EST-SSR markers

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Genetic diversity and molecular analysis among cotton genotypes by EST-SSR markers.

Genetic diversity and molecular analysis among cotton genotypes by EST-SSR markers.

Objective of this research work is to utilize EST- SSR markers for fibre quality traits to generate genetic diversity between tetraploid (Gossypium hirsutum) and diploid (Gossypium herbaceum and Gossypium arboreum) cotton species at molecular level. Twenty four (24) genotypes of cotton and thirty five (35) EST SSR primers for different fibre quality traits (fibre length, Lint percentage, Boll weight and fibre strength) were taken for this study. Almost all primers reveals amplification in both diploid and tetraploid cotton species which indicates that flanking primer sequences are conserved in both genomes of cotton. Thirty one (31) EST SSR primers generate good and enormous amplicon and produced a total of four hundred seventy eight (478) sharp, similar and variable bands in all genotypes. Average number of bands amplified by each primer was 15.419. Statistical analysis for EST SSR data was conducted using software programme NTSYS pc version 2.02e and GeneAlEx. The genetic distance (GD) among the all genotypes of cotton were also analyzed and it is ranged from 0.05 to 0.71 which indicates significant diversity between all the genotypes of both tetraploid and diploid cotton species. The average observed mean heterozygosity was 0.60 and observed mean percentage of polymorphic loci was 60%.
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The Detection of Anaphalis spp. Genetic Diversity Based on Molecular Character (using ITS, ETS, and EST-SSR markers)

The Detection of Anaphalis spp. Genetic Diversity Based on Molecular Character (using ITS, ETS, and EST-SSR markers)

Abstract— Anaphalis is the natural vegetation component in mountainous areas and is found in volcanic soils. Anaphalis is one of the species which existence is currently presumed to decrease and is feared to be extinct in nature. The purpose of this study was to detect genetic diversity of Anaphalis spp. in Bromo Tengger Semeru National Park (BTSNP) based on molecular characters by using ITS, ETS, and EST-SSR markers in supporting the conservation aspects of Anaphalis genetically. This research method was carried out by exploring the existence of Anaphalis populations, their coordinates marked by GPS, and leaf samples collected as a source of molecular analysis material. PCR products from ITS and ETS markers were sequenced, and the results’ phylogenetic were analyzed using the MEGA6 program. PCR products from EST-SSR markers were performed by scoring DNA bands (allel) and both variations and genetics population were analyzed by using the POPGENE 1.32 program. Anaphalis populations found in BTSNP are Anaphalis javanica, A. longifolia, and A. viscida. The genetic diversity of Anaphalis spp. in BTSNP has polymorphism potential that is high enough, which is 57% (ITS) and 31% (ETS-partial), with a maximum likelihood phylogenetic tree topology which is monophyletic separated into four clusters consisting one cluster outgroup and three others being an ingroup. Whereas based on the genetic diversity value of the EST-SSR sequences in Anaphalis spp. in BTSNP shows that only A. longifolia populations in the Ranu Kumbolo area that have a high genetic diversity value (0.024) compared to the other two Anaphalis species. The highest genetic distance of Anaphalis spp. BTSNP in A. longifolia is found in the population of Penanjakan and Mt. Batok areas (0.040) with the smallest gene flow rate (0.428). Further research is needed to obtain a more complete picture of Anaphalis genetic diversity by using more molecular markers, bigger population numbers, more individuals and in bigger populations in other conservation areas in supporting the Anaphalis conservation strategy program.
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Assessment of EST SSR Markers for Evaluating Genetic Diversity in Watermelon Accessions from Zimbabwe

Assessment of EST SSR Markers for Evaluating Genetic Diversity in Watermelon Accessions from Zimbabwe

The phenotypic diversity among watermelon cultivars has been attributed to point mutations in genes control- ling fruit colour, which may not be readily detected by dominantly inherited markers [7]. The use of sequence- related amplified polymorphism (SRAP) markers, known to be associated with gene sequences, produced variable marker profiles suggesting that considerable polymor- phism exists in the vicinity of coding regions of the wa- termelon genome [8]. For this reason, the development of markers related to genes controlling fruit quality in wa- termelon, by searching for oligonucleotides that occur in high frequency in 4700 watermelon EST-unigenes was initiated [8]. The markers designed from these EST- unigenes included EST (expressed sequence tag)-derived SSR (EST-SSR) markers. Availability of EST-SSR marker sequences for oligonucleotide synthesis, in- volvement of PCR amplification, the simplicity of pro- tocol that produces reliable and easily detected amplifi- cation products, their co-dominance and single locus derivation, constitutes advantages over AFLP, RFLP and RAPD markers [9]. Therefore, these markers are pres- ently gaining momentum for estimating functional ge- netic diversity in genebank collections [10].
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Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers

Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers

EST-SSRs are highly polymorphic, abundant and are accessible to research laboratories via published primers sequences [4]. These published primers are especially important resources for species like E. sibiriucs with few molecular markers available. In this study, a total of 9 EST-SSR markers from three different genuses were used for hybrid identification and genetic diversity analysis. The transferability rate of EST-SSRs was 100%. Results of this study were consistent with previous reports that EST-SSR markers have high transferability rate among species. Information on genetic diversity and hybrid population and their parents can improve our understanding of breeding materials.Based on our re- sults the percentage of polymorphism varied from 65.12 (Pop 5) to 75.68% (Pop 1), with an average of 70.51%. The average percentage of polymorphism (PPB) of five hybrid populations were lower than previous reports of SRAP (PPB = 86.5%) [28], SSR (PPB = 89.4%) [4], and SCoT (PPB = 91.9%) [29]. The major reason for relatively low PPB could be small sample size of each population. In addition, hybrid populations derived from seven par- ent genotypes, and genetic base was relatively narrow. This can be supported by results of structure analysis. In general, these accessions and their offspring did not show major genetic structure, most of accessions were assigned into mixed groups, indicating relatively narrow genetic base.
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Effective Procedure for Development of EST SSR Markers Using cDNA Library

Effective Procedure for Development of EST SSR Markers Using cDNA Library

The present study was conducted to develop EST-SSR markers using the cDNA library from rice plant. Total RNA ex- tracted from the leaves of brown plant hopper resistance gene originated from a rice cultivar “Cheongcheong” and sen- sitive rice cultivar “Nakdong” were used to synthesize a cDNA library. As a result of analyzing the cDNA library, the 17 EST-SSR primer sets were developed. This study enables to provide effective marker assisted selection (MAS) methods on the selection of white-backed planthopper resistance gene originated from a rice plant more simply, quickly and precisely. Furthermore, using this marker’s advantage of deriving from cDNA, it is possible to identify the white-backed planthopper resistance gene. In addition, this study introduces a technique for construction of a cDNA library safely without using radioactivity.
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Characterization and development of 56 EST-SSR markers derived from the transcriptome of Odontobutis potamophila.

Characterization and development of 56 EST-SSR markers derived from the transcriptome of Odontobutis potamophila.

The denaturing polyacrylamide gel electrophoresis (PAGE) and the capillary electrophoresis (CE) are the two frequently used techniques to estimate the SSR products. Denaturing PAGE does not require expensive instruments and fluorescent labels (Pagel et al., 2016). Comparatively, CE can increase the speed of electrophoresis and provide more accurate data. Therefore, in this study, we developed 56 EST-SSR markers of O. potamophila by using the CE technique, and used these markers to obtain detailed genetic background information about the wild populations of this fish species.
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Characterization and Development of EST-SSR Markers in Sweet Potato (Ipomoea batatas (L.) Lam)

Characterization and Development of EST-SSR Markers in Sweet Potato (Ipomoea batatas (L.) Lam)

Abstract: According to statistics from the Food and Agriculture Organization, the world population will increase to about 91 million (Asia 51 million, Africa 19 million). A rise in the world’s population means an increased need for food. However, climate change has caused desertification and unpredictable weather, creating problems in the supply and demand of food. Sweet potato (Ipomoea batatas) is an alternative to solving the food problem, as it is one of the world’s most important food crops, especially in developing countries. The tuberous roots of sweet potato are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for breeding this crop. Recently, molecular markers developed for sweet potato have demonstrated good potential for use in genetic selection. In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full- sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.
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Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

