With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.

Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involve the endothelin 3 gene, EDN3. A genomic region, DR1 of 127 kb, together with another region, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversion of one DR2. Quantitative PCR and copy number variation analyses on the Cemani genome sequence confirmed the duplication of EDN3. These genetic arrangements are identical in Cemani and Silkie, indicating a single origin of the genetic cause of Fm. The two DR1s harbor two distinct EDN3 haplotypes in a form of permanent heterozygosity, although they remain allelic in the ancestral Red Jungle Fowl population and some domesticated chicken breeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemani and Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguous record for selective sweep that extends in both directions from tandemly duplicated EDN3 loci. This highly homozygous tract is different in length between Cemani and Silkie, reflecting their distinct breeding histories. It is estimated that the Fm phenotype came into existence at least 6600–9100 years ago, prior to domestication of Cemani and Silkie, and that throughout domestication there has been intense artificial selection with strength s > 50% in each breed.

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BackgroundIn previous studies, the Mx Gene has been demonstrated to confer positive anti viral responses in chicken. The amino acid variation of Asn (allele A) at position 631 was specific to positive antiviral Mx/resistant, while, that of Ser (allele G) was specific to negative Mx/susceptible. This research was aimed at selecting one of the native chicken breeds which was found out to be resistant to avian influenza using molecular technique. The selected breed will then be used as the base population to improve native chicken breed in Indonesia.MethodsMarker Assisted Selection (MAS) method was used in this research to accelerate the selection process, since the disease resistance had low heritability value. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique used to select the genotype of Mx++, Mx+- and Mx-- that corresponded to the positive antiviral activity (Mx++), or those which had positive or negative activity (Mx+-) and negative antiviral activity (Mx--). There were 200 native hens and 40 cocks used in this experiment. Allele frequency of Mx Gene was calculated. The productivity indicators such as age at first laying, egg weight and hen weight at first laying and egg production were also measured. The chicken that had Mx++ and Mx+- genotypes, were selected to produce offspring.ResultsResult showed that the frequency of the resistant allele (Mx+) was 65% and 60% in laying hens and in cocks, respectively, while the frequency of the susceptible allele (Mx-) was 35% and 40% in hens and cocks, resepctively. Age, egg weight and hen weight at first laying and egg production for susceptible genotype were slightly better than for the resistant genotype which were 172,41 VS 178,81 days; 33,94 VS 32,84 g; 1450 VS 1439 g and 54,32 VS 48,30 %, respectively.

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (Gallus gallus) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar.

ABSTRAKTujuan penelitian ini adalah mempelajari keragaman genetik populasi domba di Indonesia menggunakan penciri DNA mikrosatelit. Sebanyak 18 lokus DNA mikrosatelit digunakan untuk menentukan genotipe populasi domba Indonesia. Sampel darah domba yang digunakan sebanyak 200 ekor berasal dari populasi domba garut tipe tangkas, domba garut tipe daging, domba purbalingga, domba batur dan domba jember diektraksi DNA total dengan menggunakan metode salting out. Data lokus DNA mikrosatelit dianalisis menggunakan program POPGENE 3.2. Hasil penelitian menunjukkan bahwa diperoleh sebanyak 180 alel dari 17 lokus DNA mikrosatelit, sedangkan rataan jumlah alel adalah 10 alel (6 sampai 18 alel) dari lima populasi domba Indonesia (domba garut tipe tangkas, domba garut tipe daging, domba purbalingga, domba batur dan domba jember). Nilai heterosigositas observasi (Ho) dan heterosigostas harapan (He) diperoleh masing-masing 0,5749 dan 0,6896, sedangkan nilai genetik diferensiasi untuk inbreeding antar populasi (FIS), dalam populasi (FIT) dan rataan diferensiasi genetik (FST) masing-masing 0,1006; 0,1647 dan 0,0712. Jarak genetik dan pohon genetik menunjukkan bahwa populasi domba Indonesia berbeda antara populasi domba garut tipe tangkas, domba garut tipe daging, domba purbalingga, domba batur dan domba jember. Berdasarkan hasil penelitian dapat disimpulkan bahwa diperlukan strategi program pemuliaan, pelestarian dan pemanfaatan secara berkelanjutan pada setiap populasi domba di Indonesia. Kata-kata kunci: domba Indonesia, penciri DNA mikrosatelit, keragaman genetik ABSTRACTThe purpose of this research was to study genetic diversity in Indonesian sheep population using microsatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep. Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci data were analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from 17 microsatellite loci, while average number of alleles was 6.10 alleles (6 to 18 alleles) from five Indonesian sheep populations (garut sheep of fighting type, garut sheep of meat type, purbalingga sheep, batur sheep and jember sheep population). The average of observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.5749 and 0.6896, respectively, while the genetic differentiation for inbreeding among population (FIS), within population (FIT) and average genetic differentiation (FST) were 0.1006, 0.1647 and 0.0712, respectively. Genetic distance and genetic tree showed that Indonesian sheep population was distinct from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep population. Based on this results were needed a strategy for conservation and breeding programs in each Indonesian sheep population.

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.