scholarly journals ANALISIS KERAGAMAN GENETIK TIGA STRAIN NILA MERAH (Oreochromis sp) DENGAN ANOVA RAPD

2017 ◽  
Vol 1 (1) ◽  
pp. 21
Author(s):  
Iskandariah Iskandariah ◽  
Otong Zenal Arifin ◽  
Rudhy Gustiano
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Nile Tilapia ◽  
Genetic Variance ◽  
Laboratory Research ◽  
Red Tilapia ◽  
Freshwater Aquaculture ◽  
Genetic Strain ◽  
Different Strains ◽  
Random Amplified Polymorphism Dna

Analysis Genetic Variation of Three Strains of Red Tilapia by Anova of RAPD.          Study on the genetic variance of three strains of red tilapia (Oreochromis sp) had been conducted in the Biology Molecular Laboratory, Research Institute for Freshwater Aquaculture (RIFA) Bogor.  Three different strains, Red NIFI from Thailand,  Red Tilapia from Lido lake and Red Tilapia from Bogor’s farmer were analyzed in the study.  Observation used Random Amplified Polymorphism DNA (RAPD) with OPA-03, OPA-04, OPC 14 and OPC-15 primers.  The results showed that only OPA-03 primer was able to amplify numerous samples.  Further analysis showed that the percentage of polimorphic range was between 16.67 – 38.89%, heterozygosity value 0.0378 – 0.1536 and genetic distance among strain 0.3051 – 0.6037.Keywords : RAPD, genetic, strain, nile tilapia, oreochromis ABSTRAK           Penelitian mengenai variasi genetik tiga strain nila merah dari 3 lokasi yang berbeda telah dilakukan di Laboratorium Molekuler Biologi, Balai Riset Perikanan Budidaya Air Tawar (BRPBAT) Bogor.  Strain yang diamati meliputi jenis nila Red NIFI dari Thailand, nila merah dari Danau Lido dan nila merah dari Petani Bogor. Penelitian menggunakan metode analisis Random Amplified Polymorphism DNA (RAPD), dengan menggunakan primer OPA-03, OPA-04, OPC-14 dan OPC-15.  Hasil pengamatan menunjukkan hanya OPA-03 yang dapat menghasilkan amplifikasi dalam jumlah sampel yang memadai.  Hasil analisis menunjukkan bahwa persentase polimorfik berkisar antara 20.00-40.00%, dengan nilai heterozigositas 0.0604–0.1516 dan jarak genetik antar strain 0.1770-0.4865.  Kata kunci : RAPD, genetik, strain, ikan nila, oreochromis

Habitat differentiation between estuarine and inland Hibiscus tiliaceus L. (Malvaceae) as revealed by retrotransposon-based SSAP marker

2011 ◽  
Vol 59 (6) ◽  
pp. 515 ◽  
Author(s):  
Tian Tang ◽  
Lian He ◽  
Feng Peng ◽  
Suhua Shi
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Variance ◽  
Genetic Relationships ◽  
Principal Coordinate Analysis ◽  
Geographical Isolation ◽  
Tidal Zone ◽  
Ecological Scale ◽  
Habitat Differentiation

Hibiscus tiliaceus L. (Malvaceae) is a pantropical coastal tree that extends to the tidal zone. In this study, the retrotransposon sequence-specific amplified polymorphism (SSAP) technique was used in order to understand the genetic variation between four population pairs of H. tiliaceus from repeated estuarine and inland habitat contrasts in China. The estuarine populations were consistently more genetic variable compared with the inland ones, which may be attributed to extensive gene flow via water-drifted seeds and/or retrotransposon activation in stressful estuarine environments. An AMOVA revealed that 8.9% of the genetic variance could be explained by the habitat divergence within site, as compared with only 4.9% to geographical isolation between sites, which indicates significant habitat differentiation between the estuarine and inland populations. The estuarine populations were less differentiated (ΦST = 0.115) than the inland (ΦST = 0.152) implying frequent gene interchange in the former. Accordingly, the principal coordinate analysis of genetic distance between individuals revealed that genetic relationships are not fully consistent with the geographic association. These results suggest that despite substantial gene flow via sea-drifted seeds, habitat-related divergent selection could be one of the primary mechanisms that drive habitat differentiation in H. tiliaceus at a local ecological scale.

scholarly journals EVALUASI KERAGAMAN GENTIK IKAN KALUI (Osphronemus goramy) DARI KABUPATEN LIMA PULUH KOTA, SUMATERA BARAT BERDASARKAN MARKA RANDOM AMPLIFIED POLYMORPHISM DNA (RAPD)

2017 ◽  
Vol 11 (4) ◽  
pp. 313
Author(s):  
Estu Nugroho ◽  
Azrita Azrita ◽  
Hafrizal Syandri ◽  
Refilza Refilza
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Rapd Marker ◽  
Genetic Differences ◽  
Random Amplified Polymorphism Dna

