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F. Saputra
Indonesian Research Institute for Animal Production
Agriculture, Biological Sciences & Forestry Energy

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Journal : Tropical Animal Science Journal

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Genetic Diversity of Indonesian Swamp Buffalo Based on Microsatellite Markers F. Saputra; Jakaria Jakaria; A. Anggraeni; C. Sumantri
Tropical Animal Science Journal Vol. 43 No. 3 (2020): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2020.43.3.191

Abstract

Indonesia has high genetic resources of local swamp buffalo with good adaptation across regions. However, these animals decline in both population and genetic quality. This research was conducted to study the genetic diversity of Indonesian swamp buffalo. A total of 199 DNA samples (swamp buffalo) from seven provincial populations were used in this study. Genetics identification used three microsatellite markers (CSSM66, ILSTS61, and ILSTS17). Microsatellites were visualized by Polyacrylamide Gel Electrophoresis (PAGE) 10% with silver staining method. Microsatellite data were analyzed using GenAlEx 6.41, Cervus 3.0, and POPTREE2 software. The results showed that a total of 9 alleles were found from the three loci. ILSTS61 had a high PIC (Polymorphism Information Content) compared to the other loci. The high observed heterozygosity of ILSTS61 was found in swamp buffalo from Riau Province, while the Ho value of ILSTS17 ranged from 0.000 to 0.170. This study identified two clusters for Indonesian swamp buffalo, i.e., cluster I (Aceh, North Sumatra, and Riau) and cluster II (Banten, Central Java, West Nusa Tenggara, and South Sulawesi). The two major divergent directions are considered in Indonesia swamp buffaloes across the observed provinces.
Growth Performance of Male Line of Superior Tropical Rabbit B. Brahmantiyo; N. Pratiwi; F. Saputra; Y. C. Raharjo; L. H. Prasetyo
Tropical Animal Science Journal Vol. 44 No. 3 (2021): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2021.44.3.273

Abstract

New Zealand White rabbits (NN) are known as broiler rabbits that are well adapted to the Indonesian environment. HyLa rabbits are rabbits imported from China that were selected for high reproduction and growth rates. The increased productivity of NN rabbits was achieved by crossing to HyLa rabbits. This study was aimed to evaluate HyLa and NN rabbits’ productivity and their reciprocal crosses to develop a broiler rabbit adaptive to tropical climate. Forty heads of does and 20 heads of bucks of HyLa rabbit, 30 heads of does, and 6 heads of bucks of New Zealand White rabbits (NN) were used. Reproductive performance of does (litter size at birth, litter size at weaning, mortality, and weekly does body weight) and the kit’s growth performance (weekly body weight from weaning until the age of 20 weeks) was evaluated. Data were analyzed using the SAS program, FactoMineR, and factoextra package in R 4.0.0. Rabbit’s growth data were periodically analyzed by the Gompertz model. At the age of 10 weeks, HyLa had a body weight of 1459.7 ± 373.1 g greater than HyLa x NN (1380.1 ± 389.9 g), NN x HyLa (1225.7 ± 263.4 g), and NN (985.0 ± 234.4 g). Based on the Gompertz model, NN x HyLa had an inflection point at a weight of 1,977.7 at 12 weeks. Furthermore, NN x HyLa had a better litter size than HyLa x NN. NN bucks x HyLa does have the potential to be developed as a superior rabbit adaptive to tropical climate.
Haplotype Diversity of Swamp Buffalo and River Buffalo Based on Cytochrome B Gene: A Study of Meta-Analysis F. Saputra; A. Anggraeni; A. B. L. Ishak; A. Hafid; M. Rusdin; C. Sumantri
Tropical Animal Science Journal Vol. 44 No. 4 (2021): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2021.44.4.399

