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All Journal Journal of the Indonesian Tropical Animal Agriculture
A. Setiaji
Faculty of Animal and Agricultural Sciences, Diponegoro University, Tembalang Campus, Semarang 50275, Central Java
Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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Genetic diversity and phylogenetic analysis of Indonesian local and commercial rabbit breeds based on mitochondrial D-loop Lestari, D. A.; Latifa, A. P.; Sutopo, S.; Kurnianto, E.; Setiatin, E. T.; Agustine, A. D.; Nabilah, Z.; Kamila, F. T.; Prahara, P. G.; Kamalludin, M. H.; Setiaji, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 50, No 3 (2025): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.50.3.189-198

Abstract

This study aimed to evaluate the genetic diversity and phylogenetic relationships among four rab-bit breeds raised in Central Java, namely Indonesian Local rabbit (LC), Hycole (HC), Hyla (HL), and New Zealand White (NZ), using mitochondrial D-loop region sequences. A total of 40 blood samples were collected from rabbits in three regencies in Central Java. DNA was extracted from each sample, followed by gene amplification, Sanger sequencing, and sequence analysis. A 906 bp fragment of the mitochondrial D-loop region was successfully amplified from all individuals. The overall genetic di-versity was found to be low, with mean values of k = 4.615, nucleotide diversity (π) = 0.00509 ±0.00092, and haplotype diversity (Hd) = 0.385 ± 0.070. Genetic distance analysis showed a close rela-tionship among the breeds, ranging from 0.00349 to 0.00610. Two haplotypes (A and B) were identi-fied, and both were shared across all breeds, indicating limited genetic differentiation. Phylogenetic tree reconstruction further demonstrated that the four breeds clustered closely together and were most likely derived from European lineages rather than distinct indigenous origins. In conclusion, rabbits raised in Central Java represent a genetically homogenous group with low diversity, highlighting the need for broader genetic resource management and conservation strategies to ensure long-term popula-tion sustainability.
Quantifying of morphological character for Kacang goat using principal component factor analysis Lestari, D. A.; Sutopo, S.; Kurnianto, E.; Dagong, M. I. A.; Bugiwati, S. R. A.; Mamat-Hamidi, K.; Yakubu, A.; Pandupuspitasari, N. S.; Agusetyaningsih, I.; Kamila, F. T.; Setiaji, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 49, No 4 (2024): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.49.4.316-322

Abstract

The study’s objective was to estimate the association among various linear body measurements and body weights of adult Kacang goats. The data was obtained from 209 heads of adult Kacang Goat, compressed 78 bucks and 131 ewes. The morphological evaluation was performed by measuring body weight (BW), body length (BL), chest depth (CD), chest girth (CG), chest width (CW), and withers height (WH). Factor PROCEDURE was performed to estimate the principal component. The result of factor analysis was used to determine the independent variable for linear regression analysis. BW has a favorable correlation with CG, BL, CD, CW, and WH for bucks and ewes. PC 1 accounts for 55.62% of the variation in bucks, while PC 2 accounts for an additional 18.34%. PC 1 accounts for just 0.45% of the overall variation in ewes, whereas PC 2 accounts for 0.24%. The R-squared (R2) values for bucks and ewes in the regression equation with CG as the independent variable are 0.32 and 0.41, respectively. For both bucks and ewes, the regression equation with CW as the independent variable had a higher R2 of 0.52 and 0.20, respectively. For bucks and ewes, the regression equation'sR2 values are 0.54 and 0.44, respectively, with combined CG and CW acting as independent variables. This integrated approach to analyzing body measurements in Kacang Goats provides a robust foundation for making informed decisions in goat farming.
DNA variants and population structure of Magelang ducks across generation Febriana, A.; Kurnianto, E.; Sutopo, S.; Lestari, D. A.; Setiaji, A.; Sugiharto, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 49, No 1 (2024): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.49.1.67-77

Abstract

Magelang ducks (MD) are Indonesian local ducks and are known as dual-purpose type ducks which have high egg production, duck day production (DDP), and body weight size. Nowadays, the MD is selected to establish the pure line to advance the egg production trait in the Breeding and Rearing Center of Non-Ruminant Animals Banyubiru, Central Java. The mitochondrial DNA (mtDNA) Dloop region, is highly polymorphic and could be used to analyze the population genetics. The present research aims to examine the impacts of continuous selection on population structure and genetic mutations on MD across two generations using the mtDNA D-loop region. Thirty-six blood samples from the second (G2) and third (G3) generations were examined using the sequencing method. The MEGA X and DnaSP software were applied to calculate the genetic diversity, genetic distance, and to generate a phylogenetic tree. The number of haplotypes (H), haplotype diversity (Hd), and Tajima's D are 26, 0.9746, and -1.46, respectively. The Fst value of MD is 0.156. The genetic distance among populations ranges from 0.0000 – 2.097. The UPGMA analysis constructs one clade in a phylogenetic tree between MD, Indonesian local Ducks, Indian Ducks, Vietnamese Ducks, and Chinese Ducks. The study found that the genetic variation and population structure did not significantly change between the second and third generations.
Co-Authors A. Yakubu Agusetyaningsih, I. Agustine, A. D. Bugiwati, S. R. A. E. Kurnianto E. T. Setiatin, E. T. Febriana, A. Kamalludin, M. H. Kamila, F. T. Latifa, A. P. Lestari, D. A. M. I. A. Dagong, M. I. A. Mamat-Hamidi, K. Nabilah, Z. Pandupuspitasari, N. S. Prahara, P. G. S. Sugiharto Sutopo Sutopo