Potato is one of high economically horticultural plant. The increasing of national consumption of potato becomes a challenge for potato breeders. The success of breeding programs is depending on availability of genetic diversity. The aim of this research was to analyze the genetic diversity of fourteen accessions of potato by using SSR and STS markers. PCR analysis was scored as biner data and the collected data was analyzed using NTSYS and PowerMarker. The result showed that there were 63% polymorphic (12 markers) of total markers. As many as 60 alleles with the size of 200-500 bp were identified by a range of 2-9 alleles per locus. The polymorphism level was 0.59 (0.36-0.74). Result also showed the average of major allele frequency was 49.42% (35.71-63.64%). Nine markers which have polymorphism level more than 0.5 could be used to detect genetic diversity of potato. The average of genetic diversity index was 0.65. Cluster analysis showed that 14 accessions of potato were split in two groups (coefficient 0.70). The first groups consisted of Atlantik, GM 05, Granola Kembang Merbabu 17, and the second groups consist of Repita, Maglia, Medians, CIP397078.7, CIP392781.1, Margahayu, Granola, CIP394613.139, Amabile, and Tenggo. The information of genetic diversity of this germplasm could be used as a preliminary basis for choosing crossing parents in potato breeding in Indonesia.Keywords: Potato (Solanum tuberosum L.), SSR, STS, genetic diversity. ABSTRAKKentang (Solanum tuberosum L.) merupakan salah satu tanaman hortikultura yang memiliki nilai ekonomis tinggi. Meningkatnya kebutuhan konsumsi kentang nasional menjadi tantangan bagi pemulia kentang. Tersedianya sumber keragaman genetika merupakan prasyarat keberhasilan program pemuliaan suatu varietas. Penelitian ini bertujuan menganalisis keragaman genetika empat belas aksesi kentang menggunakan marka simple sequence repeats (SSR) dan sequence-tagged sites (STS). Hasil analisis polymerase chain reaction (PCR) diberi skor sebagai data biner. Analisis data dilakukan menggunakan perangkat lunak NTSYS dan PowerMarker. Hasil penelitian menunjukkan dari 19 marka yang digunakan terdapat 12 marka (63%) yang bersifat polimorfik. Sebanyak 60 alel berukuran antara 200-500 bp dengan kisaran 2-9 alel per lokus berhasil dideteksi. Nilai polymorphic information content (PIC) menunjukkan rerata sebesar 0,59 dengan nilai tertinggi 0,74 (RGH-SSR 21) dan nilai terendah 0,36 (RGH-SSR 30). Rerata frekuensi alel utama adalah 49,42% dengan nilai terendah 35,71% (STG-0016) dan nilai tertinggi 63,64% (RGH-SSR 40). Terdapat 9 marka dengan nilai PIC >0,5 yang dapat digunakan untuk mendeteksi keragaman genetika aksesi kentang. Keragaman aksesi kentang tersebut cukup tinggi, seperti yang direfleksikan oleh nilai rerata diversitas gen, yaitu 0,65. Hasil analisis klaster menunjukkan bahwa keempat belas aksesi kentang tersebut mengelompok menjadi dua kelompok utama pada koefisien 0,70. Kelompok pertama terdiri atas varietas Atlantik, GM 05, Granola Kembang, dan Merbabu 17, sedangkan kelomp...

<p>Sebagai salah satu komoditas tanaman pangan penting di Indonesia setelah padi dan jagung, kedelai memerlukan upaya peningkatan keragaman genetik dengan cara introduksi aksesi dari negara lain terutama Cina sebagai salah satu negara asal kedelai di dunia. Marka <em>simple sequence repeat </em>(SSR) dapat digunakan untuk analisis keragaman genetik antaraksesi kedelai introduksi. Tujuan penelitian ini adalah mempelajari keragaman genotipik dan fenotipik 48 aksesi kedelai introduksi asal Cina menggunakan 15 marka SSR. Analisis DNA dilakukan menggunakan PCR dan data hasil PCR menggunakan marka SSR dianalisis menggunakan perangkat lunak XLSTAT, NTSYS, dan <em>Power</em><em>M</em><em>arker</em>. Data karakter morfologis diperoleh dari basis data <em>Germplasm Resources Information Network</em> (GRIN), <em>United States Department of Agriculture</em> (USDA) (<a href="http://www.ars-grin.gov/">www.ars-grin.gov</a>). Data ini digunakan sebagai data keragaman fenotipik yang diperlukan untuk menunjang hasil karakterisasi molekuler. Hasil penelitian menunjukkan bahwa terdapat keragaman karakter morfologis dan molekuler antaraksesi kedelai yang dipelajari. Berdasarkan hasil analisis komponen utama, karakter tinggi tanaman, bobot 100 biji, hasil biji, warna pusar biji, warna trikoma, warna bunga, dan warna polong berkontribusi besar terhadap keragaman total. Analisis molekuler menggunakan marka SSR menunjukkan bahwa terdapat variasi alel yang cukup tinggi (9–25 alel) di antara aksesi kedelai dengan rerata jumlah alel 15,6, sedangkan rerata nilai <em>Polymorphism Information Content </em>(PIC) sebesar 0,89 (0,84–0,94). Seluruh marka SSR memiliki nilai PIC&gt;0,5 yang menunjukkan bahwa marka tersebut informatif untuk studi keragaman genetik kedelai dengan rerata nilai diversitas gen sebesar 0,90. Hasil analisis filogenetik dan analisis koordinat utama menunjukkan bahwa 48 aksesi tersebut mengelompok menjadi tiga dengan koefisien kemiripan 0,84. Pada penelitian ini dilakukan pula uji asosiasi antara marka SSR dan karakter morfologis. Asosiasi yang signifikan ditemukan pada tujuh lokus marka SSR. Persentase keragaman total yang dapat dijelaskan oleh marka SSR tersebut, yaitu 17,25–78,45%. Marka GMES2225 dan Sat_286 berasosiasi dengan warna kulit biji, sedangkan marka GmF35H berasosiasi dengan tinggi tanaman. Informasi keragaman genetik akan sangat bermanfaat sebagai langkah awal untuk kegiatan seleksi tetua persilangan dengan sifat yang diinginkan dalam membantu program pemuliaan kedelai di Indonesia.</p>

