The genus Synedrella remains monotypic in spite of its wide range of distribution, in which S. nodiflora (L.) Gaertn has taxonomically been the only member of the genus so far. This leads to assumption of the very low genetic difference among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB-rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpBrbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) as well as low haplotype diversity (0.0345) and low nucleotide diversity (0.000040). In addition, the very low fixation index (FST = 0.02645; p = 1.00000) proves low genetic difference, or in other words, indicates high connectivity among populations of S. nodiflora in Java Island. At the same time provides a fact of nearly no variation among the IGS atpB -rbcL sequences. (Chiang & Schaal, 2000a, 2000bFujii et al., 1997;Small et al., 2005;Taberlet et al., 1991). How to CiteThe purpose of this study is to know genetic diversity and the level of connectivity among S. nodiflora populations in Java Island based on IGS atpB -rbcL. It is expected from the study that molecular data can be obtained to compare with the existing taxonomical status of the species as the only member of genus Synedrella, which has been based merely on phenotypical characters. METHODSS. nodiflora samples were collected randomly from ten different locations in Java Island, i.e. Bogor (n = 5), Tasikmalaya (n = 5), Ciamis (n = 5), Banyumas (n = 10), Yogyakarta (n = 5), Mojokerto (n = 5), Probolinggo (n = 6), Malang (n = 6), Lumajang (n = 5) and Jember (n = 6) ( Figure 1). The plants were taken with their roots and were put into plastic bottles previously filled with a little water prior to be planted in pots in a glass house. Genomic DNAs were isolated from uppermost leaves following CTAB method (Doyle & Doyle, 1990). The quality and quantity of the isolated DNAs were measured using genequant. Amplification of IGS atpB -rbcL was performed using universal primers, i.e. 5'-ACA TCK ART ACK GGA CCA ATA A-3' as forward primer and 5' -AAC ACC AGC TTT RAA TCC AA-3' as reverse primer (Chiang et al., 1998). A total volume of 11.5 µl PCR mixture consisting of 2 µl template DNA, 5 µl KapaTaq DNA polymerase, 4.25 µl nuclease free water (NFW) and 0.125 µl of individual primer was subjected to PCR condition as follows: pre-denaturation of 94

Background and Aim: Reproductive traits play an important role in population increases and the egg production (EP) abilities of Indonesian local ducks (ILD). The prolactin (PRL) gene is a single chain polypeptide hormone belonging to a family of growth hormone genes that are mainly synthesized in the anterior pituitary gland in all vertebrates. It has a significant effect on reproductive traits and EP. Single nucleotide polymorphisms (SNPs) present in PRL are a useful molecular marker for EP. This study aimed to identify the PRL polymorphisms based on these SNPs and to uncover the associations with reproductive traits in ILD. Materials and Methods: A total of 280 ILDs consisting of Tegal and Magelang (F0) ducks and their reciprocal crosses, namely, Gallang (F1) and Maggal (F1), were maintained and specific variables were recorded, that is, age at first egg, body weight at first egg, first egg weight, and EP, for 90 days. Allele and genotype frequencies were used to determine the Hardy- Weinberg (H-W) equilibrium. The association between the SNP genotypes of PRL and reproductive traits was analyzed using one-way analysis of variance, following the GLM procedure of SAS. The genotypic effects on the reproductive traits were determined using regression analysis. Results: This study successfully amplified a polymerase chain reaction product of 190 bp, which was used to identify the SNP. Results indicated that PRL in ILDs is polymorphic. A SNP was found at position 164 nt (c.164G >A), consisting of three different genotypes, namely, GG, GA, and AA. The genotypes of Tegal and Magelang (F0), and Gallang (F1) populations were not in H-W equilibrium. The Maggal population (F1) was in H-W equilibrium. Significant associations were detected between the genotypes and EP in all ILDs (p<0.01), following a regression line of y=2.337x+64.605, with a determination coefficient of 0.0188 (r=0.14). Conclusion: PRL can be recommended as a candidate gene for reproductive traits in ILD, especially EP.

An intergeneric cross between Phalaenopsis 2166 and Vanda ‘saint valentine’ has successfully produced protocorms that will be grown further to form seedlings. The present study aims to genetically characterize both parents by using ndhE partial gene as its sequence is shown polymorphic among five orchid genera of the subtribe Oncidiinae. The results reveal that the ndhE partial sequences of Phalaenopsis 2166 and Vanda ‘saint valentine’ are considerably homologous with those of Oncidium. However, alignment of ndhE partial sequences between both parents shows only 58% similarity, leading to the conclusion that a relatively high genetic difference between them may occur.

