Microsatellite Simple Sequence Repeat Research Articles

Microsatellite Markers and Genetic Diversity Analysis in Grape (Vitis vinifera L)

Abstract Grape (Vitis vinifera L), commonly cultivated in India, shows a wide range of ripening periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this study was to fingerprint these accessions and to construct a molecular database including the cultivars commonly grown in India. A total of 42 genotypes were analyzed using seven microsatellite simple sequence repeat (SSR) markers and their main morphological and agronomic characteristics were com-pared. A total of 45 alleles in all 42 genotypes were obtained with 7 primers with an average number of 6.4 alleles per locus. The dis-similarity matrix showed that a maximum of 110 units was obtained between the genotypes “Convent Large Black” and “Arka Hans,” while a minimum dissimilarity if 37 units were obtained between the genotypes “Anab-e-Shahi” and “Dilkhush.” In the dendrogram the microsatellite segregated the genotypes into two clusters (A and B) at 476 units with two subclusters each. The sub-clusters grouped genotypes predominantly as A1 with seeded fruits, A2 with seedless fruits, B1 with pigmented and seedless fruits, and B2 with colorless and seeded fruits. The use of seven polymorphicmicrosatellite markers and the level of genetic variability detected within Indian grapevine germplasm suggested that this is a reliable, efficient, and effective marker system that can be used for diversity analysis and subsequently in crop improvement programs

Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding.

This work aims to characterize the genetic diversity of species, early hybrids, and cultivars using microsatellite simple sequence repeat (SSR) markers, as well as analyze and identify the origin of Hemerocallis spp. early hybrids. For this research, samples were collected from different types of daylily species, early hybrids (known or hypothetically first-generation hybrids from Hemerocallis species), foreign, and Lithuanian varieties. An initial screening of SSR primers developed for Hemerocallis citrina was performed, and their suitability for testing other daylily species and hybrids was evaluated. The genetic diversity was assessed with the selected eight-primer set, and molecular SSR profiles were created. Primer SAU00097 is the most informative according to heterozygosity (0.95) and polymorphism information content (PIC) (0.17). The highest heterozygosity was observed in Lithuanian cultivars (0.713), the lowest in species (0.583). Genetic relationships between species show that only fulvous daylilies are separated into a different cluster. The highest variation among genotypes was observed in the species group (18%), while modern cultivars had the slightest variation among genotypes (1%). The putative origin of early hybrids was analyzed using a likelihood heatmap of all genotypes. Results show what species might be used in breeding for early hybrids. Several modern diploid and tetraploid daylily cultivars have triploid species as ancestors.

Metabolite Profiling of Gardenia jasminoides Ellis In Vitro Cultures with Different Levels of Differentiation.

Gardenia jasminoides Ellis is an aromatic and medicinal plant of high economic value. Much research has focused on the phytochemistry and biological activities of Gardenia fruit extracts; however, the potential of the Gardenia plant in vitro cultures used as mass production systems of valuable secondary metabolites has been understudied. This paper presents data on metabolite profiling (GC/MS and HPLC), antioxidant activities (DPPH, TEAC, FRAP, and CUPRAC), and SSR profiles of G. jasminoides plant leaves and in vitro cultures with different levels of differentiation (shoots, callus, and cell suspension). The data show strong correlations (r = 0.9777 to r = 0.9908) between antioxidant activity and the concentrations of chlorogenic acid, salicylic acid, rutin, and hesperidin. Eleven co-dominant microsatellite simple sequence repeats (SSRs) markers were used to evaluate genetic variations (average PIC = 0.738 ± 0.153). All of the investigated Gardenia in vitro cultures showed high genetic variabilities (average Na = 5.636 ± 2.157, average Ne = 3.0 ± 1.095). This is the first report on a study on metabolite profiles, antioxidant activities, and genetic variations of G. jasminoides in vitro cultures with different levels of differentiation.

