Genetic diversity of Central Javanese duck (Indonesia) based on Inter Simple Sequence Repeat markers
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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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References
Askari N, Mohammad-Abadi MR, Baghizadeh A. 2011. ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat, and sheep populations. Ir J Biotechnol 9 (3): 222-229.
Bakkappa S, Talebi E, Subramanya G. 2011. Role of molecular markers (RAPD & ISSR) in silkworm conservation. Int J Adv Biol Res 1 (1): 1-7.
Barazandeh A, Mokhtari M, Damanehand MM, Roudbari Z. 2020. Analyzing simple sequence repeats derived from expressed sequence tags in dromedary camels. Ir J Appl Anim Sci 10 (3): 555-565.
Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32 (3): 314-331.
Chang M-T, Cheng Y-S, Huang M-C. 2016. A novel non-synonymous SNP of the COLX gene and its association with duck reproductive traits. Mol Cell Probes 26 (5): 204-207. DOI: 10.1016/j.mcp.2012.05.003.
Dogan B, Duran A, Seker M, Cetin O, Martin E. 2015. Study of phylogenetic relationship of Turkish species of Klasea (Asteraceae) based on ISSR amplification. PhytoKeys 56 (1): 29-40. DOI: 10.3897/phytokeys.56.5608.
Eissa EA, Farahat GS, Mahmoud BY, El-Full EA. 2014. Productive traits and molecular genetics characterization (RAPD and ISSR) of selected long shank length and control lines in the 6th generation of Japanese quail. Egypt J Genet Cytol 43: 73-98. DOI: 10.21608/ejgc.2014.9923.
El-Sabrout K, Aggag SA. 2015. Use of inter simple sequence repeats and protein markers in assessing genetic diversity and relationships among four rabbit genotypes. World Rabbit Sci 23 (4): 283-288. DOI: 10.4995/wrs.2015.3912.
FAO. 2015. The second report on the state of the world’s animal genetic resources for food and agriculture. Rome. [also available at http://www.fao.org/3/a-i4787e.pdf]
Gradzielewska A. 2011. Application of the ISSR method to estimate the genetic similarity of Dasypyrum villosum (L.) P. Candargy Greek populations to Triticum and Secale species. Biodivers Res Conserv 21 (1): 7-12. DOI: 10.2478/v10119-011-0002-1.
Hong-yan Y, Jing F, Fang-yong N, Zhi-heng D, Xiu-juan B. 2013. Genetic diversity analysis among populations of mink from China by inter-simple sequence repeat (ISSR) markers. J Northeast Agric Univ 20 (3): 47-54. DOI: 10.1016/S1006-8104(14)60008-8.
Ismoyowati, D Purwantini. 2010. An estimation of genetic variation in Indonesian local duck using microsatellite marker. Asian J Poul Sci 4 (4): 198-204. DOI: 10.3923/ajpsaj.2010.198.204.
Ismoyowati, Indrasanti D, Sulistyawan IH. 2018. The differences of feed quality and egg production performance of Tegal and Magelang ducks on farming in Central Java. Bull Anim Sci 42 (3): 197-202. DOI: 10.21059/buletinpeternak.v42i3.34465.
Ismoyowati, Iriyanti N, Santosa SA. 2012. The differences of physical, chemical, and fatty acid profile of meat quality of male muscovy (Cairina moschata) and local duck (Anas plathyrinchos). J Indones Trop Anim Agric 37 (4): 250-256. DOI: 10.14710/jitaa.37.4.250-256.
Li HF, Yang N, Ma YH, Chen GH, Tu YJ, Tang QP, Chen KW. 2006. Study on molecular genetic diversity of native egg-laying duck breed population in China. J Shandong Agric Univ (Nat Sci Ed) 4: 536-540.
Lin RL, Chen HP, Rouvier R, Marie-Etancelin C. 2016. Genetic parameters of body weight, egg production, and shell quality traits in the Shan Ma laying duck (Anas platyrhynchos). Poult Sci 95 (11): 2514-2519. DOI: 10.3382/ps/pew222.