ABSTRACT. Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species’ transcriptome, with 626, 643, and 536 of the makers located in coding sequences, 5' untranslated regions and 3' untranslated region, respectively. The annotation of SSR-containing expressed sequence tags revealed that the transcripts were enriched for several Gene Ontology (GO) categories, including ‘protein binding’, ‘regulation of transcription’, and ‘integral to membrane’. Among the 2,553 SSRs, di- and tri-nucleotide repeat motifs were the most abundant (52.3 and 45.6%, respectively), and AC/GT and GAA/TTC were the most frequent di- and tri-nucleotide motifs, respectively. PCR amplification, using 100 SSR primer pairs, revealed that 94% of the markers were of good quality and that 83-88 of the makers could be amplified in six other Allium species. This suggests that the markers had high cross-species transferability. The substantial number of SSRs developed will provide a valuable resource for future genetic and breeding studies in Chinese chive. KEY WORDS: Chinese chive; SSR marker; transcriptome;
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In silico search, characterization and validation of new EST SSR markers in the genus Prunus

In silico search, characterization and validation of new EST SSR markers in the genus Prunus

Several reasons account for the high popularity of EST derived microsatellite markers (EST-SSRs). First, marker development from existing sequence data is fast, easy and economical. An appropriate search program can detect any type of SSR, whereas enrichment cloning captures only SSRs with predefined motifs. Second, given the pref- erential association of SSRs with the non-repetitive por- tion of plant genomes, they are a common component of ESTs [33]. Third, EST-SSRs are physically linked to expressed genes and therefore represent so-called “func- tional markers” that are of particular interest for marker- assisted selection [34]. Finally, primer target sequences residing in expressed DNA regions are expected to be relatively well conserved, thus enhancing the chance of marker transferability across taxonomic boundaries [35].
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Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

The dendrogram clustered all of the lowland ecotypes (LL) into the first. The second group contained all of the upland ecotypes (UL). Other methods have also been used to cluster upland and lowland switchgrass ecotypes. Missaoui et al adopted restriction fragment length poly- morphism (RFLP) markers to analyze the genetic rela- tionships among 21 switchgrass genotypes, resulting in three upland and eighteen lowland genotypes clusterin- ginto two different groups [53]. Huang et al identified differences between the coding sequences of a nuclear gene encoding plastid acetyl-CoA carboxylase in upland and lowland ecotypes genetic variation analysis at gene level, provided by Huang et al researching about a nu- clear gene encoding plastid acetyl-CoA carboxylase [54]. In this study, we preliminarily presented population structure analysis of 7 lowland and 127 upland geno- types using 51 ISSR, SCoT, and EST-SSR primer pairs, resulting in an apparently separate cluster among the two ecotypes, confirming the genetic differences be- tween upland and lowland ecotypes. However, as we do not have as many lowland switchgrass samples as up- land, we highly recommend more lowland ecotype or other nuclear markers should be used in conjunction with ISSR, SCoT and EST-SSR to more appropriately classify upland and lowland ecotypes.
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Characterization of variable EST SSR markers for Norway spruce (Picea abies L )

Characterization of variable EST SSR markers for Norway spruce (Picea abies L )

the most abundant, followed by penta- (23%) and hexa- nucleotide repeats (10.4%) respectively. Di- and tetranu- cleotide repeats were the least abundant with 8.3% each. Twenty-seven out of 60 planned primer pairs amplified polymorphic products in the testing population of 16 individuals, while two did not generate a fragment and 31 proved to be monomorphic [see Additional file 1]. Four of the 27 polymorphic SSR regions showing more than 2 alleles per locus (Pa_16, Pa_24, Pa_34 and Pa_40) in the testing population were excluded from further analysis. In a total of 96 individuals 135 alleles were detected in the 23 remaining loci (Table 1) ranging from 2 to 17 alleles per locus (Table 2) with a mean value of 5.6. Total number of effective alleles was and 50.645 with a minimum of 1.123, a maximum of 4.115 and a mean value of 2.202. 87% of the variable regions were based on trinucleotide repeats, the rest were penta- nucleotide repeats. Di-, tetra and hexanucleotide repeats proofed to be not polymorphic. Loci Pa_41 and Pa_53 were not polymorphic in the Mayrhofen population. Values for expected heterozygosity ranged from 0.021 to 0.780 in the Gusswerk population (mean 0.367) and from 0.123 to 0.769 in the Mayrhofen population (mean 0.385). Observed heterozygosity was found to be between 0.021 and 1.000 in the Gusswerk population (mean 0.461) and between 0.042 and 1.000 in the Mayr- hofen population (mean 0.515). Differences in observed heterozygosities between the two populations ranged from zero (Pa_44) to 0.894 (Pa_49). The minimum dif- ference of expected heterozygosities between the two populations was found at locus Pa_12 (0.002) and the maximum at locus Pa_49 (0.382). Regarding the Guss- werk population, in eleven loci the observed heterozyg- osity was significantly higher and in three loci significantly lower than the expected value. In the Mayr- hofen population we found thirteen loci with the observed heterozygosity significantly higher than the expected and in four loci it was significantly lower. Ele- ven loci showed significant departure from Hardy-Wein- berg expectations (HWE, Guo and Thompson’s exact test [P < 0.05]) within the 48 investigated individuals from the Gusswerk population. The number of loci with significant departure from HWE was higher in the Mayerhofen population (16 loci). Frequency of null alleles was variable from zero to 99.0% in the Gusswerk
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Agro morphological and molecular diversity in castor (Ricinus communis L ) germplasm collected from Andaman and Nicobar Islands, India

