Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis.

Objective: This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus). Methods: This study used gDNA of Cemani chicken isolated from liver tissue. mtDNA sequencing was performed using WGS mtDNA analysis with nanopore technology by Oxford Nanopore Technologies GridION. Bioinformatics and data analysis were then performed. Results: This study showed that the length of the mtDNA genome is 16,789 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), and a noncoding control region (Dloop). Furthermore, analysis showed there were polymorphic sites and amino acid alterations when mtDNA Cemani chicken was aligned with references from GenBank. Conclusion: Site (988T>*) in Dloop genes and (328A>G) in ND3 genes which alter glycine to stop codon, were specific markers found only in Cemani chicken.

Genetic characteristics of complete mtDNA genome sequence of Indonesian local rabbit (Oryctolagus cuniculus).

BACKGROUND: Indonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits. RESULT: This study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop). CONCLUSIONS: mtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.

Effect of insulin-like growth factor 1 gene on growth traits of Kejobong goat and its growth analysis.

AIM: This study aimed to identify the effect of the insulin-like growth factor 1 (IGF1) gene on growth, to uncover the genetic marker at the IGF1 gene, and to predict growth performance by analyzing growth models of Kejobong goats based on their genotype. MATERIALS AND METHODS: DNA and records of body weight (BW) and body measurements (BM) of Kejobong goats were collected, the IGF1 gene was amplified from the DNA template by polymerase chain reaction (PCR); the PCR products were then sequenced to determine single nucleotide polymorphisms (SNP). Linear mixed model (LMM) was used to analyze the association between SNP and growth traits. Four non-linear growth models were analyzed using non-LMM to describe the growth model and to compare the growth within genotypes. RESULTS: An SNP at intron 4 (g5752G→C) genotyped into GG and CC was significantly associated with BW and BM. Goats of genotype GG had a significantly higher BW and BM (p<0.05) than those of genotype CC. Growth analysis showed that the von Bertalanffy model was the most fit for describing BW, the Brody model for chest width and hip height, the Gompertz and Logistic models for heart girth, and the von Bertalanffy and Gompertz models for hip width. CONCLUSION: An SNP at intron 4 of the IGF1 gene was associated with the growth trait and was usable as a genetic marker candidate for improvement of growth traits of Kejobong goats while von Bertalanffy model provides proper and accurate estimates of parameters to describe the growth performance of Kejobong goats.

Amino acid sequence based on Cytochrome b gene in Kejobong goat and its genetic relationships among several local goats in Asia.

AIM: This study aimed to analyze the amino acid sequence of Cytochrome b (Cyt b) gene in Kejobong goat and its genetic relationships with local goats located in Asia. MATERIALS AND METHODS: A total of 28 heads of Kejobong goat were purposively sampled. The deoxyribonucleic acid (DNA) was extracted from blood using gSYNC DNA mini kit (Geneaid Biotech Ltd.). Cyt b gene was amplified using polymerase chain reaction (PCR) method with CytbCapF and CytbCapR primers. The amplified PCR products were sequenced for further analysis. RESULTS: There were a total 377 amino acid sequences translated from 1140 base pair (bp) of Cyt b gene, 99.20% of it were monomorphic, amino acid alterations were found at site 16th, 121st, and 231st, and Kejobong goat was in the same cluster with Southeast Asian local goats. CONCLUSION: Most of the amino acid sequence on Cyt b gene in Kejobong goat is monomorphic (99.20%), only a few nucleotide mutations were found that causing amino acid alteration in three sites (0.80%). Kejobong goat has a close genetic relationship to several local goats in Southeast Asian.