Ikan kalui merupakan nama lokal dari ikan gurami di Kabupaten Lima Puluh Kota, Sumatera Barat termasuk jenis ikan ekonomis tinggi. Terdapat lima strain ikan kalui yang tersebar di pembudidaya, yaitu Tambago, Palapah, Krista, Jepun, dan Merah. Penelitian ini dilakukan untuk mengamati keragaman genetik strain ikan kalui atau gurami dengan menggunakan penanda RAPD. Sebanyak 50 sampel DNA ikan kalui diekstraksi dari sirip dan diamplifikasi secara random dengan menggunakan empat primer terbaik dari 20 primer OPA yaitu OPA-02, OPA-04, OPA-06, dan OPA-07. Hasil menunjukkan bahwa perbedaan yang nyata secara genetik hanya terdapat antara strain ikan kalui Merah dengan Tambago dan Krista. Variasi genetik tertinggi diamati pada ikan kalui strain Krista dengan nilai heterogenitas 0,1756 kemudian diikuti berturut-turut oleh strain Merah (0,1735); Palapah (0,1480); Jepun (0,0594); dan Tambago (0,0203). Jarak rata-rata Nei genetik adalah 0,407, dengan nilai terendah yang teramati antara strain Tambago dan Palapah.Kalui is a local name of giant gouramy fish in West Sumatera Province that categorized as an high economically fish. Five strains of kalui are distributed to farmers i.e. Tambago, Palapah, Krista, Jepun and Merah. This research was conducted to observe the genetic variation of Kalui strains using RAPD marker. A total of 50 samples of whole DNA was extracted from kalui-giant gouramy finclip and randomly amplified using four of the best 20 primers (OPA i.e. OPA-02, OPA-04, OPA-06 and OPA-07). The results showed that Significant genetic differences were only observed between strain Merah-Tambago and Merah-Krista. The highest variability was observed in Krista with heterogeneity value of 0.1735 followed by Merah (0,1735), Palapah (0,1480), Jepun (0,0594) and Tambago (0,0203). The average Nei genetic distance was 0.407, with the lowest was observed between Tambago and Palapah.

scholarly journals Genetic variability of the fifth generation of nile tilapia Oreochromis niloticus using microsatellite DNA markers

2015 ◽  
Vol 10 (2) ◽  
pp. 124
Author(s):  
Gloria Ika Satriani ◽  
Dinar Tri Soelistyowati ◽  
Dian Hardianto ◽  
Ratu Siti Aliah
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Dna Markers ◽  
Microsatellite Loci ◽  
Microsatellite Dna ◽  
Nile Tilapia ◽  
Fifth Generation ◽  
Freshwater Aquaculture ◽  
Microsatellite Dna Markers ◽  
Aquaculture Development

<p>ABSTRACT</p><p><br />Fifth generations of Nile tilapia from several strains have been produced by using selective breeding program in Main Centre for Freshwater Aquaculture Development (MCFAD) Sukabumi, West Java. This research was aimed to evaluate the impact of family selection program of some highly economic traits on its genetic variability using microsatellite DNA markers. The total of 180 specimens have been collected from fifth generation of nine reciprocal mating between three families selected from fourth generation of Nile tilapia and were screened for genetic variability at three microsatellite loci (UNH 123*, UNH 172*, UNH 216*). The results showed that the amount of genetic variability on fifth generations of Nile tilapia from three strains was ranged between 33 to 100% and the highest genetic distance relationship between families was 0.3875. This research approved that females and males issued from the family which have more amount of genetic variability and higher distance to others could be considered as genetic materials to produce the next generation.</p><p><br />Keywords: microsatellite DNA, genotype, genetic variability, genetic distance, Oreochromis nilotiocus</p><p><br /> ABSTRAK</p><p><br />Beberapa strain ikan nila generasi kelima telah dihasilkan dalam program pemuliaan di Main Centre untuk Freshwater Aquaculture Development (MCFAD) Sukabumi, Barat Jawa. Riset ini bertujuan untuk mengevaluasi pengaruh seleksi famili terhadap performa karakter ekonomis penting berdasarkan keragaman genetiknya menggunakan penanda microsatellite DNA. Spesimen dari 180 individu generasi kelima hasil persilangan resiprokal antara tiga famili generasi keempat dianalisis dengan penanda tiga microsatellite loci (UNH 123*, UNH 172*, UNH 216*). Hasil penelitian menunjukkan bahwa keragaman genetik ikan nila generasi kelima berkisar antara 33 sampai 100% dan hubungan kekerabatan genetik antar famili yang paling jauh adalah 0,3875. Individu betina dan jantan yang berasal dari famili dengan tingkat keragaman genetik dan kekerabatan yang lebih tinggi dapat dipertimbangkan sebagai sumber genetik berkualitas untuk menghasilkan generasi berikutnya.<br />Kata kunci: microsatellite DNA, genotipe, keragaman genetik, jarak genetik, Oreochromis nilotiocus</p>

scholarly journals KARAKTERISASI MORFOLOGI KETURUNAN PERTAMA IKAN NILA (Oreochromis niloticus) GET DAN GIFT BERDASARKAN METODE TRUSS MORPHOMETRICS