Assessing new SSR markers for utility and informativeness in genetic studies of brown rust fungi on wheat, triticale, and rye

AbstractThe aim of the present study was to validate new simple‐sequence repeat (SSR) markers and use them to assess genetic variability among 24 isolates of Puccinia triticina collected from wheat (Pt‐wheat) and triticale (Pt‐triticale), and 15 isolates of P. recondita f. sp. secalis (Prs) collected from rye. The Pt and Prs isolates were tested for virulence on a set of 35 Thatcher wheat near‐isogenic lines, eight rye lines with known resistance genes, and 53 triticale cultivars with uncharacterized leaf rust resistance. Molecular genotypes were determined using a newly developed set of 34 SSR microsatellite primer pairs. All SSR markers tested on Pt isolates successfully amplified fragments of appropriate size. When tested on the Prs isolates, 21 out of the 34 Pt SSRs amplified expected fragments. Sixteen of these 21 SSRs were polymorphic, providing for the first time microsatellite markers to study genetic variation in Prs. Based on virulence data, variation among Prs isolates was low, probably due to the small number of rye differential lines available. Much higher variation for virulence was observed within the collection of Pt isolates from wheat and triticale, and two separate groups were established with mixed host origin. Substantial genetic variation was detected among the isolates studied with the SSR markers, assuming two different models of SSR evolution (infinite alleles model and stepwise mutation model). The newly developed set of SSR markers proved their effectiveness in detecting genetic variation and should be useful in further population genetics investigations of the two pathogens.

Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity.

SummaryAn outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site‐associated DNA sequencing (RAD‐seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole‐genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD‐seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.

Pyramiding of bacterial blight resistance genes in rice variety Jyothi (Ptb 39) through marker assisted selection

As in other rice growing locales around the world, in Kerala too, various climatic, edaphic, biological, physical, physiological and socio-economic variables impact the area, production, and productivity of the rice. Bacterial blight (BB), an important biotic stress caused by Xanthomonas oryzae pv. oryzae (Xoo) assumes a huge role in deciding rice profitability in Kerala. PTB 39 (Jyothi) and Mo 16 (Uma) are both elite rice varieties of Kerala, but extremely susceptible to the bacterial blight. Host-plant resistance is advocated as the most effective breeding strategy to combat the BB in contrast to the use of hazardous plant protection chemicals. Breeders have attempted to introgress disease resistance genes (R-genes) into rice cultivars to impart BB resistance. Markerassisted selection (MAS) enables pyramiding multiple R-genes along with rapid background recovery of the recurrent parent, while maintaining the exquisite quality characteristics of rice. Considering the impact of the disease on food security and sustainability, efforts to introgress three R-genes (xa5, xa13 and Xa21) into the variety Jyothi from donor parent Improved Samba Mahsuri (ISM) through MAS were made. Foreground selection of the BC2F4 individuals was done using the Sequence Tagged Sites (STS) as well as functional markers. Foreground selection of the BC2F4 individuals was done using the xa5 gene linked STS marker RG556. Restriction digestion of the PCR product of the STS marker with Dra1 restriction enzyme, resulted in production of alleles of size 238bp and 438bp in all the BC 2F4 individuals including the parents, indicating the presence of R-gene xa5. Amplification of DNA of the individuals with the functional marker xa5SR further confirmed the presence of R-gene xa5 in the parents as well as in the 51 BC 2F4 individuals. Foreground selection with STS marker pTA 248 to detect the presence of Xa21 gene revealed that in BC 2F4 Plant No. 9 and plant no. 21 amplicon of size 992 bp, as found in the donor parent ISM was present. And background selection was done by using rice microsatellite (RM) simple sequence repeats (SSR) markers.

Development of a low-resolution genome scan marker set for the acceleration of major gene or QTL mapping in wheat

The traditional approach to identify targeted quantitative trait loci (QTL) or genes in a mapping study is to develop partial to comprehensive genetic maps by using a fairly large number of molecular markers. This is a cumbersome and potentially expensive process in which the result is often good coverage of areas with no significant importance. Here we have developed a low-resolution genome scan marker set (LRGS) of 104 microsatellite (simple sequence repeat) markers to identify the geneor QTL-carrying chromosome(s) earlier in a mapping study using a very small number of markers. In doing so, cost and time are reduced. An indication of association or linkage of a marker with the trait of interest, often still below a statistically significant threshold, can then be further investigated by saturating only the putative targeted area with additional markers to produce a high-resolution map of the region potentially housing the gene/QTL. Secondly, the LRGS markers can be used in QTL mapping efforts to provide the necessary chromosome anchoring points for high-throughput marker types with often unknown chromosome positions. This approach, combined with an automated analysis platform, accelerates a mapping effort and reduces the cost associated with the molecular work.

