Application of Denaturing Gradient Gel ElectrophoresisApplication of Denaturing Gradient Gel Electrophoresis(DGGE) Methods on Parent-Offspring Relationship of the Coral Pocillopora damicornis

Abstract

DGGE (Denaturing Gradient Gel Electrophoresis) is the most powerful methods for mutation detection currentlyavailable. In DGGE, DNA fragments of the same length but with different sequences can be separated. Thesensitivity of DGGE to slight sequence differences is high since single base changes could be observed. Therehas been a debate about whether planulae of the coral Pocillopora damicornis are produced sexually or asexually.If produced sexually, planulae are expected to be genetically different from each other and also from theirparents. In order to detect possible genetic difference between planulae and their parents, DGGE analysis ofITS2 region of rDNA was used. If there are genetic differences, it is proved that planulae are producedsexually. A total 49 adult colonies and 78 planulae from 11 localities were used for analysis. However, only in2 families (Bise01#02 and Bise02#03YL) showed different DGGE profile, suggesting genetic difference betweenparent and offspring. The attempt to detect genetic difference in planulae of P. damicornis and their parentsusing DGGE method was not completely success since DGGE method can not prove clearly the genetic differencebetween parent and offspring. However, the possibility that DGGE method is applicable for studying coral canbe suggested. PCR-DGEE amplification may perform with new STR (short tandem repeat) polymorphic loci ofP. damicornis that currently found to answer whether planulae are produced sexually or asexually. DGGE (Denaturant Gradient Gel Electrophoresis) merupakan salah satu teknik akurat untuk mengetahui mutasiDNA. Sensivitas DGGE sangat tinggi, karena dengan menggunakan DGGE, fragmen DNA yang memiliki panjangbasa yang sama dapat dipisahkan hanya berdasarkan perbedaan satu basa penyusunnya saja. Model reproduksikarang Pocillopora damicornis telah lama menimbulkan perdebatan. P. damicornis dilaporkan memproduksi planulaesecara seksual dan aseksual. Jika diproduksi secara seksual, planula akan berbeda secara genetik denganinduknya. Analisa DGGE dikombinasikan marker ITS2 dari rDNa digunakan untuk mendeteksi perbedaan tersebut.Jika terdapat perbedaan genetik, dapat disimpulkan planulae diproduksi secara seksual. Analisa dilakukan terhadap53 koloni dan 78 planulae dari 11 lokasi yang berbeda. Dua famili (Bise01#02 and Bise02#03YL) mempunyaiprofil DGGE berbeda antara planulae dan induknya. Hal ini menunjukkan adanya perbedaan susunan gen antaraplanulae dan induknya dan kemungkinan produksi planulae dilakukan secara seksual. Namun demikian, kombinasianalisa DGGE dan marker ITS2 dari rDNA kurang memberi hasil memuaskan. Saat ini telah ditemukan STR (shorttandem repeat) spesifik untuk P. damicornis. Kombinasi penggunaan amplifikasi PCR-DGGE dengan STR diharapkanlebih akurat untuk menjawab permasalahan produksi planulae pada karang P. damicornis.