Genetic Variation of Calpastation Gene of Indigenous Bali Cattle (Bos javanicus) in Indonesia

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.

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Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2008000500014 ◽

2008 ◽

Vol 43 (5) ◽

pp. 657-659 ◽

Cited By ~ 3

Author(s):

Rogério Abdallah Curi ◽

Luis Artur Loyola Chardulo ◽

Antônio Carlos Silveira ◽

Henrique Nunes de Oliveira

Keyword(s):

Single Nucleotide Polymorphism ◽

Bos Taurus ◽

Direct Sequencing ◽

Bos Indicus ◽

Basic Structure ◽

Meat Tenderness ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Pcr Rflp ◽

Cast Gene

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

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Phylogenetic tree analysis for Bali Cattle based on partial sequence 16S rRNA Mitochondrial DNA

E3S Web of Conferences ◽

10.1051/e3sconf/202233500014 ◽

2022 ◽

Vol 335 ◽

pp. 00014

Author(s):

R. Misrianti ◽

S.H. Wijaya ◽

C. Sumantri ◽

J. Jakaria

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Phylogenetic Tree ◽

Bos Taurus ◽

Bos Indicus ◽

Partial Sequence ◽

Bos Grunniens ◽

Bos Javanicus ◽

Mitochondria Dna ◽

Bali Cattle

Mitochondria DNA (mtDNA) as a source of genetic information based on the maternal genome, can provide important information for phylogenetic analysis and evolutionary biology. The objective of this study was to analyze the phylogenetic tree of Bali cattle with seven gene bank references (Bos indicus, Bos taurus, Bos frontalis, and Bos grunniens) based on partial sequence 16S rRNA mitochondria DNA. The Bayesian phylogenetic tree was constructed using BEAST 2.4. and visualization in Figtree 1.4.4 (tree.bio.ed.ac.uk/software/figtree/). The best model of evolution was carried out using jModelTest 2.1.7. The most optimal was the evolutionary models GTR + I + G with p-inv (I) 0,1990 and gamma shape 0.1960. The main result indicated that the Bali cattle were grouped into Bos javanicus. Phylogenetic analysis also successfully classifying Bos javanicus, Bos indicus, Bos taurus, Bos frontalis and Bos grunniens. These results will complete information about Bali cattle and useful for the preservation and conservation strategies of Indonesian animal genetic resources.

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Monomorphic allele rs109231213 in 3’UTR PLAG1 gene in purebred of Bali cattle (Bos javanicus)

E3S Web of Conferences ◽

10.1051/e3sconf/202233500010 ◽

2022 ◽

Vol 335 ◽

pp. 00010

Author(s):

Sutikno Sutikno ◽

Jean Pierre Munyaneza ◽

Santiananda Arta Asmarasari ◽

Jakaria Jakaria

Keyword(s):

Body Weight ◽

Gene Polymorphism ◽

Bos Taurus ◽

Direct Sequencing ◽

Bos Indicus ◽

Specific Marker ◽

Bos Javanicus ◽

Bali Cattle

The mutation rs109231213 that is located in 3’UTR of PLAG1 gene is associated with the growth and body weight in several Bos taurus and Bos indicus breeds. This study aimed to identify SNP rs109231213 in Bali cattle (Bos javanicus). The study used 41 samples of Bali cattle. The PLAG1 gene polymorphism was analyzed using PCR and direct sequencing methods. PCR pimers were 5’- TTGCACAGAATCAGTGTGTC-3’ and 5’- AGCCTAACGTGGATCTATGG-3’. The results showed that primers successfully amplified the 331 bp fragment at annealing 60°C that contained rs109231213. SNP was monomorphic in Bali cattle with one allele (G). This study concludes that rs109231213 in 3’UTR of PLAG1 gene can be used as specific marker in purebred of Bali cattle that have never been crossed with Bos taurus and Bos indicus.

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Effect of repeated implants of oestradiol-17β on beef palatability in Brahman and Braham cross steers finished to different market end points

Australian Journal of Experimental Agriculture ◽

10.1071/ea08193 ◽

2008 ◽

Vol 48 (11) ◽

pp. 1434 ◽

Cited By ~ 9

Author(s):

J. M. Thompson ◽

R. Polkinghorne ◽

M. Porter ◽

H. M. Burrow ◽

R. A. Hunter ◽

...