Population genetic diversity and structure of a dominant tropical seagrass, Cymodocea rotundata, in the Western Pacific region

AbstractCymodocea rotundata is an ecologically important tropical pioneer seagrass species distributed in the Indo‐Pacific region. The population genetic diversity and structure of this species were analysed at 46 sites spanning the Philippines, Ryukyu Islands (northern limit) and Hainan Island, by using microsatellite simple sequence repeat (SSR) markers. Analyses revealed the persistence of C. rotundata likely relies on local population dynamics and fitness influenced by environmental gradients, with sexual reproduction prevalent in the Philippines while the Ryukyu and Hainan populations were predominantly established by clonal spread. Analysis of molecular variance showed significant genetic differentiation (P < 0.001) among three geographic regions: the Philippines, Ryukyu and Hainan. Furthermore, the mean fixation index value was very high (FST = 0.36), indicating poor dispersal potential or limited gene flow. Allelic richness and heterozygosity of C. rotundata was comparable in the Philippines and Ryukyu Islands populations. More private alleles were found in the Philippines and excess heterozygotes in the Ryukyu Islands. STRUCTURE analysis revealed that the Ryukyu and Hainan populations were mosaics of admixed alleles of individuals from the Philippines. An assignment test suggested that recruitment occurs from the Northeast Philippines to Ryukyu Islands. These results suggest that the Philippine populations are tropical seagrass hotspots and perhaps the origin of the populations in the Ryukyu and Hainan Islands. This scenario is most likely driven by the Kuroshio Current and island integration events during plate tectonic activities. The Philippine Archipelago is considered of high importance for conservation objectives and management plan of seagrasses. Likewise, the Ryukyu Islands are also important in terms of conserving regional diversity because locally adapted genotypes have important evolutionary potential in the face of environmental change.

Genetic Diversity Analysis in Date Palm (Phoenix dactylifera L) Germplasm using Microsatellite Markers

The Date Palm (Phoenix dactylifera L), germplasm commonly cultivated in Egypt, shows a wide range ofrepining periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this studywas to genetic diversity analysis and relationships for 45 date palm genotypes and to construct a molecular databaseincluding the cultivars commonly grown in Egypt. An analysis of thirty three microsatellite simple sequence repeat(SSR) loci out of thirty five markers was performed to define allele diversity, heterozygosity and genetic structure. Theaverage number of alleles per locus was 32.3. Heterozygosity per locus was 0.64 (Dpalm-103) to 0.96 (Dplam-100, 256,mpdCIR08 and mpdCIR078) with an average of 0.89. The highest heterozygosity (0.768) was detected in Avanda,followed by Amhat (0.758) while Khalas had lowest heterozygosity value (0.455).The genetic similarity values rangedfrom 0.041 to 0.260. The obtained dendrogram showed three main clusters and generally, a good structuring of 45genotypes and accessions. The use of 33 polymorphic microsatellite markers and the level of genetic variabilitydetected within Egyptian date palm germplasm suggested that this is reliable, efficient and effective marker system thatcan be used for diversity analysis and subsequently in crop improvement programs.