Abstract

Buffalo (Bubalus bubalis) is well known as a domesticated buffalo in Asia. The genetic diversity of buffaloes in Asia needs to be studied to ensure a proper breeding program. A meta-analysis study on the cytochrome b gene of the mitochondrial genome from various published data was conducted to evaluate genetic variation and haplo-geography of Asian buffaloes. A meta-analysis is used to provide a comprehensive view of the data. A total of 1369 swamp buffaloes Cytochrome B sequences (from Indonesia (79), Bangladesh (98), China (909), India (4), Laos (96), Taiwan (29), Thailand (54), and Vietnam (100)) and 91 river buffaloes (from China (42), Nepal (42), and Pakistan (7)) were used in this study. Cytochrome B sequences (678 bp) of Syncerus caffer, Bubalus arnee, Bubalus depressicornis, Bubalus quarlesi, Bubalus mindorensis, swamp buffalo, and river buffalo were determined for their haplotypes using DnaSP v6 program. Haplotypes were analyzed by Principal Coordinate Analysis (PCoA) using Adegenet Package and Hierarchical Clustering on Principal Components (HCPC) methods using Factoextra and FactoMineR Package in R-4.0.0 program. Bayesian analysis of genetic differentiation was implemented in BAPS 6.0. Furthermore, we found 56 haplotypes for swamp buffaloes in eight Asian countries and 5 haplotypes for river buffaloes in Pakistan. We also found 5 haplotypes for outgroup (B. arnee, S. caffer, B. depressicornis, B. quarlesi, B. mindorensis). Therefore, we found 66 haplotypes in total with outgroup sequences. Based on the PCoA results, three clusters were found. However, the HCPC found eight clusters. Based on HCPC, countries in East and South Asia have four maternal lineages. This is evidence that buffalo domestication has first occurred in East-South Asia. In conclusion, we found four maternal lineages of swamp buffalo and two maternal lineages of river buffalo from ten countries. We also found one maternal lineage for Syncerus caffer and one maternal lineage for B. depressicornis, B. quarlesi, and B. mindorensis.
Genetic Diversity of Various Goat Breeds in East Java Based on DNA Microsatellite Markers T. E. Susilorini; D. Wulandari; A. Furqon; W. A. Septian; F. Saputra; S. Suyadi
Tropical Animal Science Journal Vol. 45 No. 3 (2022): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2022.45.3.247

Abstract

Information on genetic diversity using microsatellite markers was essential to formulate effective conservation and breeding strategies. This study aims to identify the genetic diversity and relationships between Kacang, Senduro, Peranakan Ettawa (PE), Boer, and Saanen goats in the East Java region, Indonesia, using 12 microsatellite markers. A total of 86 goat blood DNA samples, which consisted of Kacang (n=41), Senduro (n=23), Boer (n=13), PE (n=5), and Saanen (n=4), were used in this study. The DNA was extracted based on Genomic DNA Mini Kits protocols for analysis fragment in microsatellite DNA region using specific primer recommended by the ISAG/FAO. A total of 96 alleles were identified in this study. The observed heterozygosity ranged from 0.470±0.135 (Kacang) to 0.592±0.211 (PE) and the expected heterozygosity ranged from 0.589±0.251 (Saanen) to 0.762±0.084 (PE). F statistical analysis include inter-population inbreeding rate (Fis) 0.2583 (25.83%), inbreeding rate in population (Fit) 0.3238 (32.38%), and genetic differentiation (Fst) 0.0882 (8.82%). The 11 microsatellite markers were highly informative (PIC>0.5), except the INRA063 locus markers were quite informative (PIC 0.25-0.5). The research showed that Kacang, Senduro, and PE goats had a close genetic distance and formed a cluster. Kacang and Saanen goats showed a long genetic distance at 26.9%. In conclusion, the genetic relationship among goat breeds in East Java was divided into three clusters where Boer and Saanen goats formed their cluster.
Co-Authors A. Anggraeni A. B. L. Ishak A. Furqon A. Hafid B. Brahmantiyo C. Sumantri D. Wulandari Jakaria Jakaria L. H. Prasetyo Muh. Rusdin N. Pratiwi Suyadi Suyadi T. E. Susilorini W. A. Septian Y. C. Raharjo