<p>Jarak pagar (<em>Jatropha</em><em> </em><em>curcas</em> L.) merupakan salah satu tanaman yang potensial sebagai penghasil energi alternatif bahan bakar fosil. Informasi mengenai keragaman genetik genus <em>Jatropha</em> spp. sangat penting untuk menentukan arah kegiatan pemuliaan ke depan. Tujuan penelitian ini adalah menganalisis keragaman genetik 20 aksesi plasma nutfah <em>Jatropha</em> spp. asal Indonesia dan Thailand menggunakan 20 marka SSR. Sebanyak 129 alel berhasil dideteksi dengan rentang 4-9 alel per lokus dan rerata 6,5 alel. Nilai diversitas gen sebesar 0,53 hingga 0,86 dengan rerata 0,75, sedangkan nilai PIC sebesar 0,49 hingga 0,84 dengan rerata 0,71. Sebanyak 12 marka memiliki nilai PIC &gt; 0,70 dan bersifat informatif untuk membedakan individu jarak. Rerata frekuensi alel utama yang diperoleh sebesar 37% dengan rentang 18–55%. Sebanyak 7 marka SSR mampu membedakan genotipe heterozigot dengan nilai heterozigositas sebesar 0,05 hingga 0,11 dengan rerata 0,03. Hasil analisis filogenetik menunjukkan bahwa 20 aksesi <em>Jatropha</em> spp. memisah menjadi dua klaster utama pada koefisien kesamaan 0,70. Klaster pertama terdiri atas 17 aksesi <em>J. curcas</em>,<em> </em>sedangkan klaster kedua terdiri atas 3 aksesi, yaitu <em>J. podagrica</em>, <em>J. gossypifolia</em>, dan <em>J. multifida</em>. Data keragaman genetik yang diperoleh pada penelitian ini dapat dimanfaatkan sebagai dasar pemilihan tetua persilangan dalam rangka menghasilkan varietas unggul baru dengan karakter kadar minyak tinggi sesuai yang diharapkan.</p>

Chili pepper (Capsicum annuum) is one of the high economical horticultural comodity in Indonesia and its genetic diversity contributes to the success of breeding programs. Simple sequence repeat (SSR) markers can be used to analyze genetic diversity among chili pepper genotypes. The aim of this research was to analyze the genetic diversity of twenty-seven genotypes of chili pepper by using 24 SSR markers. The collected data was analyzed using cluster analysis and principle coordinate analysis (PCoA). The result showed that high allele variation (4–17 alleles) was observed among chili pepper genotypes tested, with an average allele number and Polymorphism Information Content (PIC) value was 7.708 and 0.758 (0.598–0.920) respectively. All of SSR markers showed PIC value >0.5 which indicated that these markers were suitable for chili pepper diversity studies with a high differentiation and with the average value of genetic diversity was 0.78. The clustering and principle coordinate analysis showed that twenty-seven genotypes of chili pepper were divided into two groups (coefficient of similarity 0.74 in cluster analysis) indicating a high genetic variability among them. Genetic diversity analysis in this study will be useful as an initial basis of selection for appropriate parents with desired traits to assist the breeding program of chili pepper in Indonesia.