DNA Fingerprinting and Characterization of some Egyptian Date Palm Cultivars Using Simple Sequence Repeats (SSRs)

The Date Palm (Phoenix dactylifera L), germplasm commonly cultivated in Egypt, shows a wide range ofrepining periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this studywas to fingerprint 45 date palm genotypes and accessions and to construct a molecular database including the cultivarscommonly grown in Egypt. An analysis of thirty three microsatellite simple sequence repeat (SSR) loci out of thirty fivemarkers was performed to define distinct specific alleles across all loci, genetic similarity within cultivars in eachregion of five different locations and possibility of linking morphological traits with molecular data. In general, theresults indicated the possible use of SSR analysis to detect cultivar-specific markers for forty five Date palm cultivarsand accessions under investigation that can be used to discriminate among the cultivars and genotypes. The geneticdistance among populations compared to each other (Hayani, Samany and Zagholol) which presented at differentlocations in this study, may or may not correlate with the geographical distance between them in some species,depending on natural and artificial factors involved in shaping the population genetic structure of the species. Based onour findings, it is clear that there is some discordance between the data corresponding to molecular variability and thoserelated to the variability available for breeding purposes (phenotypic variability). However, the use of 33 polymorphicmicrosatellite markers to study Egyptian date palm germplasm suggested that this is reliable, efficient and effectivemarker system that can be used for diversity analysis, and subsequently in crop improvement programs.

Assessment of genetic diversity and population structure of mung bean (Vigna radiata) germplasm using EST-based and genomic SSR markers

Mung bean is an important legume crop in tropical and subtropical countries of Asia and has high nutritional and economic value. However the genetic diversity of mung bean is poorly characterized. In this study, our goal was to develop and use microsatellite simple sequence repeat (SSR) markers for germplasm evaluation. In total, 500 novel expression sequence tag EST-based SSRs (eSSRs) and genomic SSRs (gSSRs) were developed from mung bean transcriptome and genome sequences. Of these, only 58 were useful for diversity evaluation in a panel of 157 cultivated and wild mung bean accessions from different collection sites in East Asia. A total of 2.66 alleles were detected on average per locus which shows that polymorphism is generally low for the species. The average polymorphic information content (PIC) of gSSRs was higher than eSSRs and most of the polymorphic gSSRs were composed of di- and tri-nucleotide repeats (52.4% and 38.1% of all loci, respectively). The genotypes were differentiated into nine subgroups by cluster analysis, and the wild mung bean accessions separated well from the cultivated accessions. Analysis of molecular variance indicated that 22% of variance was observed among populations and 78% was due to differences within populations. Clustering, population structure analyses showed that non-Chinese cultivated and wild mung bean accessions were separated from Chinese accessions, but no geographical distinctions existed between genotypes collected in China. Interestingly, the average PIC value of cultivated mung bean (0.36) was higher than that of wild mung bean (0.25) showing that further collecting and wide crosses are necessary for mung bean improvement.

Genetic diversity and population structure of pencil yam (Vigna lanceolata) (Phaseoleae, Fabaceae), a wild herbaceous legume endemic to Australia, revealed by microsatellite markers

Pencil yam (Vigna lanceolata Benth.) (Phaseoleae, Fabaceae) is a herbaceous legume endemic to Australia. A previous morphological study suggested that pencil yam is a complex species of two or more related taxa with seven distinct morphological types (morphotypes) and, thus, taxonomic revision is necessary. In this study, we assessed genetic diversity and determined the genetic structure of a pencil yam collection of 62 accessions from seven morphotypes using 18 microsatellite (simple sequence repeat) markers with the aim to provide information for taxonomic study. In total, 138 alleles were detected with a mean of 7.67 alleles per locus. Polymorphism information content per marker varied between 0.06 and 0.90 with a mean of 0.61, while the overall gene diversity was 0.62. Bayesian clustering, principal coordinate, and neighbor-joining analyses consistently revealed that these accessions are grouped into two subpopulations with difference in number of alleles, allelic richness, and gene diversity. The population structure was not related to either morphotype or geographical origin. Gene diversity of V. lanceolata was higher than that of wild Vigna radiata (L.) Wilczek and wild Vigna umbellata (Thunb.) Ohwi & Ohashi, comparable with that of wild Vigna mungo (L.) Hepper, Vigna exilis Tateishi & Maxted, and Vigna grandiflora (Prain) Tateishi & Maxted, and lower than that of wild Vigna angularis (Willd.) Ohwi & Ohashi. These results indicated that the taxonomy of V. lanceolata should be revised and that its gene diversity was moderate compared with the other wild Vigna species.

