&lt;b&gt;Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia

Susanti, Retno; Iswari, Retno Sri; Fibriana, Fidia; Sari, Retno

doi:10.4025/actascianimsci.v39i4.34352

Cited by 5 publications

(4 citation statements)

References 24 publications

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“…The haplotypes indicate the low diversity of these ducks based on the COI gene where COI serves as the identity/barcode of duck species. In comparison with the ducks D-loop genes, the diversity of duck species shows 23 haplotypes (Susanti et al 2017). COI can serve as a barcode if the variation is very small within species.…”

Section: Discussionmentioning

confidence: 99%

“…Compared to the D-loop gene, the COI gene of Javanese duck show only a few polymorphic sites and haplotypes formed. The analysis of 718 nucleotides from D-loop genes in 35 samples of Central Javanese duck showed 32 polymorphic sites and 23 haplotypes (Susanti et al 2017). Based on Table 1, it can be seen that the types of ducks that show variations are 2 Tegal Branjangan ducks (haplotype B and E) and 2 Pekin duck (haplotype C and D).…”

Section: Coi Gene Sequence Analysismentioning

confidence: 96%

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The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool

et al. 2018

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Susanti R, Iswari RS, Fibriana F, Indriawati. 2018. The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool. Biodiversitas 19: 997-1003. The local duck DNA barcoding is still rarely conducted in Indonesia while DNA barcoding is extensively used as a tool of species identification and delineation tool. This study aimed to analyze the sequence and patterns of Central Javanese ducks mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Feather samples of seven breeds of native duck were collected from traditional husbandries in Central Java. The samples were employed for DNA extraction and COI gene amplification. Five haplotypes were obtained from 35 samples, i.e., haplotype A, B, C, D, and E. Also, 9 variable sites with synonym substitution was detected in four nucleotides number 55, 61, 100, and 109; whereas five synonym substitutions were identified in the nucleotides number 36, 48, 51, 66, and 756. In conclusion, this study annotates that COI mtDNA gene is essential for local ducks barcoding system.

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Section: Discussionmentioning

confidence: 99%

Section: Coi Gene Sequence Analysismentioning

confidence: 96%

The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool

et al. 2018

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“…In Indonesia, genetic diversity of duck turned into finished through numerous molecular techniques which include microsatellite (Susanti et al 2021b) and mitochondrial DNA (Susanti et al 2017;Susanti et al 2018), but there are no reports concerning the use of ISSR marker on domesticated duck. Inter-simple sequence repeats (ISSRs) are domains inside the genome clamped by microsatellite sequences (simple sequence repeats; SSRs).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Central Javanese duck (Indonesia) based on Inter Simple Sequence Repeat markers

et al. 2022

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Abstract. Susanti R, Kartikasari AD, Sasi FA, Arlinda DD. 2022. Genetic diversity of Central Javanese duck (Indonesia) based on Inter Simple Sequence Repeat markers. Biodiversitas 23: 1807-1813. Genetic resources of local livestock need to be documented and conserved to prevent genetic erosion of the germplasm. This study aimed to determine the genetic diversity of domestic ducks (Anas platyrhynchos domesticus) in Central Java, Indonesia, based on Inter Simple Sequence Repeat (ISSR) markers. There were seven types of Central Javanese ducks used in this research. DNA was extracted from feathers samples. To give rise to ISSR profile of duck DNA, 5 different ISSR markers were used. Annealing temperature used in PCR was the result of the optimization. The ISSR-PCR results showed that all primers (100%) were polymorphic. From a total of five ISSR primers, resulted in 44 obvious bands in all duck samples, with 41 (91.78%) bands being polymorphic. The quantity of alleles was numerous from 7-14 polymorphic loci, the mean quantity of alleles according to locus was 8.8, and the average PIC score for the Central Javanese duck was 0.777. The relationship investigation showed that the Central Javanese local duck was clustered into two primary offshoots, one heading to Pengging duck breeds and another one consisting of all other Central Javanese local duck. The genetic diversity among Central Javanese local duck based on ISSR primer was high. The ISSR loci were polymorphic for Central Javanese duck and may be useful for study of genetic diversity and genome evolution of Central Javanese ducks in the future.

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“…Most current genetic data resources in terms of studying duck are available only for heritability and genetic relationship of some traits (Bochno et al 2000) and epidemic disease cases (Susanti et al 2008). Moreover, molecular data availability only comes from mitochondrial DNA sequence to study evolution and phylogenetic (Jin et al 2014(Jin et al , 2012Susanti et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic Characterization of the Central Javanese Duck using Microsatellite Markers

Susanti¹,

Yuniastuti²,

Agustin³

2021

JSM

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Duck conservation strategy based on genetic characteristics has been undertaken to preserve indigenous breeds and produce high quality offspring. In addition, the genetic characteristic analysis provides further information for studying avian influenza viruses. The aim of this research was to study the genetic characterisation of indigenous Central Javanese duck in Indonesia using microsatellite markers. Microsatellite or simple sequence repeats (SSR) or short tandem repeats (STR) of various breeds of Central Javanese duck were analysed on 35 local ducks which consisted of seven variants of Javanese ducks in Central Java. Ten pairs of duck microsatellite primers were used to amplify the DNA from feathers. Nine out of 10 microsatellite loci (90%) demonstrated polymorphic patterns containing 50 alleles. The number of alelles varied from two to 10 alleles at various polymorphic microsatellite loci with an average of 5.56 alelles per locus. From the study, CAUD013 locus was determined as the highest heterozygosity with 0.882 score while CAUD030 locus was the lowest one with 0.034 score.Similarly, CAUD030 locus had the lowest PIC score (0.30) whereas the CAUD013 locus had the highest PIC value (0.869). Hence, it was showed that microsatellite markers were highly polymorphic in several loci for the Central Javanese duck and may be useful for genetic description of other native duck in terms of species conservation.

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<b>Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia

Cited by 5 publications

References 24 publications

The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool

The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool

Genetic diversity of Central Javanese duck (Indonesia) based on Inter Simple Sequence Repeat markers

Genetic Characterization of the Central Javanese Duck using Microsatellite Markers

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