Agro morphological and molecular diversity in castor (Ricinus communis L ) germplasm collected from Andaman and Nicobar Islands, India

EST-SSR analysis. The genomic DNA was iso- lated from young leaf samples by cetyl-trimethyl ammonium bromide (CTAB) method (Doyle & Doyle 1990) with minor modifications as per the requirement. DNA was quantified electrophoreti- cally using λ-DNA on 0.8% agarose gel. Twenty-nine EST-SSR markers of castor developed at DOR, Hy- derabad, were used for Polymerase Chain Reaction (PCR) amplification. Reactions were carried out in a volume of 20 μl containing ~ 25 ng of template DNA, 0.08mM dNTPs, 1× reaction buffer (contain- ing 1.5mM MgCl 2 ) (Bangalore, Genei), 5 Pmoles of each forward and reverse primer and 1U of Taq DNA polymerase. Amplification was performed using the Eppendorf Mastercycler gradient version 2.1, programmed according to Williams et al. (1990) with minor modifications. The PCR cycle profile followed had initial denaturation at 94°C for 5 min and then 30 cycles of 30 s denaturation at 94°C, 30 s primer annealing at 56°C and 30 s extension at 72°C and 10 min at 72°C for the final product extension.
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Vol 71, No 3 (2019)

Vol 71, No 3 (2019)

Abstract: Chrysanthemum morifolium cv. ‘Huaihuang’ has great medicinal and commercial value. However, limited genomic and transcriptional information restricts the further research of ‘Huaihuang’. In this study, using ‘Huaihuang’ leaf as the sample, we performed RNA-Seq and obtained numerous unigene sequences for functional characterization, and developed new EST-SSR markers. The results show that 176 unigenes were assigned to the ‘antioxidant activity’ in GO annotations, 998 unigenes were assigned to ‘Secondary metabolite biosynthesis, transport and catabolism’ in the KOG database, 381 unigenes were assigned to ‘Biosynthesis of other secondary metabolites’, and 377 unigenes were assigned to ‘Metabolism of terpenoids and polyketides’ in the KEGG database. A number of genes involved in the biosynthesis of flavones and terpenes, such as CHS, CHI, FLS, HMGR and MVD, were found in the transcription data of ‘Huaihuang’. Also, 36 new polymorphic EST-SSR markers were developed and validated. Using them, the genetic diversity was analyzed and a dendrogram of six clades was constructed among 15 medicinal chrysanthemum varieties. The excavated unigenes and identified new EST- SSR markers will provide useful resources for the study of biosynthesis of active components, genetic diversity analysis, population structure identification and in molecular breeding research of ‘Huaihuang’ and related species.
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Confirmation of Pearl Millet Napiergrass Hybrids Using EST Derived Simple Sequence Repeat (SSR) Markers

Confirmation of Pearl Millet Napiergrass Hybrids Using EST Derived Simple Sequence Repeat (SSR) Markers

Prospects for deploying perennial grasses that are currently considered leading candidates for dedicated energy crops over large acreages are debatable because of several limitations, including vegetative propagation or small seed size, low biomass production during the first growing season, and incomplete assessments of crop invasiveness risk. Pearl Millet-Napiergrass hybrids (“PMN”; Pennisetum glaucum [L.] R. Br. × P. purpureum Schumach.), in contrast, are large-seeded, sterile feedstocks capable of high biomass production during establishment year. Novel methods are war- ranted for confirmation of PMN hybrids, as traditional morphological observations can be inconclusive and chromo- some number determination using cytological methods is laborious and time consuming. Six putative PMN lines were produced in this study, and 10 progeny from each line were evaluated using morphological traits, seed fertility, flow cytometry, and expressed sequence tag-simple sequence repeat (EST-SSR) markers. All putative hybrid lines were ster- ile and failed to produce seed. The PMN hybrids could not be distinguished from either parent using flow cytometry due to highly similar nuclear genome DNA contents. A number of paternal napiergrass-specific EST-SSRs were identi- fied for each PMN line, and four paternal-specific EST-SSRs conserved across all napiergrass accessions were selected to screen the putative PMN hybrids. These EST-SSRs confirmed that all F 1 individuals analyzed were PMN hybrids.
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Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (Carica papaya L )

Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (Carica papaya L )

Complete papaya genome has been sequenced by Ming et al. [5], which gen- erated enormous amount of ESTs and other DNA sequences which are freely accessible at NCBI (http://www.ncbi.nlm.nih.gov) and the availability of several SSR mining tools like MISA [13], TROLL [36], SciRoKo [37], Msat commander [38], etc., makes it possible to utilize available ESTs for the development of genic SSRs which could be applied for papaya crop improvements. Only few studies of microsatellite analysis from genomic sequences [39] and from ESTs [40] have been performed in papaya. Moreover, only limited genic or EST-SSR markers, which emerge from transcribed portion of the genome, therefore becomes more important, are available in C. papaya . Therefore, the present study was underta- ken to develop genic SSRs by utilizing the available EST database of C. papaya. The study has following two objectives: 1) In-silico approach to mine SSRs from the available papaya ESTs from the NCBI database and, 2) to develop EST-SSR primers. These developed primers could be used for estimation of genetic diver- sity, cross-transferability across species and genera, in comparative-genomics study and in identification of sex specific markers in papaya.
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EST-SSR: A New Class of Genetic Markers in Cotton

EST-SSR: A New Class of Genetic Markers in Cotton

Recent advances in genomic technologies have generated a large number of expressed sequence tags (ESTs) in cotton. Many of these ESTs are available in public databases, which offer an opportunity to identify simple sequence repeats (SSR) in ESTs by data mining. These sequences may provide an estimate of diversity in the ex- pressed portion of the genome and may be useful for comparative mapping, for tagging important traits of interest, and for additional map-based cloning of important genes. One hundred and thirty-three SSR-containing ESTs (EST-SSRs) were identified by analyzing 9,948 sequences be- longing to Gossypium hirsutum L. in GenBank. The EST-SSR sequences and the related EST sequences without SSRs were clustered to reduce redundancy and to develop consensus sequences. Primers were designed for 84 of these EST-SSRs and were tested for their ability to amplify and detect diversity among three lines of G. hirsutum and one line of G. barbadense L. An average of three amplicons was obtained per primer pair. The intraspecies polymorphism rate among the G. hirsutum cotton cultivars was 26% and interspe- cific polymorphism between G. hirsutum and G. barbadense was 52%. The presence of SSRs in the EST-SSR markers was confirmed by cloning and sequencing of the amplified products of randomly selected primer pairs from four different lines. To explore the potential use of the EST-SSR loci for comparative mapping, these sequences were compared against different plant species using BLAST assuming an e-value of 1E -10 or less as a
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Comparative study of EST-SSR, SSR, RAPD, and ISSR and their transferability analysis in pea, chickpea and mungbean

Comparative study of EST-SSR, SSR, RAPD, and ISSR and their transferability analysis in pea, chickpea and mungbean

have used 10 EST-SSR markers (developed from EST data of pea available on NCBI), in amplification of 3 legumes plants (Table 2). All 10 EST-SSR markers showed more amplification capability in all 3 legumes, contained better capacity for quantifying the genetic diversity through total number of effective alleles. Around 80% of EST-SSR showed amplification in pea, followed by 60% in chickpea and 50% in mung bean.