Keyword(s):

Meat Quality ◽

Shear Force ◽

Bos Taurus ◽

Bos Indicus ◽

Meat Tenderness ◽

Sensory Testing ◽

Anterior Portion ◽

End Points ◽

Longissimus Lumborum ◽

Quality Measurements

The effect of repeated implantation with 20 mg oestradiol-17β (Compudose 100) on carcass and meat quality traits was investigated using 478 Bos indicus and B. indicus × Bos taurus cross steers finished on either pasture or grain to achieve carcass weight for one of three market end points (domestic, 220 kg; Korean, 280 kg; or Japanese, 340 kg). In the oestradiol-17β treatment group, animals were administered implants at ~100-day intervals, with the number of implants administered to any steer ranging from one to eight. Cattle were slaughtered and at boning the anterior portion of the M. longissimus lumborum was removed and frozen after aging for 1 day for later objective meat quality measurements (shear force, compression and cook loss %). The adjoining portion was aged for 14 days before consumer sensory testing using the Meat Standards Australia protocols. Each sample was scored for tenderness, juiciness, like flavour and overall liking by 10 untrained consumers. Implanting increased carcass weights and ossification scores (P < 0.05) and reduced marbling scores in comparison to non-implanted carcasses. For tenderness, like flavour, overall liking and MQ4 scores there was a significant (P < 0.05) interaction between B. indicus content and oestradiol-17β treatment, whereby high B. indicus content cattle that were implanted with oestradiol-17β had the lowest sensory scores. The number of implants administered did not affect carcass weights or marbling scores, whereas ossification scores increased in carcasses as the number of implants increased. The number of implants administered had no effect (P > 0.05) on sensory scores, or objective meat tenderness.

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Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v25i2.2496 ◽

2020 ◽

Vol 25 (2) ◽

pp. 39

Author(s):

Peni Wahyu Prihandini ◽

A Primasari ◽

M Luthfi ◽

J Efendy ◽

D Pamungkas

Keyword(s):

Genetic Diversity ◽

Bos Taurus ◽

Phylogenetic Analyses ◽

Bos Indicus ◽

Haplotype Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Bos Javanicus ◽

Reverse Primer ◽

Relationship Of

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt b, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of Bos taurus, Bos indicus, and Bos javanicus were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt b were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with Bos javanicus. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with Bos javanicus.

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Genetic polymorphism analysis of 5' untranslated region of thyroglobulin gene in Bali cattle (Bos javanicus) from three different regions of Indonesia

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.42.3.175-184 ◽

2017 ◽

Vol 42 (3) ◽

pp. 175

Author(s):

S. Anwar ◽

A.C. Putra ◽

A.S. Wulandari ◽

P. P. Agung ◽

W.P.B. Putra ◽

...

Keyword(s):

Genetic Polymorphism ◽

Untranslated Region ◽

Candidate Snps ◽

Polymorphism Analysis ◽

Bos Javanicus ◽

Pcr Rflp ◽

Thyroglobulin Gene ◽

Polymerase Chain ◽

Reference Sequences ◽

Bali Cattle

The g.422C>T nucleotide variations in the 5’ untranslated region (5’UTR) of TG gene (called as TG5) has been reported to be associated with level in intramuscular fat (IMF) content or marbling in beef cattle. The objective of this study was to confirm genetic polymorphism of TG5 gene in Bali cattle populations from three different regions as the main resources of Bali cattle in Indonesia. A total of 200 head of Bali cattle have been performed genotyping on TG5 gene using polymerase chain reaction-restriction fragment lenght polymorphism (PCR-RFLP) method and sequence analysis. Results of the study confirmed that TG5 was monomorphic in Bali cattle wherever their origin regions. Moreover, nine candidate SNPs were detected within 5’UTR of TG gene in Bali cattle compared to Genbank reference sequences, although no SNP variations among Bali cattle sample studied. The new other genetic markers within an entire TG gene suggested to be explored and verified for their polymorphisms in Bali cattle. The nine candidate SNPs were also required further verification and validation in a larger sample to be regarded as new SNPs between Bali cattle and Genbank reference sequences.

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Polymorphisms of the Myostatin gene (MSTN) and its associationwith growth traits in Bali cattle

Indian Journal of Animal Research ◽

10.18805/ijar.v0iof.7609 ◽

2017 ◽

Author(s):

Hary Nugroho ◽

Woro Busono ◽

Sucik Maylinda

Keyword(s):

Growth Traits ◽

Restriction Enzymes ◽

Gene Frequencies ◽

Gene Markers ◽

Myostatin Gene ◽

Pcr Rflp ◽

Chest Girth ◽

Bali Cattle ◽

Strong Candidate ◽

Almost All

This research aims to develop a method for selection based on myostatin gene markers. The experiment was conducted in Bali cattle. Blood samples were collected from 100 cattle irrespective of age. PCR-RFLP was applied with primers for amplifying the 1346bp of the Myostatin gene were (F) 5’-CCCTACAGAGGCCACTTCAA-3’ and (R) 5’-CTCGCTGTTCTCATTCAGATC-3’, sand HaeIII restriction enzymes. PCR-RFLP results showed that not all genotypes present in the population, despite populations that were observed quite polymorphic (PIC = 49.5%) with the conditions of gene frequencies. The results showed that almost all variables influenced by myostatin genotype where the genotype BB is better, except the chest girth showed a better result in genotype AB. It suggested that MSTN is strong candidate gene that influenced growth traits. Moreover, it is also expected that this MSTN could be used in marker-assisted selection.