Abstract. Asadi, Dewi N, Nugroho K, Terryana RT, Mastur, Lestari P. 2020. Evaluation of SSR and important agronomical characters of promising mutant lines of soybean. Biodiversitas 21: 299-310. Improved soybean (Glycine max (L.) Merr.) varieties resistant to major pest or disease, and in accordance with consumer preferences are important in breeding programs to raise their productivity. Identification of superior promising mutant lines of soybean before releasing them needs multiple environment trials complemented with molecular assay. This study aimed to assess morpho-agronomical and molecular characters using SSR markers of promising mutant lines of soybean (Glycine max (L.) Merr.). A total of 14 SSR markers were used to evaluate 20 mutant lines along with their parental lines and check varieties, and eight different locations were chosen to field evaluation of 11 selected lines induced by gamma-ray. Values of Polymorphism Information Content, allele number, and gene diversity index were high, indicating the great genetic diversity among these mutant lines, and far distant from their parental lines. Phylogenetic tree also supported the distinguishable among gamma ray-induced mutant lines compared to the parental lines. The significant interaction between promising line and environment showed their high adaptability and stable yield in various environments. Biosoy-8 (2.713 ton/ha) and Biosoy-11 (2.631 ton/ha) revealing the high yields lines supported with the molecular information could be potential to be released as new varieties and can direct their efficient utilization for field application or further improvement scheme.

A B S T R A C TThe use of molecular marker is an efficient approach to analyze the genetic diversity and it can be used widely in biological studies. The characterization of rice germplasms by using molecular markers technique is more precise because it is not influenced by environmental factors. The purpose of this study was to analyze the genetic diversity of 24 varieties of lowland and upland rice by using 15 SSR markers. The results showed as many as 86 alleles were detected in 24 rice varieties, with the average number of alleles per marker was 5.73 and the range of alleles per locus was 2-10. The average of major allele frequency was 43% with the lowest score was 26% on RM6997 and RM536 markers and the highest score was 65% on RM60 marker. A total of 14 SSR markers were able to discriminate heterozygous alleles within a range between 0.17 (RM105) to 1.00 (RM201, RM263, RM416, RM518 and RM223). The value of gene diversity ranged from 0.48 (RM60) to 0.81 (RM536) with an average of 0.70. The value of PIC (Polymorphic Information Content) ranged from 0.38 (RM105) to 0.78 (RM536) with an average of 0.65. The phylogenetic analysis showed that 24 rice varieties separate into two main clusters in the coefficient of 0.63. The first cluster consists of 12 lowland varieties and the second cluster consists of 12 upland varieties. The genetic diversity data in this study were expected could be a valuable information in the rice plant breeding activities in the future.

Sugar palm (Arenga pinnata Merr.) originating from Indonesia, is classified as underutilized plant but has potential as water conservation and high productivity sugar producer. Therefore, it is important to have baseline genetic diversity information for this plant species. In this study, seven simple sequence repeat (SSR) markers were used to analyse genetic diversity of sugar palm trees among the populations collected from their natural areas, especially in Cianjur Regency located in West Java and Banten Province. To measure their genetic diversity, phylogenetic tree and principal coordinate analysis were performed using using recommended softwares. The results revealed that high allele variation (23-33 alleles) was observed among sugar palm samples tested, with an average allele number and polymorphism information content (PIC) value was 27.143 and 0.942 (0.937-0.951) respectively. All of SSR markers showed PIC value >0.9 which indicated that these markers were suitable for sugar palm diversity studies with a high differentiation. The UPGMA cluster analysis based on Nei’s standard genetic distance and principle coordinate analysis produced two main groups that wereCianjur and Banten populations, indicating the geographical differentiation.. Taken together, the generated information about genetic diversity of sugar palm in this study could importantly contribute to assist sugar palm breeding program in Indonesia.

<p>Shallot (Allium cepa var. aggregatum) is one of the most important vegetable crops grown in Indonesia. The limited knowledge available on the genetic diversity and the threat of plant disease have been major problems to maintain high shallot production in Indonesia. Development of molecular markers linked to disease resistance is required for molecular breeding activity in this crop. This study aimed to assess the genetic diversity at conserved domain of resistance gene analog (RGA) in a set of 36 Indonesian shallot genotypes to complement morphological characterization. Twelve morphological and fifteen molecular markers traits were investigated in an attempt to characterize and to discriminate the Indonesian shallots genotypes. Characterization at orphological level indicated that phenotypic variance was highest for total bulb weight (TWB, cv = 99.39%) and the least for the plant height (PH, cv = 28.16%). The correlation analysis between traits showed that TWB and number of bulb (NB), TWB and bulb weight per plant (WB), NB and WB, and WB and PH were positively correlated. Molecular analysis revealed a total of 1,512 alleles with an average of 1.946 alleles per locus. The Polymorphism Information Content (PIC) values ranged from 0.253 to 0.676 and six out of 15 RGA markers were highly informative with PIC values ≥0.50. Based on cluster analysis, the 36 Indonesian shallot genotypes were clearly discriminated into six major groups. These results revealed that the RGA-based markers could support the morphological characterization in evaluating the genetic diversity of shallots. </p>