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Kristianto Nugroho

Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian

Author-ID : 2693438

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Genetic Diversity Analysis and Development of DNA Fingerprints of 20 Indonesian Local Chili Pepper Varieties Based on SSR Markers Rerenstradika Tizar Terryana; Nadia Della Savitri Ayu Ningrum; Kristianto Nugroho; Darmawan Saptadi; Helmi Kurniawan; Puji Lestari
Jurnal AgroBiogen Vol 16, No 2 (2020): December
Publisher : Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/jbio.v16n2.2020.p45-58

Chili pepper is one of the most valuable horticultural crops, widely cultivated in Indonesia. Analysis of its genetic diversity is needed to develop successful breeding programs of local varieties. Simple sequence repeat (SSR), a robust molecular marker used for genetic diversity analysis in plant species, offers potential, reliable DNA fingerprinting method to assess genetic variation and varietal identification of chili pepper. Fifteen SSR markers were used in this study to analyze the genetic diversity and develop profiling identification of DNA fingerprint of local chili pepper varieties. Twenty local and two improved varieties of three chili pepper species, consisting of 3, 1, and 18 varieties of Capsicum frutescens, C. chinense, and C. annuum, respectively, were assessed for their SSR polymorphism. A total of 87 alleles was obtained from the polymorphism analysis with high alleles variation (2–16 alleles) with average total allele of 5.8 and average polymorphism information content (PIC) of 0.59 (0.34–0.83). Clustering and Principle Coordinate Analyses (PCoA) classified the varieties into two groups with coefficient of similarity of 0.65 indicating their high genetic variability. Most local varieties belonged to the same cluster and separated from the two improved varieties. Based on PIC values and dendrogram with selected markers, five SSR markers, i.e. EPMS441, EPMS331, EPMS335, GPMS194, and CaSSRBio1.1, were identified as SSR marker set for DNA fingerprinting purposes. SSR marker set used in this study was successful in developing the varietal identity of local chili pepper varieties, as indicated by unique code of each variety.

KERAGAMAN GENETIK 24 VARIETAS PADI SAWAH DAN PADI GOGO (Oryza sativa L.) INDONESIA BERDASARKAN MARKA SSR Kristianto Nugroho; Slamet Slamet; Puji Lestari
Scripta Biologica Vol 4, No 1 (2017)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

The 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.

METODE EKSTRAKSI DNA CABAI (Capsicum annuum L.) MENGGUNAKAN MODIFIKASI BUFFER CTAB (CETHYL TRIMETHYL AMMONIUM BROMIDE) TANPA NITROGEN CAIR Kristianto Nugroho; Rerenstradika T Terryana; Puji Lestari
Scripta Biologica Vol 4, No 2 (2017)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

Chili pepper is an agricultural commodity having high economic value. The production and supply of chili pepper frequently did not match the increased demand; it caused the market price fluctuated. It is important to create new varieties of chili pepper with high production trait to overcome the scarcity. Therefore the plant breeding activities for chili pepper should be done intensively in both conventional and molecular-based to obtain varieties of chili pepper with expected qualities. In molecular breeding, DNA extraction is the crucial steps of the process. If extracted DNA has an excellent quality and quantity, the next processes normally could be completed with the high-quality result. To date, most methods of DNA extraction used liquid nitrogen to destroy the tough carbohydrates of plant tissue. Liquid nitrogen is nitrogen gas in a fluid state which quite difficult to be distributed to the remote laboratory wit no available storage facility. This study aimed to obtain a modified DNA extraction method, in particular for chili pepper, which capable to produce DNA with high quality and quantity without using liquid nitrogen. The sample used consisted of eight F2 plants including their hybrid-parental of the Kencana and the 0207. This research applied modified Doyle and Doyle method for extraction. Modification of extraction buffer is done through the addition of the 1% (w/v) PVP (Polyvinylpyrrolidone) and 0.2% (v/v) β-mercaptoethanol. The results showed that the DNA extracted using this method has good quality and quantity, capable of being amplified by using SSR (Simple Sequence Repeat) primer and could be digested by restriction enzyme EcoRI. Besides, this method can reduce dependence on the use of liquid nitrogen, in particular for remote laboratories with no available storage facility.

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