explained by the genetic divergence of its parents. Probably for understanding and manipulating heterosis the genetic divergence must be dissected to select “positive” markers, i. e. those that allow identifying the part of heterogeneity associated with the expression of heterosis in F1.

Genome‐Wide Reduction of Genetic Diversity in Wheat Breeding

ABSTRACTPublic concerns about crop uniformity introduced by modern plant breeding and genetic vulnerability to biotic and abiotic stresses have been one of the major forces driving long‐term efforts in plant germplasm conservation for future food security. However, such concerns have gained little empirical support, as recent molecular diversity analyses of improved crop gene pools did not reveal much reduction from early to recent breeding efforts. We conducted a genome‐wide examination of 75 Canadian hard red spring wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 370 simple sequence repeat (or SSR) markers that were widely distributed over all 21 wheat chromosomes. A total of 2280 SSR alleles were detected. Allelic reduction occurred in every part of the wheat genome and a majority of the reduced alleles resided in only a few early cultivars. Significant allelic reduction started in the 1930s. Considering 2010 SSR alleles detected in the 20 earliest cultivars, 38% of them were retained, 18% were new, and 44% were lost in the 20 most recent cultivars. The net reduction of the total SSR variation in 20 recent cultivars was 17%. This clear‐cut evidence not only supports the contention that modern plant breeding reduces the genetic diversity of Canadian wheat, but also underlies the need for conserving wheat germplasm and introducing genetic diversity into wheat breeding.