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 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 Confirmation of Alleles Inheritance in F1 Progenies Derived from a Cross of Calcutta-4 [Musa acuminata ssp. burmannicoides] and Musa acuminata ssp. microcarpa Based on SSR Markers

2020 ◽  
Vol 16 (1) ◽  
pp. 17
Author(s):  
Dea Rosalia ◽  
Puji Lestari ◽  
Andy Soegianto ◽  
Darmawan Saptadi ◽  
Agus Sutanto ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Disease Resistance ◽  
Ssr Markers ◽  
Selection Process ◽  
Musa Acuminata ◽  
Chi Square ◽  
Genetic Studies ◽  
Ssr Primers ◽  
Chi Square Analysis ◽  
Selection Of

<p>Banana breeding to produce improved varieties with disease resistance haracters and other desired traits could sustain its yield. Alleles harbored by parents could be passed on to the offsprings through hybridization, but need to be confirmed using molecular markers. This study aimed to confirm allele inheritance in F1 progenies derived from a cross of Calcutta-4 (Musa acuminata ssp.  burmannicoides) and M. acuminata ssp. microcarpa based on SSR markers. Eleven pairs of SSR primers were used to amplify DNA of 44 progenies using the PCR technique. The results showed that six SSR markers (MaSSR 1.1, MaSSR<br />5.1, MaSSR 6.1, MaSSR 7.1, MaSSR 8.1, and MaSSR 11.1) were polymorphic in both parents. Four markers (MaSSR 1.1, MaSSR 5.1, MaSSR 6.1, and MaSSR 8.1) had PIC &gt;0.7, indicating their informativeness to distinguish these progenies and other genetic studies of banana germplasms. A total of 44 F1 individuals were confirmed to harbor alleles inherited from their parents,<br />suggesting as true progenies from the cross of Calcutta-4 and M. acuminata ssp. microcarpa. This population demonstrated 100% success of hybridization performed. Chi-Square analysis revealed that segregation of all markers did not match to Mendelian ratio 1:2:1, except for MaSSR 1.1 (x2 = 5,62) and MaSSR 6.1 (x2 = 3,77) markers. The genetic traceability of banana F1 progenies demonstrating the usefulness and feasibility of SSR markers in this study provided information on selection of true progenies which may be valuable for breeders to assist selection process in future banana breeding program in Indonesia.</p>

scholarly journals Application of molecular markers in sunflower breeding

Genetika ◽  
2007 ◽  
Vol 39 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Dejana Saftic-Pankovic
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Inbred Lines ◽  
Vegetable Crops ◽  
Large Variability ◽  
Parental Lines ◽  
Early Phases ◽  
Selection Of

The results of the application of molecular markers in sunflower breeding obtained in the Institute of Field and Vegetable Crops in the last decade are reviewed. Our results on genetic distance (GD=7-75%) between sunflower inbred lines obtained with RAPD and SSR markers, indicate large variability and provide important information for the selection of parental lines for future crosses. Interspecific hybridization is often used in sunflower breeding. As only some populations of H. giganteus and H. maximiliani are resistant to sunflower diseases, the investigation of genetic variability in/between two species is of interest. The results obtained with SSR markers are presented. The successful hybridization between H. rigidus and H. annuus was confirmed with RAPD markers, and the variability between F1 and BC1F1 plants is discussed. Desirable alleles and haplotypes can be detected with molecular markers both in early phases of plant development and in early phases of the production of improved lines, which reduces or completely eliminates the large number of testing cycles for desirable phenotypes. CAPS markers for resistance to downy mildew, that can be used in marker assisted selection are presented. .

Identification of SSR marker associated with rust resistance in cowpea (Vigna unguiculata L.) using bulk segregant analysis

2016 ◽  
Vol 39 (1) ◽  
Author(s):  
M. S. Uma ◽  
Niranjan Hegde ◽  
Shailaja Hittalmani
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Rust Disease ◽  
Ssr Primers ◽  
Single Marker ◽  
Significant Regression ◽  
Resistant Genotypes ◽  
Selection Of

Bulked segregant analysis was undertaken to tag gene(s) controlling rust resistance using molecular markers in cowpea, to permit rapid selection of superior desirable rust resistant genotypes in the breeding program. For this purpose, the C-152, cultivated variety with high yielding, semi determinate plant type, good protein content and highly rust susceptible was crossed with genotype IC202778, the landrace from Himachal Pradesh, India having determinate, semi spreading and rust resistant characters. The parental genotypes were analyzed with 92 SSR markers for detection of polymorphism and only 13 markers showed polymorphism between the parents. Using each of these 13 SSR primers, we carried out bulked segregate analysis on F<sub>2</sub> plants representing two extremes of rust disease resistance and susceptible trait. Three SSR markers VuUGM02, VuUGM08 and VuUGM19 were found to be associated with rust resistance. This was further confirmed through selective genotyping. The co-segregation data on these molecular markers and rust resistance on F<sub>2</sub> plants were analysed by means of single-marker linear regression approach. Significant regression suggested linkage between VuUGM02 and rust resistance gene.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

Controlled photo-discharge of dust in a complex plasma

2021 ◽  
Vol 87 (2) ◽  
Author(s):  
Michael McKinlay ◽  
Edward Thomas
Keyword(s):  
High Intensity ◽  
Dusty Plasmas ◽  
Lanthanum Hexaboride ◽  
Magnetized Plasma ◽  
Background Plasma ◽  
Proof Of Concept ◽  
Langmuir Probes ◽  
Complex Plasma ◽  
Dust Charge ◽  
Selection Of

