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 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

Mapping of digested and undigested random amplified microsatellite polymorphisms in barley

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 991-998 ◽  
Author(s):  
Jörg Becker ◽  
Manfred Heun
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Linkage Maps ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Alternative Approach ◽  
Microsatellite Mapping ◽  
Simple Sequence

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)n simple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.

scholarly journals IDENTIFICATION OF POLYMORPHISM ON SIMPLE SEQUENCE REPEATS MARKERS ASSOCIATED WITH BROWN PLANTHOPPER RESISTANCE GENES IN TWENTY RICE GENOTYPES AND THEIR GENETIC RELATIONSHIP

2015 ◽  
Vol 2 (1) ◽  
pp. 98
Author(s):  
Nono Carsono ◽  
Yessikha V. Barus ◽  
Santika Sari ◽  
Winny D. Widarmi ◽  
Danar Dono ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Resistance Genes ◽  
Genetic Relationship ◽  
Polymorphic Information Content ◽  
Durable Resistance ◽  
Brown Planthopper ◽  
Bph Genes ◽  
Rice Genotypes ◽  
Brown Planthopper Resistance ◽  
Simple Sequence

<p>Brown planthopper is one of the most destructive insect pest of rice in Indonesia and other Asian countries. Pyramiding some brown planthopper resistance genes is a valuable approach to create more durable resistance against the pest. The objective of this study was to identify polymorphisms of Brown Planthopper Resistance genes (Bph) on 20 genotypes of rice, and to obtain genetic relationship among genotypes tested. The experiment was conducted from June to September 2012 at Green House and Laboratory of Plant Analysis and Biotechnology, Faculty of Agriculture, Universitas Padjadjaran, Jatinangor. Twenty genotypes were analyzed, and two of them were used as check varieties. Simple Sequence Repeat (SSR) markers were applied to detect Bph3, Bph4, Qbph3, and Qbph4 genes. Polymorphic levels were analyzed by calculating PIC (Polymorphic Information Content). The grouping of rice genotypes were done based on principal components analysis (PCA) of SSR data, and the genetic relationship based on the presence of Bph genes was estimated using UPGMA (Unweighted Pair Group With Arithmetic mean). Results showed that RM313, RM8072, RM8213, RM5953, RM586, and RM589 markers were polymorphic. Rice genotypes PTB 33, Diah Suci, Cibogo, Cisantana, Digul, Ciherang, Inpari 13, Inpari 10, and Memberamo had Bph3, Qbph3, Bph4, and Qbph4. Meanwhile Bph3, Qbph3, and Bph4 were supposed to be belonged by IR 64, Aek Sibundong, Batang Gadis, IR 66, and Mekongga. Kalimas and Tukat Penatu had Bph3, Qbph3, dan Qbph4. IR 74 had Bph3 and Qbph3, and Fatmawati had Bph3 and Bph4. UPGMA clustering resulted in two main clusters, in which the first cluster consisted of 2 subclusters. PTB-33 was closely related with Memberamo, Tukat Penatu, Digul, Diah Suci, and Kalimas. The SSR markers used in this study were proven to be valuable in molecular detection of Bph genes and in estimating genetic relationsips of rice genotypes. PTB-33 was a good donor of resistance genes, as well as Memberamo, Tukat Penatu, Digul, Diah Suci, and Kalimas which were identified as promising donors in rice breeding resistance to brown planthopper. </p><p><strong>Keywords :</strong> Bph gene, Brown Planthopper, Genetic relationship, SSR markers.</p>

Development of EST–SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 684-691 ◽  
Author(s):  
B. Pranavi ◽  
G. Sitaram ◽  
K.N. Yamini ◽  
V. Dinesh Kumar
Keyword(s):  
Ssr Markers ◽  
Castor Bean ◽  
Expressed Sequence Tag ◽  
Ricinus Communis ◽  
Rapid Development ◽  
Genetic Purity ◽  
Ricinus Communis L ◽  
Purity Testing ◽  
Expressed Sequence ◽  
Simple Sequence

Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST–SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.

Genetic mapping and variability of seven soybean simple sequence repeat loci

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 763-769 ◽  
Author(s):  
M. Morgante ◽  
A. Rafalski ◽  
P. Biddle ◽  
S. Tingey ◽  
A. M. Olivieri
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Rflp Markers ◽  
Sequence Motifs ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Simple Sequence

Microsatellites or simple sequence repeats are stretches of short tandemly repeated DNA sequence motifs, dispersed throughout the genomes of most eukaryotes. Simple sequence repeat polymorphisms (SSRPs) have recently been reported in plants. Here we present the genetic map position of seven different soybean (Glycine max (L.) Merr. and Glycine soja Sieb. and Zucc.) SSRPs contained in sequenced genes, four of which represent newly mapped positions for these genes. The other three SSRPs coincided with independently established RFLP map positions for the corresponding genes. When a set of 61 soybean accessions was screened at four of these loci by using agarose gels, the average number of alleles per locus was 7.75, the effective number of alleles (ne) was 2.57, and the level of allele differentiation (δT) was 0.62. Allelic variation decreased sharply with increasing levels of domestication, with the level of differentiation going from 84% in the wild soybean to 43% in the elite germplasm. Variation levels observed on a subset made of 19 of the 61 lines were always higher for SSRPs than for RFLP markers, with the average number of alleles per locus going from 4.25 to 2.15. In comparison with RFLP markers, SSRPs are more informative and are easier to analyse but require more effort to develop.Key words: simple sequence repeats, soybean, variability, mapping, domestication, microsatellites.

Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 104-110 ◽  
Author(s):  
J. Provan ◽  
G. Corbett ◽  
W. Powell ◽  
J. W. McNicol
Keyword(s):  
Simple Sequence Repeats ◽  
Wild Rice ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Cultivated Rice ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Wild Accessions ◽  
Simple Sequence

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

scholarly journals Optimization of the choice of molecular markers for identification of commercially used rice varieties in India using rapid DNA extraction protocol

2016 ◽  
Vol 8 (2) ◽  
pp. 1028-1034
Author(s):  
Pravas Ranjan Kole ◽  
Rajeev Singh Rana ◽  
Kangila Venkataramana Bhat
Keyword(s):  
Molecular Marker ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Identification ◽  
Sequence Repeat ◽  
Genetic Purity ◽  
Traditional Practice ◽  
Rice Varieties ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

The present investigating aimed at the development of molecular marker for cultivar identification and genetic purity assessment. A total of four SSR markers and six SRAP primer were developed for the identification of sixteen different commercial varieties of rice. Traditional practice like grow-out-test based on morphological traits is time consuming and sometimes environmentally influenced. After development of molecular marker, it is using as an alternative to grow –out –test because of its rapid, accurate detection. We have assessed the potential of simple sequence repeat and sequence-related amplified polymorphism markers in distinguishing rice varieties and four simple sequence repeat markers namely CT-14, CT-25 CT XY-1 and ATC-3 and six sequence-related amplified polymorphism markers primers could be clearly distinguished sixteen commercially cultivar rice varieties. In addition to single markers, it’s better to try with marker combinations, which were amenable for PCR and capable of distinguishing the varieties. Larger differences for each crop were found between cultivers from different seed companies than within the same company. These DNA markers can provide an easier and faster reliable genetic identification of rice cultivars.

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