De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae).

Veratrilla baillonii Franch is an important Chinese medicinal herb for treating liver-related diseases, which has been over-collected in the recent decades. However, the effective conservation and related population genetic study has been hindered because of the lack of genome sequences and genetic markers in the natural population. We have conducted RNA-seq on V. baillonii. We performed de novo assembly of these data to characterize the V. baillonii transcriptome, resulting in 133,019 contigs with size >200 bp. These contigs were annotated using the NCBI nonredundant database and Gene Ontology (GO) terms. From these contigs, we developed novel microsatellite simple sequence repeat (SSR) markers, identifying a total of 40,885 SSRs. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetranucleotides) accounted for 99.8% of all SSRs, with mononucleotide repeats most common, followed by dinucleotide (16.2%) and trinucleotide repeats (14.7%). We selected 151 SSRs for experimental validation, of which 74 were confirmed by polymerase chain reaction. Fourteen SSRs were determined to be polymorphic by screening 40 individuals from six distant populations. The number of alleles per locus ranged from two to four, and the expected heterozygosity varied from 0.2637 to 0.8571, suggesting that these SSR markers are highly polymorphic and effective for further genetic analysis in the nature population. In addition, we explored the genetic structure of V. baillonii using five SSRs in four geographic populations and found that the identified genotypes were clustered into two phylogenetic clades: the Mekong River clade and Jinsha River clade. This result indicates that these two regions may harbor highly divergent genetic lineages and enriched genetic diversity. The de novo transcriptome sequences and new SSR markers discovered by this study provide an initial step for understanding the population genetics of V. baillonii, and a valuable resource for effective conservation management.

Genetic divergence in soybeans based on phenotypic traits and microsatellite markers

Background The success of a breeding program depends on the existence of genetic variability [1]. Therefore, breeders have recommended to the formation of the population-based study, the interbreeding between superior cultivars and divergent, resulting in hybrid combinations of higher heterotic effect, so that in segregating generations it has a greater chance of obtaining transgressive genotypes [2]. Microsatellite markers or Simple Sequence Repeat (SSR) have been widely used to estimate genetic diversity in soybean due to their high degree of polymorphism, codominant inheritance, PCR-based detection, allelic diversity and the knowledge of the location of the marker in the genome the species [3]. In this report we present results of agronomic traits and microsatellite markers to evaluate the genetic diversity of 35 soybean genotypes to determine their potential as parents for breeding programs.

Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex.

BackgroundThe moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex.ResultsMolecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex.ConclusionsWe propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research.

Development of 16 microsatellite markers in Eusideroxylon zwageri by next-generation sequencing

The Ulin, Eusideroxylon zwageri, is a useful tropical tree now threatened by excessive logging. We used next-generation sequencing to isolate and characterize 16 polymorphic and codominant microsatellite (simple sequence repeat) markers in 32 E. zwageri trees in east Kalimantan, Indonesia. The number of alleles for each locus ranged from 2 to 19 and observed and expected heterozygosities ranged from 0.13 to 0.91 and from 0.18 to 0.92, respectively. These microsatellites may be useful for genetic studies and conservation of E. zwageri.

Assessment the genetic diversity of common bean Phaseolus vulgaris collection by microsatellite SSR markers

Common bean plants (Phaseolus vulgaris L.) are the most important edible beans for their high nutritional value as an important source of dietary protein. However, in spite of the importance of this crop species, its genetics has not been fully characterized. Advances in molecular biology techniques have provided the basis for uncovering virtually unlimited numbers of DNA markers. Polymerase Chain Reaction (PCR) -based markers are more convenient and accurate determination of the genetic relationships. The utility of PCR-DNA based marker is generally determined by the technology that is used to reveal DNA-based polymorphism between and within different organisms. Thus, the present investigation aimed to assess the genetic variability among the different varieties of common bean based on the genetic distances that obtained by simple sequence repeat (SSR) or microsatellite techniques. SSR-DNA markers will identify closely related genotypes of different varieties of common bean. In the present study, a total of eleven bean varieties, nine of P. vulgaris L., one of Phaseolus coccineus, and one of Phaseolus lunatus namely: Bean CORA, Judia cilena, Diamant, palati, Distinction, Contender, Fagiolo Nano, Ambra, Bronco, Merit, Lima bean were selected SSR markers that were relatively more efficient in detecting similarities among Pharsalus genotypes studied with similarities up to 95%. SSR profiling provides useful information on the level of polymorphism and genetic diversity in common bean. Key words: Phaseolus vulgaris L., common bean, polymerase chain reaction, dietary protein.

