scholarly journals Seleksi Berbasis Marka Molekuler pada Padi Generasi F2 Guna Merakit Galur Padi Harapan Tahan Wereng Coklat

Agrikultura ◽  
2016 ◽  
Vol 27 (1) ◽  
Author(s):  
Nono Carsono ◽  
Gigih Ibnu Prayoga ◽  
Neni Rostini ◽  
Danar Dono
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Yield Loss ◽  
Insect Pest ◽  
Brown Planthopper ◽  
F2 Population ◽  
Significant Yield ◽  
F2 Generation ◽  
F2 Progeny ◽  
Simple Sequence

ABSTRACTMolecular Marker-based Selection on F2 Progeny for Development of Promising Rice Lines Resistant to Brown PlanthopperBrown planthopper (BPH) is the major insect pest of rice and accounts for significant yield loss. This experiment was aimed to develop BC1F1 and F3 brown planthopper resistant rice lines. Selection on the basis of SSR markers can be done by using two polymorphic SSR markers, i.e., RM586 dan RM8213, which screened from eight SSR markers for BPH resistant. Sixty-three F2 genotypes from IP-1 (derived from IR-64 x PTB-33) population and twenty F2 genotypes from PP-11 (derived from Pandan Wangi x PTB-33) population were selected and will be used for further research by selfed and backcrossed to recipient parents. Chi-squares test for segregation of DNA bands in F2 generation showed that RM8213 fitted with 1:2:1 Mendelian ratio for controlling photosynthetic rates and trichomes length in IP-1 population. This information could be used in programs to develop a durable brown planthopper resistant rice cultivar.Keywords: BPH, F2 population, Moleculer marker, SSRABSTRAKWereng coklat merupakan salah satu hama utama pada tanaman padi yang mampu menurunkan produksi padi secara nyata. Penelitian ini bertujuan untuk memperoleh galur-galur padi F2 yang memiliki marka-marka yang berasosisasi dengan ketahanannya terhadap wereng coklat. Seleksi pada galur padi F2 hasil persilangan telah dilakukan melalui teknik marka molekuler Simple Sequence Repeat (SSR) menggunakan dua marka SSR yang menunjukkan polimorphisme yaitu RM586 dan RM8213 dari delapan marka yang diskrining. Sebanyak 63 genotip dari populasi IP-1 (hasil persilangan IR-64 x PTB-33) dan 20 genotip dari populasi PP-11 (hasil persilangan Pandan Wangi x PTB-33) untuk disilangkan sendiri maupun disilang balik dengan tetua recipient. Selain itu, hasil analisis Chi-Kuadrat untuk segregasi pita DNA menunjukkan bahwa primer RM8213 memiliki rasio 1:2:1 (dominasi tidak sempurna) dalam mengontrol karakter laju fotosintesis dan panjang trikoma terhadap wereng coklat pada populasi IP-1. Informasi yang diperoleh dari penelitian ini nantinya dapat digunakan untuk program perakitan kultivar padi tahan wereng coklat yang durable.Kata Kunci: Marka molekuler, Populasi F2, SSR, Wereng coklat

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.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

2016 ◽  
Vol 106 (4) ◽  
pp. 362-371 ◽  
Author(s):  
P. Cheng ◽  
X. M. Chen ◽  
D. R. See
Keyword(s):  
Ssr Markers ◽  
Stripe Rust ◽  
Simple Sequence Repeat ◽  
Puccinia Striiformis ◽  
The United States ◽  
Grass Species ◽  
Cereal Crops ◽  
Sequence Repeat ◽  
Grass Hosts ◽  
Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

scholarly journals Use of simple sequence repeat (SSR) markers for screening blue disease resistance in cotton germplasm exchange

2015 ◽  
Vol 14 (41) ◽  
pp. 2871-2875 ◽  
Author(s):  
Faustine Christopher ◽  
Vieira Hoffmann Lucia ◽  
Ismail Tibazarwa Flora ◽  
Lukonge Everina
Keyword(s):  
Disease Resistance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Germplasm Exchange ◽  
Simple Sequence

scholarly journals Pengujian Kemurnian Genetik Benih Padi Galur F3 (Pandanwangi x PTB33) Terseleksi Menggunakan Marka Molekuler Simple Sequence Repeats (SSR)

Agrikultura ◽  
2015 ◽  
Vol 26 (2) ◽  
Author(s):  
Syindy Raffini Nasihin ◽  
Wieny H. Rizky ◽  
Nono Carsono
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence Repeat ◽  
Brown Planthopper ◽  
Plant Analysis ◽  
Current Experiment ◽  
Genetic Purity ◽  
Experimental Station ◽  
Purity Testing ◽  
Brown Planthopper Resistance ◽  
Simple Sequence

