scholarly journals Development and characterization of EST-SSR markers for Taxus mairei (Taxaceae) and their transferability across species

2016 ◽  
Vol 65 (1) ◽  
pp. 67-70 ◽  
Author(s):  
X. Wu ◽  
Y. Wen ◽  
S. Ueno ◽  
Y. Tsumura
Keyword(s):  
Molecular Markers ◽  
Genetic Analysis ◽  
Ssr Markers ◽  
Taxus Cuspidata ◽  
Genetic Analyses ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Taxus Mairei ◽  
Ssr Loci

AbstractTaxusis an important genus which is well-known for Taxol. Its genetic analyses were lagged behind those of other conifers due to lack of suitable molecular markers. In this paper, we explored polymorphic loci forTaxus maireiand tested their transferability across species based on 150 EST-SSR loci already developed forTaxus cuspidatapreviously. The results showed that 103 loci were polymorphic, the number of alleles per locus ranged from 2 to 11 over 16 individuals. The observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0 to 1 and 0.0625 to 0.891, respectively. ThePICvalues ranged from 0.11 to 0.754 with an average of 0.453. The average cross-species transferability was 96.07% among 5 species. Most of these loci can be used as universal markers inTaxusgenus. The PCA results showed these markers have strong power to identify different species. These markers will be useful for further studies on genetic analysis and conversation ofTaxus mairei.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

scholarly journals Development and characterization of microsatellite loci for Cedrela fissilis Vell (Meliaceae), an endangered tropical tree species

2014 ◽  
Vol 63 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
F. B. Gandara ◽  
E. V. Tambarussi ◽  
Alexandre Magno Sebbenn ◽  
E. M. Ferraz ◽  
M. A. Moreno ◽  
...  
Keyword(s):  
Genomic Library ◽  
Population Level ◽  
Fixation Index ◽  
Allele Number ◽  
Neotropical Tree ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Ssr Loci ◽  
Polymorphic Microsatellite

Abstract The timber of the Neotropical tree Cedrela fissilis is used in construction, shipbuilding, carpentry and for medical purposes. In this study, polymorphic microsatellite (SSR) markers derived from an enriched genomic library were characterized using 120 adult trees from four different C. fissilis populations. No substantial genotypic linkage disequilibrium was detected among all possible pairs of SSR loci. The number of alleles per locus ranged from 2 to 20, the average allele number ranged from 8 to 9.7, depending on the population. The observed heterozygosity among the different SSR loci varied from 0.0 to 1.00 , the expected heterozygosity varied from 0.07 to 0.95 On the population level, the average observed and expected heterozygosities ranged from 0.50 to 0.63 and from 0.64 to 0.70, respectively. The average fixation index among populations ranged from 0.09 to 0.24. Thus, the SSR loci revealed high poly - morphism rates and can be used to study the genetic diversity,structure, mating system, and gene flow in C. fissilis.

scholarly journals The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

BMC Genetics ◽  
2011 ◽  
Vol 12 (1) ◽  
pp. 41 ◽  
Author(s):  
Robertha AV Garcia ◽  
Priscila N Rangel ◽  
Claudio Brondani ◽  
Wellington S Martins ◽  
Leonardo C Melo ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Genetic Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence

Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

2014 ◽  
Vol 12 (3) ◽  
pp. 323-329 ◽  
Author(s):  
Guillermo Padilla ◽  
Rafel Socias i Company ◽  
Amando Ordás
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Average Value ◽  
La Palma ◽  
Expected Heterozygosity ◽  
Commercial Cultivars ◽  
Soft Shell ◽  
Genetic Profiles ◽  
Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

scholarly journals Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

2020 ◽  
pp. 1-12
Author(s):  
Laila Dabab Nahas ◽  
Alsamman M. Alsamman ◽  
Aladdin Hamwieh ◽  
Naim Al-Husein ◽  
Ghinwa Lababidi
Keyword(s):  
Drought Tolerance ◽  
Bread Wheat ◽  
Ssr Markers ◽  
Web Sites ◽  
Wheat Breeding ◽  
Genic Ssr ◽  
Drought Tolerant ◽  
Ssr Loci ◽  
Weather Changes

