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All Journal Livestock and Animal Research Jurnal Agripet
Ferdy Saputra
Indonesian Research Institute for Animal Production
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Veterinary

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Multivariate analysis of five chicken breed in Indonesia based on microsatellite allele frequency Ferdy Saputra; Tike Sartika; Anneke Anggraeni; Andi Baso Lompengeng Ishak; Komarudin Komarudin; Nurul Pratiwi
Livestock and Animal Research Vol 19, No 1 (2021): Livestock and Animal Research
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (399.538 KB) | DOI: 10.20961/lar.v19i1.43459

Abstract

Objective: This study tries to examine several multivariate methods in classifying genetic diversity using microsatellite allele frequency data.Methods: This study used microsatellite allele frequency data from White Leghorn (n = 48), Kampung (n = 48), Pelung (n = 24), Sentul (n = 24), and Black Kedu (n = 25) from Indonesian Research Institute for Animal Production. Allele frequency data were analyzed by the Neighbor-Joining (NJ) method using the POPTREE2 program. The data was also analyzed by the Principal Component Analysis (PCA), Correspondence Analysis (CA), and Hierarchical Clustering on Principal Components (HCPC) methods using the factoextra and FactoMineR packages in the R 4.0.0 program.Results: Correspondence Analysis (CA) found Sentul is more closer to Black Kedu. However, based on NJ, PCA, and HCPC showed Sentul is closer to Kampung. Based on the value of Dimension 1, Correspondence Analysis (80.7%) can explain greater variation than PCA (58.9%). However, CA method generated different results compared to NJ, PCA, and HCPC. NJ, PCA, and HCPC found four chicken clusters, namely cluster 1 (White Leghorn), cluster 2 (Pelung), cluster 3 (Black Kedu), and cluster 4 (Kampung and Sentul).Conclusions: In conclusion, HCPC is a better multivariate method for analyzing allele frequency data than PCA and CA. HCPC can be used to analyze allele frequency data better than PCA, because HCPC is a combination of methods from hierarchical clustering and principal components.
Indonesian River Buffalo Molecular Phylogeny Compared to Other Mammals Based on STAT1 Sequence Fuad Hasan; Armyn Hakim Daulay; Ferdy Saputra; Isyana Khaerunnisa
Jurnal Agripet Vol 22, No 1 (2022): Volume 22, No. 1, April 2022
Publisher : Agricultural Faculty

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17969/agripet.v22i1.20889

Abstract

ABSTRACT. Genes differ in sequence, size, and functional domains among species. According to studies, STAT1 provides information on the rate of evolution that correlates with its function in the immune system. STAT1 is also considered a genetic marker for economic traits in mammals. Studying sequence comparison is an important issue in bioinformatic study and can explain phylogenetic. Therefore, this study aimed to identify the molecular phylogeny of river buffalo (Bubalus bubalis) and other mammals based on STAT1 gene sequences. This study used 7 STAT1 sequences from Ensembl (Bos grunniens, Bos indicus, Bos Mutus, Capra hircus, Cervus hanglu yarkandensis, Moschus moschiferus) and previous studies (Bubalus bubalis). The sequences were analyzed using the MEGA X 10.2.6 software to observe the nucleotide composition and the phylogeny (based on UPGMA). The adegenet package in the R 4.0.0 software is used to observe the STAT1 sequence dimensionally among mammals. The STAT1 sequence has almost similar diversity among the livestock of the same genus. Based on the STAT1 sequence, Bubalus bubalis has closer genetic proximity to the genus Bos than to another genus. In conclusion, we found STAT1 is more dynamic in evolution and more conserved and found in the similar related genus.(Filogeni kerbau Indonesia dibandingkan mamalia lain berdasarkan runutan nukleotida gen STAT1)ABSTRAK. Gen berbeda dalam urutan, ukuran, dan domain fungsional di antara spesies. Menurut penelitian sebelumnya, STAT1 memberikan informasi tentang laju evolusi yang berkorelasi dengan fungsinya dalam sistem kekebalan. STAT1 juga dianggap sebagai penanda genetik untuk sifat bernilai ekonomi pada mamalia. Studi perbandingan urutan merupakan isu penting dalam studi bioinformatika dan dapat menjelaskan filogenetik. Oleh karena itu, penelitian ini bertujuan untuk mengidentifikasi filogeni molekuler kerbau sungai (Bubalus bubalis) dan spesies mamalia lain berdasarkan sekuens gen STAT1. Penelitian ini menggunakan 7 sekuen STAT1 yang diambil dari Ensembl (Bos grunniens, Bos indicus, Bos mutus, Capra hircus, Cervus hanglu yarkandensis, Moschus moschiferus) dan penelitian sebelumnya (Bubalus bubalis). Sekuen dianalisis menggunakan program MEGA X 10.2.6 untuk melihat komposisi nukleotida dan filogeni (berdasarkan UPGMA). Adegenet package dalam program R 4.0.0 digunakan untuk mengamati urutan STAT1 secara dimensional diantara mamalia. Sekuen STAT1 memiliki keragaman yang hampir sama di antara ternak dari genus yang sama. Berdasarkan sekuen STAT1, Bubalus bubalis memiliki jarak genetik yang lebih dekat dengan genus Bos dibandingkan dengan genus lainnya. Sebagai kesimpulan, kami menemukan STAT1 lebih dinamis dalam evolusi dan lebih terkonservasi serta ditemukan dalam genus terkait yang serupa.
Co-Authors Andi Baso Lompengeng Ishak Anneke Anggraeni Armyn Hakim Daulay Fuad Hasan Isyana Khaerunnisa Komarudin Komarudin Nurul Pratiwi Tike Sartika