ABSTRACTSeed Purity Testing of F3 Progeny of Rice Lines Derived from a Cross between Pandanwangi x PTB-33 Estimated by Simple Sequence Repeat MarkersSeeds with high purity is required to produce maximum crop yield. Genetic purity of selected F3rice seed progenies derived from a cross between Pandanwangi x PTB33 was estimated by SSR(simple sequence repeats) molecular markers. Objective of current experiment was to obtain riceseed with high genetic purity (100%) in terms of homogeneity of alleles. The experiment wasconducted at Laboratory of Plant Analysis and Biotechnology, meanwhile field experiment wasperformed at Ciparanje Experimental Station, Faculty of Agriculture, Universitas Padjadjaran.Based on primer designed by Bradbury (aromatic trait) and primers RM589 and RM586 (supposedto correlate with brown planthopper resistance gene), seeds of F3 selected had 100% geneticpurity. SSR markers applied for each offspring were able to demonstrate the purity of the seed.Genotypes with 100% genetic purity can be continued for propagating their seeds.Keywords: F3, seed purity, seed rice, SSR markersABSTRAKBenih dengan kemurnian genetik tinggi sangat diperlukan untuk produksi tanaman yangmaksimal. Kemurnian genetik padi generasi F3 hasil persilangan Pandanwangi x PTB-33 diestimasidengan menggunakan marka molekuler SSR. Percobaan ini bertujuan untuk mendapatkan generasiF3 yang memiliki kemurnian genetik 100%. Penelitian dilaksanakan di Kebun PercobaanCiparanje, Fakultas Pertanian Universitas Padjadjaran dan Laboratorium Analisis dan BioteknologiTanaman. Hasil analisis menggunakan primer Bradbury menunjukkan 100% benih murniberdasarkan karakter aromatik, begitupun berdasarkan karakter ketahanan terhadap wereng(primer RM589 dan RM586) menunjukkan 100% benih murni. Marka molekuler SSR yangdigunakan untuk verifikasi kemurnian mampu menunjukkan kemurnian genetik benih padi yangtinggi. Genotip PP dapat dilanjutkan untuk pengujian dan atau perbanyakan benih sumber.Kata kunci: benih padi, F3, marka SSR, uji kemurnian genetik

scholarly journals A Way Forward to Combat Insect Pest in Rice

2021 ◽  
Vol 25 (1) ◽  
pp. 1-22
Author(s):  
MP Ali ◽  
B Nessa ◽  
MT Khatun ◽  
MU Salam ◽  
MS Kabir
Keyword(s):  
Yield Loss ◽  
Production Systems ◽  
Insect Pests ◽  
Insect Pest ◽  
Brown Planthopper ◽  
Mobile App ◽  
Rice Production ◽  
Economic Losses ◽  
Pest Species ◽  
Management Options

The damage caused by insect pest is the continual factor for the reduction of rice production. To date, 232 rice insect pest species are identified in Bangladesh and more than 100 species of insects are considered pests in rice production systems globally, but only about 20 - 33 species can cause significant economic loss. The major goal of this study is to explore all the possible ways of developed and proposed technologies for rice insect pests management and minimize economic losses. Insect pests cause 20% average yield loss in Asia where more than 90% of the world's rice is produced. In Bangladesh, outbreak of several insects such as rice hispa, leafroller, gallmidge, stem borers and brown planthopper (BPH) occurs as severe forms. Based on previous reports, yield loss can reach upto 62% in an outbreak situation due to hispa infestation. However, BPH can cause 44% yield loss in severe infestested field. To overcome the outbreaks in odd years and to keep the loss upto 5%, it is necessary to take some preventive measures such as planting of resistant or tolerant variety, stop insecticide spraying at early establishment of rice, establish early warning and forecasting system, avoid cultivation of susceptible variety and following crop rotation. Subsequent quick management options such as insecticidal treatment for specific insect pest should also be broadcasted through variety of information systems. Advanced genomic tool can be used to develop genetically modified insect and plants for sustainable pest management. In addition, to stipulate farmers not use insecticides at early crop stgae and minimize general annualized loss, some interventions including training rice farmers, regular field monitoring, digitalization in correct insect pests identification and their management (example; BRRI rice doctor mobile app), and demonstration in farmers field. Each technology itself solely or combination of two or more or all the packages can combat the insect pests, save natural enemies, harvest expected yield and contribute to safe food production in Bangladesh. Bangladesh Rice J. 25 (1) : 1-22, 2021

scholarly journals Mapping of Resistance Genes to Brown Planthopper in Untup Rajab, an Indonesian Local Rice Variety

2018 ◽  
Vol 14 (2) ◽  
pp. 75
Author(s):  
Muhamad Yunus ◽  
Diani Damayanti ◽  
Ahmad Dadang ◽  
Ahmad Warsun ◽  
Dani Satyawan ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Quantitative Resistance ◽  
Insect Pest ◽  
Rice Variety ◽  
Brown Planthopper ◽  
Snp Markers ◽  
Chromosome 8 ◽  
F2 Population ◽  
Resistant Varieties ◽  
Test Population

<p>Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective approach to control the insect pest is by using resistant varieties. Exploring for resistance genes is, therefore, a prerequisite for effective breeding program for BPH resistance. This study aimed to map BPH resistance genes in Untup Rajab, an Indonesian local rice variety. Genetic map was constructed using an F2 population from a cross between TN-1 and Untup Rajab, and SNP markers from RiceLD SNP Chip. Phenotyping was performed using bulk seedling test on F2:3 seedlings against two BPH populations, i.e. X1 and S1. Four QTLs<br />were identified on chromosomes 5, 6, 8, and 11 with PVE values of 7.63%, 9.40%, 17.66%, and 3.05%, respectively. Relatively normal distribution of resistance phenotype and the relatively low PVE values indicate that Untup Rajab has a quantitative resistance to BPH with two different resistance loci identified for each BPH test population. The QTL on chromosome 8 overlaps with OsHI-LOX gene, which is associated with resistance to BPH, and adjacent to another QTL for resistance to green leafhopper. The QTL on chromosome 6 was found near OsPLDα4 and OsPLDα5 genes which are related to BPH resistance. Meanwhile, the QTL intervals on chromosome 5 and 11 did not overlap with any known BPH QTLs or genes, which make them attractive candidates for novel BPH resistance gene discovery.</p>

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>

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