2016 ◽  
Vol 2 (3) ◽  
pp. 373
Author(s):  
Otong Zenal Arifin ◽  
Titin Kurniasih
Keyword(s):  
Genetic Distance ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Main Part ◽  
Morphological Character ◽  
Freshwater Aquaculture ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Cluster Dendrogram ◽  
Degree Of Similarity ◽  
Research Institute

Penelitian yang bertujuan untuk mendapatkan informasi karakter morfometrik dan variasi morfologi ikan nila (Oreochromis niloticus) keturunan pertama populasi GET dan GIFT telah dilaksanakan di Balai Riset Perikanan Budidaya Air Tawar, Bogor. Tujuh famili nila GET dan dua famili nila GIFT, dengan jumlah sampel masing-masing 30 ekor (15 jantan dan 15 betina) dievaluasi menggunakan metode truss morfometrik pada empat bagian tubuhnya. Dari 21 karakter truss yang diukur, terdapat delapan karakter yang dapat dipakai untuk membedakan kesembilan famili yang dievaluasi. Nilai sharing komponen dalam famili tertinggi adalah pada famili GET 18C (86,7) dan terendah pada famili 18A (43,3) serta 09C (43,3), sedangkan nilai sharing komponen antar famili tertinggi diperoleh antara famili GET 18A dengan famili GIFT 10 dengan nilai 40,0. Berdasarkan kluster dendrogram jarak genetik dengan tingkat kemiripan 70% didapatkan tiga kelompok yang berbeda secara morfologi. Kelompok 3 terutama famili GET 09C adalah famili tersendiri dan terpisah dari famili lainnya. Jarak genetik terbesar adalah antara famili GET 09C dengan famili GET 18C dengan nilai 0,026; sedangkan jarak genetik terkecil terdapat di antara famili GIFT 10 dengan famili GET 18A dengan nilai 0,001.Research aimed at elucidating morphological character and variation between GET and GIFT nile tilapia (Oreochromis niloticus) have been conducted at Research Institute for Freshwater Aquaculture, Bogor. Seven GET and two GIFT nile tilapia families, which consisted of 30 individu in each family (15 males and 15 females), were measured using truss morphometrics methods on four main part of their body. There were eight morphometrics characters can be used to differentiate the nine families, from 21 characters used. The highest within family sharing component was founded at GET 18C (86.7), whereas the lowest one was at 18A (43.3) and 09C (43.3). The highest between family sharing component was between GET 18A and GIFT 10 (40.0). Based on genetic distance cluster dendrogram (with degree of similarity 70%), there were three separated groups has been classified. Group 3rd, especially GET 09C was far isolated from other families. The highest genetic distance was between GET 09C and GET 18C (0.026), while the lowest one was between GIFT 10 and GET 18A (0.001).

scholarly journals KARAKTERISTIK GENOTIPE HIBRIDA HUNA BIRU (Cherax albertisii) DENGAN HUNA CAPITMERAH (Cherax quadricarinatus)

2016 ◽  
Vol 5 (2) ◽  
pp. 191
Author(s):  
Irin Iriana Kusmini ◽  
Estu Nugroho ◽  
Alimuddin Alimuddin ◽  
Mulyasari Mulyasari
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Rapd Analysis ◽  
Cherax Quadricarinatus ◽  
Random Amplified Polymorphism Dna

Pada pengelolaan induk di hatchery sering terjadi silang dalam (inbreeding) yang dapat menyebabkan terjadinya penurunan keragaman genetik. Salah satu program untuk meningkatkan keragaman genetik adalah dengan hibridisasi. Penelitian bertujuan untuk mengetahui keragaman genetik turunan persilangan antara huna biru Cherax albertisii dengan huna capitmerah Cherax quadricarinatus. Metode penelitian menggunakan analisis RAPD (Randomly Amplified Polymorphism DNA). Hasil penelitian menunjukkan nilai heterozigositas hibrida lebih tinggi (0,187-0,290) dibanding nonhibrida (0,0997-0,2211). Hibridisasi antara jantan huna capitmerah dengan betina huna biru (RA) menghasilkan nilai heterozigositas yang lebih tinggi dibandingkan dengan persilangan antara betina huna capitmerah dengan jantan huna biru (AR).Management of fish broodstock in hatchery can reduced genetic variation. One program that can be conducted to increase the genetic variation is hibridization. The aim of this research was to find out genetic variation (heterozigosity) of the offspring of Cherax albertisii-Cherax quadricarinatus hybrid. The methods used in this research was RAPD analysis (Random Amplified Polymorphism DNA). The result showed that heterozigosity value of hybrid (0.187-0.290) was higher than that of non hybrid (0.0997-0.2211). Hybridization of redclaw male with blue crayfish female (RA) gave better result in heterozigosity value and genetic distance than that of redclaw female with blue crayfish male (AR).