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries

scholarly journals Lokus SSR Berasosiasi Karakter Tahan Penyakit Mati-Pohon Durian Berdasarkan Bulked Pseudo-Segregant Analysis (SSR Loci Associated to Resistance Traits to Durian Die-Back based on Bulked Pseudo-Segregant Analysis)

2020 ◽  
Vol 30 (1) ◽  
pp. 9
Author(s):  
Panca Jarot Santoso ◽  
I Nyoman Pugeg Aryantha ◽  
Sony Suhandono ◽  
Adi Pancoro
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
High Intensity ◽  
Ssr Marker ◽  
Plant Genetics ◽  
Molecular Assays ◽  
Pythium Vexans ◽  
Dna Pools ◽  
Ssr Loci ◽  
Selection Of

<p>Penyakit mati-pohon disebabkan cendawan Pythiaceae khususnya Phytophtora palmivora, Pythium vexans, dan Pythium cucurbitacearum menjadi salah satu kendala utama dalam budidaya durian. Di antara upaya pengendaliannya adalah melalui pemuliaan dan seleksi tanaman tahan berbasis molekuler menggunakan marka SSR. Penelitian untuk mengidentifikasi lokus SSR yang berasosiasi dengan karakter tahan penyakit mati-pohon pada durian telah dilaksanakan di Laboratorium Genetika Tumbuhan SITH-ITB dari bulan April sampai dengan Desember 2014. Penelitian dilaksanakan secara bulked pseudo-segregant analysis dua pool DNA durian tahan dan rentan. Amplifikasi lokus SSR menggunakan 77 pasang primer mikrosatelit berlabel fluorescent. Produk amplifikasi dibaca menggunakan GeneMarker v.2.4.0., setiap puncak pancaran fluorescent yang memiliki nilai intensitas tinggi dipilih sebagai alel. Pembandingan panjang alel dilakukan di antara dua pool dan pembanding aksesi tahan. Lokus yang memiliki alel berbeda antara dua pool tetapi memiliki alel sama dengan pembanding dianggap sebagai marka yang berasosiasi dengan sifat tahan durian terhadap Pythiaceae. Hasil analisis ditemukan tiga lokus mDz03F10, mDz4B2, dan mDz3B1 dengan motif berturut-turut (GAA)3.A(GA)4, (GAGT)2ttGAGT, dan (TTTTATG)2(GCCC)2 teridentifikasi sebagai marka yang berasosiasi dengan karakter tahan Pythiaceae. Hasil analisis ini memerlukan satu langkah validasi untuk meyakinkan keterpautan marka dengan karakter target sebelum digunakan sebagai marka molekuler.</p><p><strong>Keywords</strong></p><p>Durian; SSR; BpSA; Tahan; <em>Pythiaceae</em></p><p><strong>Abstract</strong></p><p>Die-back disease caused by Pythiaceae especially Phytophtora palmivora, Pythium vexans, and Pythium cucurbitacearum is one of the obstacles in durian cultivation. An effort to control this disease is through breeding and selection of resistant plants based on molecular assays such as SSR markers. Research to identify SSR loci associated with durian die-back resistance was done at Plant Genetics Laboratory, SITH-ITB from April to December 2014. The research was conducted through bulked pseudo-segregant analysis of two DNA pools, resistance, and susceptible durians. Amplification of SSR loci was carried out by using 77 fluorescent labeled primers. Amplification products were analyzed using GeneMarker v.2.4.0. Fluorescent peak with high intensity was considered as a selected allele. Comparison of allele length was executed amongst two pools and resistance reference. A locus showed different allele between two pools, while it given the same allele to reference was considered as SSR marker associated with Phytiaceae resistance. The analysis were found three loci, mDz03F10, mDz4B2, and mDz3B1 with motif of (GAA)3.A(GA)4, (GAGT)2ttGAGT, and (TTTTATG)2(GCCC)2 recpectively identified as SSR markers associated to die-back resistance. This result, therefore, requires further validation to convince markers association to target traits before they are used as molecular markers.</p>

scholarly journals Characterization of Genetic Diversity of Stone Fruit Rootstocks Used in Chile by Means of Microsatellite Markers

