East African origins for Madagascan chickens as indicated by mitochondrial DNA.

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.

The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesian Cemani and Chinese Silkie breeds.

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.

Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers.

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.

Selection of Mx gene genotype as genetic marker for Avian Influenza resistance in Indonesian native chicken.

BACKGROUND: In 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. METHODS: Marker 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. RESULTS: Result 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.

Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci.

Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.