Genetic variation within and between strains of outbred Swiss mice

1993 ◽  
Vol 27 (2) ◽  
pp. 116-123 ◽  
Author(s):  
Shuliang Cui ◽  
Clive Chesson ◽  
Rory Hope
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Genetic Distances ◽  
Branching Pattern ◽  
Allozyme Electrophoresis ◽  
Polymorphic Variation ◽  
Swiss Mice ◽  
Allelic Substitution ◽  
Different Strains ◽  
Nei's Genetic Distance

The aim of this survey was to measure levels of genetic variation within and between 5 different strains of outbred Swiss mice. Ten to 15 animals from each strain (NIH, Q(S), ARC, IMVS and STUD) were typed, using allozyme electrophoresis, at 10 gene loci: Mod-1, Idh-1, Gpi-1, Es-1, Es-3, Hbb, Pep-3, Gr-1, Got-2 and Pgm-1. Polymorphic variation in at least one of the 5 strains was detected at all 10 loci. The proportion of polymorphic loci ranged from 0·3 (NIH) to 0·8 (IMVS) with a mean of 0·52. Average expected heterozygosities ranged from 0·08 (NIH) to 0·37 (IMVS) with a mean of 0·21. The inbred strain SWR was, as expected, homozygous at all 10 loci. The amount of allelic substitution between pairs of strains was quantified using Nei's genetic distance, and a dendrogram based on these genetic distances showed a close overall similarity in its branching pattern to the known genealogy of the strains. This survey showed that a considerable degree of genetic variation persists in the 5 strains examined, a level of variation similar to that previously detected by Rice and O'Brien (1980) in 3 other outbred Swiss strains.

scholarly journals Characterization of Deleterious Mutations in Outcrossing Populations

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 945-956 ◽  
Author(s):  
Hong-Wen Deng
Keyword(s):  
Genetic Variation ◽  
Genetic Variance ◽  
Estimation Bias ◽  
Deleterious Mutations ◽  
Environmental Variance ◽  
Higher Power ◽  
Sib Mating ◽  
The Mean ◽  
Simulation Results

Abstract Deng and Lynch recently proposed estimating the rate and effects of deleterious genomic mutations from changes in the mean and genetic variance of fitness upon selfing/outcrossing in outcrossing/highly selfing populations. The utility of our original estimation approach is limited in outcrossing populations, since selfing may not always be feasible. Here we extend the approach to any form of inbreeding in outcrossing populations. By simulations, the statistical properties of the estimation under a common form of inbreeding (sib mating) are investigated under a range of biologically plausible situations. The efficiencies of different degrees of inbreeding and two different experimental designs of estimation are also investigated. We found that estimation using the total genetic variation in the inbred generation is generally more efficient than employing the genetic variation among the mean of inbred families, and that higher degree of inbreeding employed in experiments yields higher power for estimation. The simulation results of the magnitude and direction of estimation bias under variable or epistatic mutation effects may provide a basis for accurate inferences of deleterious mutations. Simulations accounting for environmental variance of fitness suggest that, under full-sib mating, our extension can achieve reasonably well an estimation with sample sizes of only ∼2000-3000.

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

scholarly journals Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255438
Author(s):  
Vitor M. Marquioni ◽  
Marcus A. M. de Aguiar
Keyword(s):  
Population Genetics ◽  
Analytical Solution ◽  
Genetic Distance ◽  
Mean Field ◽  
Neutral Evolution ◽  
Genetic Evolution ◽  
Epidemic Spreading ◽  
Different Strains ◽  
Over Time ◽  
Good Agreement

Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains of nucleotides that can mutate inside the host. Under the hypothesis of neutral evolution we compute analytically the average pairwise genetic distance between all infecting viruses over time. We also derive a mean-field version of this equation that can be added directly to compartmental models such as SIR or SEIR to estimate the genetic evolution. We compare our results with the inferred genetic evolution of SARS-CoV-2 at the beginning of the epidemic in China and found good agreement with the analytical solution of our model. Finally, using genetic distance as a proxy for different strains, we use numerical simulations to show that the lower the connectivity between communities, e.g., cities, the higher the probability of reinfection.

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