2012 ◽  
Vol 137 (5) ◽  
pp. 302-310 ◽  
Author(s):  
María José Arismendi ◽  
Patricio Hinrichsen ◽  
Ruben Almada ◽  
Paula Pimentel ◽  
Manuel Pinto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Stone Fruit ◽  
Identification System ◽  
Expected Heterozygosity ◽  
Commercially Important ◽  
Taxonomic Groups ◽  
Simple Sequence

Stone fruit (Prunus L.) production in Chile covers ≈43,000 ha and includes a wide variety of soils and climates requiring a large diversity of rootstocks. The most commercially important rootstock cultivars are 26 genotypes from three different taxonomic groups belonging to the subgenera Amygdalus (L.) Benth. Hook. (peach group), Prunus Focke [= Prunophora (Neck.)] Focke (plum group), and Cerasus (Adans.) Focke (cherry group) with eight, seven, and 10 individuals, respectively. To determine their genetic diversity, characterization by microsatellite markers [simple sequence repeat (SSR)] was conducted. Of a total of 20 SSR markers evaluated, 12 generated amplified products that were consistent in the three taxonomic groups. The number of alleles per marker ranged from 18 for PSM-3 to four in CPPCT-002. Clustering analysis, by both traditional hierarchical and model-based approaches, indicate that all genotypes are clustered in their respective taxonomic groups, including the interspecific hybrids. Genetic diversity, measured as the average distances (expected heterozygosity) between individuals in the same cluster, was higher in Cerasus (0.78) followed by Prunus (0.72) and Amygdalus (0.64). Total number of alleles observed was 133, of which 14, 33, and 35 from six, 10, and 10 loci were unique for the peach, plum, and cherry rootstock groups, respectively. Alleles shared among peach/plum, plum/cherry, and peach/cherry rootstock genotypes were 13, 14, and 18 from nine, seven, and seven loci, respectively. Only six alleles from five loci were common to the three taxonomic groups. In addition, to develop a rootstock identification system based on SSR markers, a minimum set of three markers (PMS-3, BPPCT-037, and BPPCT-036) able to differentiate the 26 genotypes was identified. This study is the first step toward establishing a stone fruit rootstock breeding program in Chile.

scholarly journals Characterization of quince (Cydonia oblonga Mill.) cultivars using SSR markers developed for apple

2009 ◽  
Vol 15 (4) ◽  
Author(s):  
J. Halász ◽  
V. Hoffman ◽  
Z. Szabó ◽  
J. Nyéki ◽  
T. Szabó ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Bottleneck ◽  
The Self ◽  
Cydonia Oblonga ◽  
Allele Number ◽  
The World ◽  
Ssr Loci ◽  
A Minor

Quince (Cydonia oblongaMill.) is a minor fruit crop, which is primarily used for marmalade, jam and sauce.Very few quince cultivars are known all over the world and in many cases similar names are used for presumably different cultivars. The aim of the present study was to evaluate and characterize the genetic diversity of 36 quince cultivars and selections with SSR markers. Seven out of 8 SSR markers designed from apple sequences could successfully yield amplification also in quince cultivars. Number of alleles per locus ranged from 2 to 3 alleles. These allele numbers are quite low when compared to apple. It is supposed to be the consequence of a genetic bottleneck. In spite of the low allele number per locus, the 36 quince cultivars formed 30 different genotypes. The ratio of homozygosity was low, which might be coupled with the self-(in)compatibility phenotype of quinces. SSR markers proved unable to differentiate putatively closely related cultivars (e.g. ‘Bereczki’ and ‘Bereczki bôtermő’). In general, the level of polymorphism among the tested quince genotypes was much restricted due to the low allele number detected. However, it must be considered that the number of analysed SSR loci is not enough high to estimate the overall heterozygosity of the quince genome. Further experiments are needed and the SSR markers proved to be a reliable and useful tool for such analyses.

scholarly journals Molecular Characterization of Kiwifruit (Actinidia) Cultivars and Selections Using SSR Markers

2004 ◽  
Vol 129 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Yiqi Zhen ◽  
Zuozhou Li ◽  
Hongwen Huang ◽  
Ying Wang
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Rapd Markers ◽  
Reliable Method ◽  
Cultivar Identification ◽  
Direct Count ◽  
Polymorphic Loci ◽  
Single Genotype

Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa, while 33 and 36 were specific to A. chinensis and A. deliciosa, respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (Ho) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and Ho = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and Ho = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.

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