Development of 10 novel polymorphic microsatellite markers for the Indo-Pacific horned starfish, Protoreaster nodosus

Ten novel polymorphic nuclear microsatellite simple sequence repeat (SSR) markers were isolated from an Indo-Pacific horned starfish, Protoreaster nodosus. The isolated SSR markers provided polymorphisms of 2–9 alleles per locus in three populations obtained from Indonesia and the Philippines. The expected and observed heterozygosities ranged from 0.049 to 0.691 and from 0.050 to 0.800, respectively. Pairwise FST values among three populations ranged from 0.018 to 0.050 (global FST=0.031). All P. nodosus individuals collected from three populations exhibited different genotypes for the ten identified SSR markers, indicating that P. nodosus reproduces sexually. Then the developed SSR markers will be useful for studying the population and conservation genetics of P. nodosus.

Molecular characterization of pea (Pisum sativum L.) using microsatellite markers

Nineteen pea (Pisum sativum L.) accessions have been characterized using Simple Sequence Repeats (SSRs). The mains objectives of this study were to examine SSR polymorphism among cultivars and to assess genetic diversity among them. Eight microsatellites, from the Pisum microsatellite consortium (Agrogene ®, France) have been used. Five of the eight SSRs studied gave good electrophoretic profiles and helped us to amplify a number of alleles per locus varying from 3 (PSMPA5 and PSMPA6) to 13 (PSMPSAD126) with a total of 34 and an average number of 6.8 alleles per locus. The Polymorphism Information Content (PIC) varied from 0.18 for PSMPSAD134 to 0.85 for PSMPSAD126, with an average value of 0.62. The five microsatellites analyzed allowed us to separate 18 out of the 19 genotypes studied, and only the two most polymorphic markers (PSMPSAA205 and PSMPSAD126), permit to discriminate among the same genotypes (18) separated using the 5 SSRs. Genetic distances computed have been used to draw the corresponding dendrogram and to distribute genotypes according to their genetic relationship. The genotypes classified within the same group share several agro-morphological characters. Finally, the present study attests that SSR microsatellites are good tools for identifying genotypes and for the assessment of genetic diversity in pea.

Assessment of in silico BAC-based simple sequence repeat (SSR) marker development for tomato (Solanum lycopersicum L.)

Tomato landraces are less sensitive to environmental stresses and grown mainly under rain fed conditions. They are still grown in small farms due to quality and special demand of consumers. These landraces are valuable sources of genetic traits, and plant breeders can use breeding programs for crop improvement. One of the primary needs of the crop improvement is the estimation of genetic diversity. Development of microsatellite simple sequence repeat (SSR) markers from map-referenced bacterial artificial chromosomes (BAC) clones is a very effective means of targeting markers to marker scarce positions in the genome. This study was aimed at developing a set of functional SSR markers via in silico analysis of publicly available tomato DNA sequences. As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) were scored and showed 100% polymorphic patterns. The calculated polymorphism information content (PIC) values for the SSR markers developed ranged from 0.62 to 0.97 (mean 0.89). The SSR motifs CT(26) AT(27) and TTC(6) TTA(4) had the highest PIC value (0.97), while CAA(5)A(8) had the lowest PIC value (0.62). According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is related to hydroxyproline-rich glycoprotein, which is a family protein from Arabidopsis thaliana . On the other hand, the SSR with tri-nucleotide repeat motif AAC(4)A(11) was related to a putative homologous protein to A7Q2S4 from Vitis vinifera . Keywords: Tomato landraces, in silico simple sequence repeat (SSR) markers, DNA markers, genetic diversity