Sri Sulandari

• Universitas Ngurah Rai

Thirty-three individuals from four populations of green junglefowl (Gallus varius) were collected throughout Indonesia: 14 from Central Java, 4 from Eastern Java, 3 from Sumbawa island and 12 from Flores island. The mitochondrial DNA D-loop the samples were analysed for sequence diversity. Twenty-five haplotypes with 28 polymorphic sites were ident...

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...

Expected heterozygosity at individual SNP sites in the nine regions in chicken breeds. (a) Domesticated chickens, RJF, and GJF, (b) Ayam Cemani, (c) Silkie chicken. (TIF)

Characteristic morphological traits of several Indonesian chickens and Chinese Silkie. (a) Female Cemani, (b)—(d) female Kedu, (e)—(i) male Kedu, (j) male white Silkie and (k) male black Silkie. (TIF)

NJ trees for the nine regions in domesticated chicken breeds, and RJF. The phylogenetic relationship differs greatly from region to region. Two GJF haplotype sequences were used as outgroups. (TIF)

STRUCTURE analysis of each of the nine regions of GJF, RJF, Cemani, Silkie and other domesticated chickens. For regions 3–5, Cemani and Silkie exhibit nearly identical genetic components, whereas in other regions, there are no noticeable structural differences among chicken breeds and RJF. (TIF)

Sequences of primers used in this study. (PDF)

Segregating sites in EDN3 haplotypes. (PDF)

Nucleotide diversity between Cemani and Silkie based on NGS data. Bars with R1–R9 indicate the positions of the nine regions. Green square parentheses indicate the position of EDN3, and a red bar indicates the 71.4-kb region with low divergence between the two breeds. (TIF)

Reaction mixtures and PCR conditions used in this study. (PDF)

Sequence information for duplication boundaries generated by the A2 and B2 primer sets. The A2 and B2 sequences of Cemani (CM6_A2 and CM6_B2) are identical to those of Silkie (SIB17_A2 and SIB17_B2). The boundary was determined by comparison between A1 (CM31_A1) and A2 (upper panel), and between B1 (CM6_B1) and B2 (lower panel). (TIF)

Variable sites in the 71.4-kb region in Cemani, Silkie and Taiwanese L2 as compared to the reference genome. The region ranges from nt 11,183,600 to 11,255,000 and includes part of DR1. Insertions and deletions are excluded. The colored columns indicate the Silkie (green)- or Cemani (red)-specific mutations. (PDF)

Results of the HKA test in each of the nine regions of Cemani (a), Silkie (b), and other domesticated chickens (c). The significant reduction in DNA polymorphism is found in Cemani and Silkie only for DDX27 in region 3, EDN3 in region 4, and TH1L in region 5 are compared. (TIF)

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. D...

ESM Table 2. Genetic diversity measures for each chicken population from Indonesia, South Asia, Continental Africa, and Madagascar.

ESM Figure 1. Principal Coordinate Analysis (PCoA) via covariance matrix of pairwise genetic distances of D haplotypes observed in Africa (blue), South Asia (brown), Indonesia (green), and Madagascar (purple).

ESM Figure 2. Median-joining network depicting the relationship of the E haplotypes observed in East Africa and Madagascar (blue), South Asia (black) and Indonesia (green).

This study was conducted to evaluate the genetic diversity and phylogeny of Gembrong goat. For this purpose, 21 goats from endangered breed in Karangasem Bali were used. Molecular analysis of genetic diversity and phylogeography used hypervariable segment 1 of mitochondrial DNA control region. The result showed that genetic variability of Gembrong...

Sumatran elephants (Elephas maximus sumatranus) is endemic of Asian elephants in Indonesia, an endangered animal and listed on Appendix I of CITES. Therefore, information on the status and distribution of the population of Sumatran elephants, including the distribution of genetic diversity is necessary to facilitate the development of adequate cons...

A total of 1178 individuals of nearly complete sampling of 49 populations belong to 14 most popular Indonesian indigenous chicken breeds, geographically localized in different islands, were genotyped using 20 microsatellite DNA markers to investigate their molecular diversity and genetic relationship. In total, 259 alleles were observed among 49 po...

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...

Gembrong goat is animal genetic resources which endemic in Bali island and only exists in Karangasem regency. The current population status of the gembrong goat is critical. Therefore, the population development of in-situ or ex-situ needs to be conducted. Close relative mating tend to occur in conditions such as in a small population, critical sta...

Captive breeding of endangered species is often difficult, and may be hampered by many factors. Sexual monomorphism, in which males and females are not easily distinguishable, is one such factor and is a common problem in captive breeding of many avian and reptile species. Species-specific nuclear DNA markers, recently developed to identify portion...

Visually identifying the sex of a bird can be difficult. It cannot be done in half the world’s species when they are adults, and virtually none can be sexed as chicks. Despite this, the sex of a bird is vital for captive breeding. An increased number of birds are being sexed using DNA amplification techniques. In this approach, the CHD-W and CHD-Z...

The 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 populatio...

The Mitochondrial DNA (mtDNA) D-loop segment was PCR amplified and subsequently sequenced for a total of 335 individuals from Indonesian native chicken. The individuals were drawn from sixteen populations of native chicken and three individuals of green jungle fowls (Gallus varius). Indonesian native chicken populations were: Pelung Sembawa, PL (n...

Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymo...

ZEIN, M.S.A., S. SULANDARI, MULADNO, SUBANDRIYO and RIWANTORO. 2012. Genetic diversity and phylogenetic relationship of Indonesian Local goats using microsatellite DNA markers. JITV 17(1): 25-35. Genetic diversity is important information in the process of conservation and sustainable utilization of animal genetic resources. Thirteen microsatellite...

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 b...

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 (...

An A/G Single Nucleotide Polymorphism (SNP) at position 1,892 of the Mx gene coding sequence has been linked to susceptibility/resistance to avian viral infection in vitro . Using PCR-RFLP and sequencing methods, 1,946 samples from 109 populations from Asia, Africa and Europe; grouped as indigenous village, commercial, fancy chicken as well as wild...

It has previously been demonstrated that a G/A Single Nucleotide Polymorphism (SNP) at nucleotide position 1,892 of coding sequence of chicken Mx gene confers susceptibility/resistance to avian viral diseases. The aim of this study was to assess the geographical distribution of G/A alleles in relation to different genetic backgrounds of a wide rang...

The current poultry is a domesticated chickens used for both meat and egg production. Pedigree investigation is an important part to understand the process of chicken domestication in Indonesia. Molecular DNA approach using D-loop Mitochondrial DNA marker (hypervariable 1 segment) was used in this analysis. The objective of the study was to constru...

ABSTRAK Ayam Nunukan merupakan ayam lokal khas Kalimantan Timur, yang penyebarannya banyak terdapat di Pulau Tarakan dan Nunukan. Ayam ini mempunyai ciri spesifik warna bulu coklat kemerahan (buff) dengan pola bulu Columbian (bagian ujung sayap dan ekor berwarna hitam) serta bulu utama sayap dan ekor tidak berkembang (bersifat lambat tumbuh bulu) y...

ABSTRAK Ayam Gaok merupakan plasma nutfah ayam lokal khas Madura yang mempunyai potensi untuk dikembangkan. Ciri spesifik ayam Gaok adalah warna bulu betina bervariasi dengan leher lurik hitam putih. Warna bulu jantan lebih seragam memiliki warna dasar kehijauan dengan bulu penutup dan bulu leher putih silver kekuningan, bulu ekor hitam kuning kehi...