Maharani D, Hariyon DNH, Putra DDI, Lee JH, Sidadolog JHP. 2019. Phenotypic characterization of local female duck populations in Indonesia. J Asia Pac Biodivers 12 (4): 508-514. DOI: 10.1016/j.japb.2019.07.004.
Matitaputty PR, Wijaya CH, Bansi H, Laudadio V, Tufarelli V. 2015. Influence of duck species and crossbreeding on sensory and quality characteristics of Alabio and Cihateup duck meat. CyTA J Food 13 (4): 522-526. DOI:10.1080/19476337.2015.1011239.
Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York. DOI: 10.7312/nei-92038.
Parthasarathy U, Nandakishore OP, Nirmal-Babu K, Kumar S, Parthasarathy VA. 2013. Comparative effectiveness of inter simple sequence repeat and randomly amplified polymorphic DNA markers to study genetic diversity of Indian garcinia. Afr J Biotechnol 12: 6443-6451. DOI: 10.5897/AJB2013.13053.
Rajkumar U, Gupta BR, Reddy AR. 2008. Genomic heterogeneity of chicken populations in India. Asian-australas J Anim Sci 21 (12): 1710-1720. DOI: 10.5713/ajas.2008.80299.
Rohlf FJ. 1998. NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.0 User Guide. Applied Biostatistic Inc., New York.
Silva MSFS, Borges AAS, Santos SRN, Moura VG, Silvana GR, Dias ACS, Araujo AM, Filho JWGO. 2020. SSR and ISSR markers in assessing genetic diversity in Gallus gallus domesticus: A quantitative analysis of scientific production. Ciênc Rural 50 (7): e20190401. DOI: 10.1590/0103-8478cr20190401.
Sneath PHA, Sokal RR. 1973. Numerical Taxonomy: The Principles and Practice of Numerial Classification. Freeman, San Fransisco.
Son J, Park K, Lee S, Kim J, Kim N. 2012. Species relationships among Allium species by ISSR analysis. Hortic Environ Biotechnol 53 (3): 256-262. DOI: 10.1007/s13580-012-0130-3.
Suci DM, Fitria Z, Mutia R. 2017. Meat fatty acid and cholesterol content of native Indonesian muscovy duck fed with rice bran in traditional farm. Anim Prod 19 (1): 37-45. DOI: 10.20884/1.jap.2017.19.1.586.
Susanti R, Dafip M, Christijanti W, Yuniastuti A. 2021a. The interaction of intestinal bacteria and feed: A case study of intensive-duck husbandry in Central Java. J Indones Trop Anim Agric 46 (2): 154-165. DOI: 10.14710/jitaa.46.2.154-165.
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 (3): 997-1003. DOI: 10.13057/biodiv/d190331.
Susanti R, Iswari RS, Fibriana F, Sari RI. 2017. Mitochondrial D-loop sequence variation among Central Javanese duck in Indonesia. Acta Sci Anim Sci 39 (4): 449-456. DOI: 10.4025/actascianimsci.v39i4.34352.
Susanti R, Yuniastuti A, Fibriana F. 2020. Metagenome analysis of gut microbial in both the caged and non-caged ducks. J Phys Conf Ser 1524: 012076. DOI:10.1088/1742-6596/1524/1/012076.
Susanti R, Yuniastuti A, Kartikasari AD. 2021b. Microsatellite markers for assessment of genetic characterization of the Central Javanese duck. Sains Malays 50(1): 53-61. DOI: 10.17576/jsm-2021-5001-06.
Tamzil MH, Indarsih B. 2017. Measurement of phenotype characteristics of Sasak ducks: Indian runner ducks of Lombok Island Indonesia. Anim Prod 19 (1): 13-19.
Tunca RI, Taskin A, Buyuk M. 2015. Genetic analyses of some central anatolian domestic duck populations with inter simple sequence repeat (ISSR): A preliminary study. Pak J Zool 47 (6): 1709-1714.
Tunca RI, Taskin A. 2016. A comparison of genetic variations among native and some local chicken populations in Turkey. Indian J Anim Res 50 (5): 652-657. DOI: 10.18805/ijar.10278.
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