Phylogenetic analysis of Aceh cattle breed of Indonesia through mitochondrial D-Loop region

Sari, Eka Puspita; Han, Jin‐Hee; Noor, Ronny Rachman; Sumantri, Cece; Margawati, Endang Tri

doi:10.1016/j.jgeb.2015.12.001

Cited by 12 publications

(13 citation statements)

References 10 publications

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“…Interestingly, with a few samples observed in this study, we also detected specific haplotypes including Hap_17 (in Pasundan cattle), Hap_18 and Hap_19 (in Pacitan cattle), with only one individual of each haplotype (Table 2). Specific haplotypes were also found in Aceh cattle inferred from D-loop sequences (Sari et al 2016). In addition, Adinata et al (2017)…”

Section: B I O D I V E R S It a Smentioning

confidence: 84%

Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

Hartatik

Hariyono

Adinata³

2018

Biodiversitas

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Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

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Section: B I O D I V E R S It a Smentioning

confidence: 84%

Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

Hartatik

Hariyono

Adinata³

2018

Biodiversitas

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“…Currently, D-loop mitochondrial based on partial sequencing for investigation of genetic diversity was reported in some cattle breeds such as Aceh cattle (Sari et al, 2016), Bali cattle and Madura cattle (Nijman et al, 2003). Besides, the D-loop mitochondrial analysis was also carried out in Bali cattle, Madura cattle, PO cattle, and Pesisir Sumatra Barat cattle (Sutarno, 2010) as well as SO cattle (Agung and Hermansyah, 2018) using polymerase chain reaction-fragment length polymorphism (PCR-RFLP).…”

Section: For This Reason D-loop Mitochondrial Is Oftenmentioning

confidence: 99%

“…Previously, the clustering of cattle breeds based on genetic distance and the genetic tree was commonly performed using Bos taurus and Bos inducus (Chung, 2013;Xuan et al, 2010), since reference related to Bali cattle as Bos javanicus cluster has been scarcely available. Genetic diversity of cattle breeds could be researched not only according to partial fragment of D-loop mtDNA (Correia et al, 2017;Sari et al, 2016), complete fragment of dloop mtDNA (Lorenzo et al, 2018), but also whole sequence of mtDNA genome (Pramod et al, 2018). Yet, it is noteworthy that the results of the analysis using entire fragments are expected to collect comprehensive relationships between individuals within species or among species closely related with divergence time (Rehman et al, 2017).…”

Section: Genetic Distance and Genetic Tree In Bali Cattle And So Cattlementioning

confidence: 99%

Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

Jakaria

Musyaddad

Rahayu

et al. 2019

J. Indonesian Trop. Anim. Agric.

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This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

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“…Until recently, research on Simeulue buffalo which concerned in genetic studies has only been carried out by Sari (2014). The study revealed that Simeulue buffalo had a close relationship with Riau buffalo and they situated in a separate cluster from Aceh buffalo in Central Aceh and Aceh Besar.…”

Section: Introductionmentioning

confidence: 98%

Body size characteristics and polymorphism in GH and GHRH genes of Simeulue Buffalo of Aceh, Indonesia

Eriani

Rahmi

Jamil³

et al. 2018

Biodiversitas

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Eriani K, Rahmi R, Jamil I, Rosnizar R, Azhar A. 2019. Body size characteristics and polymorphism in GH and GHRH genes of Simeulue Buffalo of Aceh, Indonesia. Biodiversitas 20: 236-242. This study was done to determine body size characteristics, to identify the presence of polymorphism in the GH/MspI and GHRH/HaeIII genes, and to analyze the relationship between GH and GHRH gene polymorphisms to body size characteristics in Simeulue buffalo. Experimental animals used were 45 Simeulue buffalo randomly sampled from three subdistricts, i.e., Salang, Alafan and Simeulue Cut, fifteen from each subdistrict. Body size characteristics measured were withered height, body length, chest circumference, chest depth, and hip height. A 5 mL whole blood was collected from fifteen out of forty five by using EDTA as an anticoagulant. Extraction of genomic DNA and analysis of GH/MspI and GHRH/HaeIII polymorphisms was done using GeneAid DNA extraction kit and polymerase chain reaction-restriction length fragment polymorphism (PCR-RFLP) method, respectively. The data of body size characteristics which includes mean value, standard deviation, and coefficient of variation were analyzed descriptively. The molecular data represented by DNA banding pattern was used to calculate allele and genotype frequencies, expected (He) and observed (Ho) heterozygosities, and Hardy-Weinberg equilibrium. The relationship between genotype and body size characteristic was analyzed using t-test. The results showed that coefficient of variation in body size characteristics was low, ranging from 5.39-16.06% in the age category of 4-6 years old and ranging from 5.25-11.27% in the age category of 2- 4 years old. The results of the molecular analysis indicated that GH/MspI locus was monomorphic by the presence of one (+/+) genotype. GHRH/HaeIII locus was polymorphic as shown by the presence of 3 genotypes namely AA (0.13), AB (0.80) and BB (0.07). Expected heterozygosity (0.80) was higher than observed heterozygosity (0.49). The frequency of GHRH/HaeIII agreed with Hardy Weinberg equilibrium. GHRH/HaeIII polymorphism did not significantly influence (P>0.05) body size characteristics of Simeulue buffalo.

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Phylogenetic analysis of Aceh cattle breed of Indonesia through mitochondrial D-Loop region

Cited by 12 publications

References 10 publications

Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

Body size characteristics and polymorphism in GH and GHRH genes of Simeulue Buffalo of Aceh, Indonesia

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