A B S T R A C TPeanut is one of food crops commonly consumed in Indonesia. This species comprises several cultivars such as Kancil, Bison, Jerapah, Talam, and Tuban, each of which has its individual advantages and disadvantages. The vast variation among peanut cultivars leads to the need of study on genetic diversity and relationship among them using particular molecular marker. This study aims to see whether variation on DNA sequences among some peanut cultivars amplified with atpB-rbcL primers exists or not and to know the relationship among the cultivars based on the amplicon sequences. The method involves some sequential steps, i.e. genomic DNA isolation using CTAB protocol, amplification of DNA sequence using atpB-rbcL primers and sequencing of the amplification products. Data on sequences were edited manually using Bioedit version 7.0.4.1. Sequence alignment was performed using ClustalW, which is also implemented in Bioedit version 7.0.4.1. Arlequin 2.0 was used to calculate nucleotide diversity . Phylogenetic analysis was performed using Maximum Parsimony in MEGA 5.0. The results showed that considerably high variation in DNA sequences of some peanut cultivars amplified with atpB-rbcL primers are observed. On the other hands, very close genetic relationship among cultivars is found. KEY WORDS: DNA sequence variation, intraspecific diversity analysis, rbcL-atpB primers Penulis korespondensi: YANI YULIANI |

Humpback grouper is one of the most popular fish group in the international live trade in Asia-Pacific regions. The price for one kilogram live of humpback grouper, especially in Spermonde Archipelago South of Sulawesi, is range from 350.000-400.000 IDR, whereas in the retail level in Hong Kong the price was about 92 US$. This condition leads to the reduction of nature population due to overexploitation. Population decreasing due to overexploitation may cause loss of genetic diversity within population and lead to reduce of potential adaptive, population resistance, and productivity. Therefore, it is important to do some efforts to avoid adverse effect of overexploitation on humpback grouper population in Indonesia. One of the valuable efforts is providing genetic information such as phylogeography and genetic diversity of humpback grouper Cromileptes altivelis. Analysis was based on 618 base pairs fragment of cytochrome c oxidase I gene from 36 individuals (sequences) of Cromileptes altivelis collected at four different sites (e.g. Pulau Seribu, Jepara, Situbondo and Spermonde Archipelago). The results showed that humpback grouper population has a high haplotype and nucleotide diversity. However, high genetic diversity and polymorphisms could not reveal population fragmentation (Φ stt = 0.000). It is suggested that high gene flow rather than population sub structuring was occurred. High level genetic diversity and polymorphisms are vital related to adaptive potential to environmental alteration.

Mud clams Polymesoda erosa in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD). Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The result proved that the used RAPD marker has high polymorphisms. The mud clam population was also showed a high level of heterozigosity and genetic diversity.  This has important implication for the management plan towards ustainable use of P. erosa in the Segara Anakan Cilacap.   Key words: mud clam, RAPD, polymorphism, genetic diversity

Abstract. Susanto AH, Dwiati M, Pratiwi S. 2020. Molecular characteristics of two phenotypically identical species of Asteraceae based on the intergenic spacer trnT(UGU)-trnL(UAA). Biodiversitas 21: 5164-5169. Ogiera (Eleutheranthera ruderalis) and nodeweed (Synedrella nodiflora) are two different weed species belonging to the family Asteraceae commonly found in tropical regions. At a glance, both species show highly identical morphology, thus leading to difficulty in distinguishing between them. Therefore, molecular data based on particular markers are required. Here, we use an intergenic spacer (IGS) in the cpDNA, i.e., trnT(UGU)-trnL(UAA), as the molecular marker to reveal the difference between the two species. A pair of PCR universal primers, i.e., B48557 as the forward primer and A49291 as the reverse primer, were employed to amplify the marker. Sequence alignment was performed by the use of ClustalW implemented in Bioedit version 7.0.4.1. The results revealed that some differences with respect to both indel and base substitution were observed. Overall, this led to longer IGS trnT(UGU)-trnL(UAA) sequences of E. ruderalis than those of S. nodiflora. Although no direct relationship between the genetic and phenotypic dissimilarities was proven, coincidence seemed likely to exist. This provides molecular evidence that the two phenotypically similar species are genetically different from each other.

Giant gouramy, Osphronemus gouramy Lac. is a popular fish species in Indonesia, especially in Java and Sumatera as this freshwater fish species has a high economic value of stable price. Fish farmers in Bogor divide giant gouramy into six strains based on egg productivity, growth rate, and maximum weight of the adult. They are soang, jepang, blue saphire, paris, bastar, and porselin. These various strains lead to the need of study on the genetic relationship among them, which can be performed by the use of RAPD (Random Amplified Polymorphic DNA) marker. This study aims to determine primers producing consistent and polymorphic RAPD markers, determine specific RAPD markers, and know the genetic relationship among several giant gouramy strains. The strains used in this study are soang, jepang, and blue saphire. Survey method was applied employing purposive random sampling technique. Total genomic DNA was isolated using Genjettm genomic DNA purification kit (Fermentas), which was then used as template to amplify RAPD markers with primers OPA-07, OPA-09, OPA-11, OPA-20, OPAH-01, OPAH-08, OPAH-09, and OPAC-14. The variables examined were patterns and numbers of specific DNA fragments as the PCR amplification products. Selected primers were determined descriptively on the basis of specific DNA bands appearing on the agarose gel. Genetic diversity was predetermined by changing qualitative band pattern into quantitative binnary data. Genetic relationship was analyzed using cladistic method with PAUP software. The results showed that only five of the eight primers produce consistent and polymorphic RAPD markers, i.e. OPA-11, OPA-20, OPAH-1, OPAH-8, and OPAH-9. Specific RAPD markers which can be used to distinguish several gouramy strains are those amplified with OPA-20 of 786 bp, OPA-20 of 1,176 bp, OPAH-8 of 1,000 bp and OPAC-14 of 1,607 bp. Nervertheless, it was found that RAPD markers cannot be used to clearly determine genetic relationship among gouramy strains.