One of the limitations in studying dusty plasmas is that many of the important properties of the dust (like the charge) are directly coupled to the surrounding plasma conditions rather than being determined independently. The application of high-intensity ultraviolet (UV) sources to generate discharging photoelectric currents may provide an avenue for developing methods of controlling dust charge. Careful selection of the parameters of the UV source and dust material may even allow for this to be accomplished with minimal perturbation of the background plasma. The Auburn Magnetized Plasma Research Laboratory (MPRL) has developed a ‘proof-of-concept’ experiment for this controlled photo-discharging of dust; a high-intensity, near-UV source was used to produce large changes in the equilibrium positions of lanthanum hexaboride ( $\textrm {LaB}_6$ ) particles suspended in an argon DC glow discharge with negligible changes in the potential, density and temperature profiles of the background plasma. The shifts in equilibrium position of the dust are consistent with a reduction in dust charge. Video analysis is used to quantify the changes in position, velocity and acceleration of a test particle under the influence of the UV and Langmuir probes are used to measure the effects on the plasma.

scholarly journals Application of Microsatellite and Inter Simple Sequence Markers for Certifying Trueness to Type of Grafted Ramets and Clustering of Persian Walnut Varieties

2021 ◽  
Author(s):  
Masoomeh Hosseini Nickravesh ◽  
Kourosh Vahdati ◽  
fatemeh amini ◽  
Reza Amiri ◽  
Keith Woeste
Keyword(s):  
Ssr Markers ◽  
Issr Markers ◽  
Principal Coordinate Analysis ◽  
Dna Fingerprint ◽  
Polymorphic Ssrs ◽  
Persian Walnut ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
Ssrs Markers ◽  
Simple Sequence

Abstract The utility of seventeen Microsatellite (SSR) markers and fifteen inter simple sequence repeats (ISSR) markers for the identification of twenty eight ramets of 11 varieties of walnut (Juglans regia) was explored. Thirty nine individual genomes were screened using 61 and 38 scorable fragments from SSR and ISSR markers, respectively. The least polymorphic SSR locus was WGA004 (two alleles) and the most polymorphic (5 alleles) was WGA276. Polymorphism information content values ranged from 0.08 (WGA004) to 0.43 (WGA032) in SSR markers and from 0.11 (AGA (AC)7) to 0.49 (CAC(TGT)5) in ISSR markers, with an average of 0.29 and 0.19, respectively. In most cases, grafted varieties with identical names also had the same microsatellites profile. The principal coordinate analysis and clustering (UPGMA) based on the combined marker set emphasized two failures in grafting or off-types, ramets identified as Serr 4 (S4) and Vina 1 (V1). The presence of two off-type ramets in the walnut research orchard emphasizes the importance of using molecular certification for proving true-to-type of walnut orchards. Using 13 polymorphic SSRs, we tabulated a DNA fingerprint chart of 11 walnut varieties. Except for ‘Chandler’, each cultivar could be distinguished using a combination of only two SSR loci. The 13 SSRs markers evaluated in this study could be used in future to identify clones produced from the varieties.

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

Target and Non–target site Mechanisms Confer Resistance to Glyphosate in Canadian Accessions ofConyza canadensis

Weed Science ◽  
2017 ◽  
Vol 66 (2) ◽  
pp. 234-245 ◽  
Author(s):  
Eric R. Page ◽  
Christopher M. Grainger ◽  
Martin Laforest ◽  
Robert E. Nurse ◽  
Istvan Rajcan ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Resistance Mechanisms ◽  
Target Site ◽  
Conyza Canadensis ◽  
Weed Species ◽  
Target Site Resistance ◽  
Selection For ◽  
Simple Sequence ◽  
Growing Region ◽  
Selection Of

Glyphosate-resistant populations ofConyza canadensishave been spreading at a rapid rate in Ontario, Canada, since first being documented in 2010. Determining the genetic relationship among existing Ontario populations is necessary to understand the spread and selection of the resistant biotypes. The objectives of this study were to: (1) characterize the genetic variation ofC. canadensisaccessions from the province of Ontario using simple sequence repeat (SSR) markers and (2) investigate the molecular mechanism (s) conferring resistance in these accessions. Ninety-eightC. canadensisaccessions were genotyped using 8 SSR markers. Germinable accessions were challenged with glyphosate to determine their dose response, and the sequences of 5-enolpyruvylshikimate-3-phosphate synthase genes 1 and 2 were obtained. Results indicate that a majority of glyphosate-resistant accessions from Ontario possessed a proline to serine substitution at position 106, which has previously been reported to confer glyphosate resistance in other crop and weed species. Accessions possessing this substitution demonstrated notably higher levels of resistance than non–target site resistant (NTSR) accessions from within or outside the growing region and were observed to form a subpopulation genetically distinct from geographically proximate glyphosate-susceptible and NTSR accessions. Although it is unclear whether other non–target site resistance mechanisms are contributing to the levels of resistance observed in target-site resistant accessions, these results indicate that, at a minimum, selection for Pro-106-Ser has occurred in addition to selection for non–target site resistance and has significantly enhanced the levels of resistance to glyphosate inC. canadensisaccessions from Ontario.

Sign in / Sign up

Export Citation Format

Share Document