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All Journal Jurnal Penelitian Tanaman Industri Jurnal Tanaman Industri dan Penyegar Jurnal Penelitian Tanaman Industri (Littri)
Rubiyo Rubiyo
Pusat Penelitian dan Pengembangan Perkebunan
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Industrial & Manufacturing Engineering

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Pendugaan Parameter Genetik Ketahanan Tanaman Kakao terhadap Penyakit Busuk Buah Rubiyo Rubiyo; Sudarsono Sudarsono
Jurnal Tanaman Industri dan Penyegar Vol 2, No 3 (2011): Buletin Riset Tanaman Rempah dan Aneka Tanaman Industri
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Rapid method for cocoa breeding as an effort to produce high productivity and quality cocoa clones which are resistant to main disease infected by Phytophtora palmivora, pathogen causing black pod disease, needs to be investigated. For that reason, providing the information about various genetic parameters will really assist to solve the problems in cocoa cultivation and farming in Indonesia. One of the estimation methods of some genetic parameters which is eligible to be used is diallel crossing analysis. The research aimed at estimating genetic parameter of cocoa resistance to the disease caused by P. palmivora, using half dialel crossing. The cross used five cocoa clones as parental clones ( ICCRI 3, TSH 858, DR 1, ICS 13 and Sca 6). The clones represented selected clones resulted from resistance evaluation of previous research, with the resistance level from vulnerable to resistant. The number of genotypes in this research were 15, consisting of 10 F1, and 5 parental clones. Research took place from 2007 to 2008 in Experimental Plot of Kaliwining, Indonesian Coffee and Cocoa Research Center, Jember East Java. Seedlings from the crossing used for the research of every combination consisted of 20 seedlings replicated 3 times. Inoculum type used was mycellia, from selected inoculum in research I. Inoculation was done in leaf and to maintain the moisture (90%) it was covered by plastic. Observation was conducted 3 days after inoculation on the spot area caused by P. palmivora infection. The research indicated that there was no gene interaction in determining resistance to the disease caused by P. palmivora which mostly influenced by additive gene actions. Kd / kr was 1,3594 indicated that there were more dominant gene in parental. Heritability values in a broad and narrow sense belong to high group.
ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker Surti Kurniasih; Rubiyo Rubiyo; Asep Setiawan; Agus Purwantara; Sudarsono Sudarsono
Jurnal Penelitian Tanaman Industri Vol 17, No 4 (2011): Desember 2011
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jlittri.v17n4.2011.156-162

Abstract

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 < 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (<7.50). The rest of the cacao clones were in the third group with diversity coefficient of>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.Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity AbstrakMarka 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<3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman < 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman > 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.Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas
ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker Surti Kurniasih; Rubiyo Rubiyo; Asep Setiawan; Agus Purwantara; Sudarsono Sudarsono
Jurnal Penelitian Tanaman Industri Vol 17, No 4 (2011): Desember 2011
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jlittri.v17n4.2011.156-162

Abstract

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 < 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (<7.50). The rest of the cacao clones were in the third group with diversity coefficient of>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.Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity AbstrakMarka 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<3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman < 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman > 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.Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas
Co-Authors Agus Purwantara Setiawan, Asep S Sudarsono Sudarsono Sudarsono Sudarsono Surti Kurniasih