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Construction of EST SSR Databases for  Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L ) Distinctness Test

Construction of EST SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L ) Distinctness Test

The objectives of this study were to construct a database of expressed sequence tag (EST)-simple sequence repeat (SSR) markers to identify lettuce cultivars. A set of 370 EST-SSR primer pairs were applied for fingerprinting the lettuce cultivars. Fifty-eight EST-SSR markers showed hy- per-variability and were able to differentiate 92 cultivars. A total of 176 polymorphic amplified fragments were obtained by the 58 markers, and two to eight SSR alleles were detected for each l˚Cus with an average of three alleles per locus. Average polymorphism information content (PIC) was 0.425, ranging from 0.022 to 0.743. Cluster analysis was based on Jaccard’s distance coeffi- cients using the method of unweighted pair group. In this method we used arithmetical averages (UPGMA) algorithm categorized 4 major groups, which were in accordance to morphological traits. The eight cultivars of three groups with 100% genetic similarity through SSR analysis were inves- tigated by phenotypic traits. These cultivars including these pairs are very similar in 27 morpho- logical characteristics. Therefore, these EST-SSR markers could be used to select similar cultivars through management of reference collection to complement distinctiveness test of lettuce cultivars.
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Developmenrt of EST SSR and genomic SSR markers to assess genetic diversity in Jatropha Curcas L

Developmenrt of EST SSR and genomic SSR markers to assess genetic diversity in Jatropha Curcas L

Results: In total, 187 out of 419 expressed sequence tag (EST)-SSR and 54 out of 182 genomic (G)-SSR markers from cassava were polymorphic among the J. curcas accessions. The EST-SSR markers comprised 26.20% dinucleotide repeats, 57.75% trinucleotide repeats, 7.49% tetranucleotide repeats, and 8.56% pentanucleotide repeats, whereas the majority of the G-SSR markers were dinucleotide repeats (62.96%). The 187 EST-SSRs resided in genes that are involved mainly in biological and metabolic processes. Thirty-six EST-SSRs and 20 G-SSRs were chosen to analyze the genetic diversity among 45 J. curcas accessions. A total of 183 polymorphic alleles were detected. On the basis of the distribution of these polymorphic alleles, the 45 accessions were classified into six groups, in which the genotype showed a correlation with geographic origin. The estimated mean genetic diversity index was 0.5572, which suggests that our J. curcas germplasm collection has a high level of genetic diversity. This should facilitate subsequent studies on genetic mapping and molecular breeding.
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Molecular characterization of Turkish onion germplasm using SSR markers

Molecular characterization of Turkish onion germplasm using SSR markers

The EST-SSRs markers produced 110 bands, out of which 105 were polymorphic (95%). The number of bands ranged from 1 to 14, with an average of 5.79 amplicons per marker. The size of the alleles was observed to be between 137 bp and 350 bp. The ACM238 produced the highest number of bands (14). The EST-SSRs markers showed a higher percentage of amplification than in previous reports (Jakše et al. 2005; Khar et al. 2011; Mallor et al. 2014; Mitrová et al. 2015). The bands of ACM315 (290 bp), ACM238 (153 bp) and ACM300 (184 bp, 207 bp, 216 bp) were excluded from further evaluation because of being monomorphic across the studied set of 96 acces- sions. Similarly, ACM300 produced monomorphic bands in Spanish onions (Mallor et al. 2014). The observed allele sizes in this study for the EST-SSR markers were similar to expected values (McCallum et al. 2008) but not exactly the same. Other authors reported different allele sizes compared to those described in the original publications. For example, ACM004 gave bands between 201 bp and 212 bp in Czech onion varieties (Mitrová et al. 2015); 220 bp and 230 bp in Spanish onion accessions (Mallor et al. 2014); and 201 bp and 210 bp in Indian onion accessions (Khar et al. 2011). We observed 224 bp and 256 bp bands in Turkish onion accessions using the same marker. Such different values may result from the reading sensitivity of different devices. In addition, this reflects the diversity and genetic vari- ation of varieties originating from different regions of the world (Jakše et al. 2005; McCallum et al. 2008; Mitrová et al. 2015). The gSSRs produced 198 bands, and all of them were polymorphic. The number of bands ranged from 1 to 15, with an average of 7.33 amplicons per marker. The size of the alleles was observed to be between 90 bp and 390 bp. The AMS014 produced the highest number of bands (15) while AMS002, AMS005 and AMS030 produced the lowest number of bands (1). The band sizes of the gSSRs were similar to previous reports but not exactly the same. This difference is thought to arise for similar reasons to those causing variation in EST-SSRs. In this study, the polymorphism ratio of gSSRs was higher than that of EST-SSRs (i.e. 100% vs. 95%). This result is consistent with previous studies revealing higher polymorphism levels in gSSR than in EST-SSR markers for different plants (La Rota et al. 2005; Liu et al. 2012). This is because gSSRs mostly reside in nongenic regions (Varshney et al. 2005). The markers with PIC values equal to 0.7 or higher are highly informative for genetic studies and are
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