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Effect of the g.98535683A > G SNP in the CAST gene on meat traits of Nellore beef cattle (Bos indicus) and their crosses with Bos taurus

Meat Science ◽

10.1016/j.meatsci.2016.09.003 ◽

2017 ◽

Vol 123 ◽

pp. 64-66 ◽

Cited By ~ 6

Author(s):

Cruz Elena Enriquez-Valencia ◽

Guilherme Luis Pereira ◽

Jessica Moraes Malheiros ◽

Josineudson Augusto I.I. de Vasconcelos Silva ◽

Lúcia Galvão Albuquerque ◽

...

Keyword(s):

Beef Cattle ◽

Bos Taurus ◽

Bos Indicus ◽

Cast Gene

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Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation

The ISME Journal ◽

10.1038/s41396-019-0529-2 ◽

2019 ◽

Vol 14 (1) ◽

pp. 302-317 ◽

Cited By ~ 7

Author(s):

Peixin Fan ◽

Beilei Bian ◽

Lin Teng ◽

Corwin D. Nelson ◽

J. Driver ◽

...

Keyword(s):

Genetic Variation ◽

Gut Microbiota ◽

Bos Taurus ◽

Bos Indicus ◽

Nucleotide Polymorphisms ◽

Paternal Genome ◽

Host Genetics ◽

Microbe Interactions ◽

Host Genetic

Abstract Multiple synergistic factors affect the development and composition of mammalian gut microbiota, but effects of host genetics remain unclear. To illuminate the role of host genetics on gut microbiota, we employed animals with a graduated spectrum of genetic variation with minimal environmental influences. We bred 228 calves with linearly varying breed composition from 100% Angus (Bos taurus) to 100% Brahman (Bos indicus), as a proxy for genetic variation, and then raised the offspring in the same environment with identical diets. We hypothesized each breed would harbor distinct gut microbiota due to genetic influence. We found that the gut microbiota of preweaning calves at 3 months old is significantly affected by host genetics, profoundly by paternal genome. We also demonstrate that single nucleotide polymorphisms in host mucin-encoding genes, critical for gut mucosal health, are significantly correlated with both breed composition and mucin-degrading gut bacteria. We further demonstrate host genetics indirectly changes gut microbiota composition via microbe–microbe interactions. These findings indicate a strong contribution by host genetics in shaping the gut microbiota during early life stages, shedding light on impact of animal breeding on gut microbiota, which is associated with animal growth and health.

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Genetic polymorphisms related to meat traits in purebred and crossbred Nelore cattle

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2009001200015 ◽

2009 ◽

Vol 44 (12) ◽

pp. 1660-1666

Author(s):

Rogério Abdallah Curi ◽

Marina Rufino Salinas Fortes ◽

Luis Artur Loyola Chardulo ◽

Antonio Carlos Silveira ◽

Mário De Beni Arrigoni ◽

...

Keyword(s):

Gene Polymorphism ◽

Bos Taurus ◽

Association Studies ◽

Large Subunit ◽

Meat Tenderness ◽

Nucleotide Polymorphisms ◽

Genetic Groups ◽

Fragmentation Index ◽

Pcr Rflp ◽

Nelore Cattle

The objective of this work was to estimate the allelic and genotypic frequencies of CAST/XmnI, a calpastatin gene polymorphism, and CAPN530, a calpain 1 large subunit gene polymorphism, in different beef genetic groups (Nelore and Nelore x Bos taurus), and to investigate associations between these polymorphisms and carcass and meat traits. Three hundred animals - comprising 114 Nelore, 67 Angus x Nelore, 44 Rubia Gallega x Nelore, 41 Canchim, 19 Brangus three-way cross and 15 Braunvieh three-way cross- were genotyped by PCR-RFLP and phenotyped for rib-eye area (REA), back-fat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The occurrence of the two alleles of the CAST/XmnI and CAPN530 single nucleotide polymorphisms (SNPs) in a B. indicus breed, which permitted association studies in purebred and crossbred Nelore cattle, was first shown in the present work. No relationship was found between the CAST or CAPN1 SNPs and growth-related traits (REA) or fat deposition (BT and IF), since calpastatin and µ-calpain are not physiologically involved with these traits. Moreover, the association results between genotypes and aged meat tenderness (assessed by SF and MFI) showed that these markers are useless in assisted selection for purebred Nelore and their crosses with B. taurus.

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