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Sumba Ongole (SO) cattle are Ongole cattle from India which were imported to Indonesia during the Dutch colonial era and were well adapted on Sumba Island, East Nusa Tenggara, Indonesia. Sumba Ongole (SO) cattle are known for high meat production. This research was conducted to identify one point mutation of g.415C/A (F94L marker) in the myostatin (MSTN) gene (exon 1) using PCR-RFLP method with TaqI restriction enzyme (T*CGA). DNA samples of SO bulls and cows (Total 153) from Sumba Island were used in this study. Results revealed that all samples in this study had CC genotype with C allele as the common allele. The mutation point of g.415C/A was not found in this study. However, one mutation point of g.400G/A was detected in this study without amino acid changes (synonymous). It was concluded that MSTN/TaqI gene in the present study is monomorphic and cannot be used as the genetic marker for productive traits of SO cattle.

Birth weight and calving interval are included of productivity traits that can be increased by selection program. However, the standard of desirable birth weight in cattle during the selection program is important to prevent dystocia incident risk. This study was aimed to select Bali cattle (Bos javanicus) based on Estimated Breeding Value of birth weight (EBVBW) and Most Probable Producing Ability of birth weight (MPPABW) and calving interval (MPPACI). Total of 758 records data of BW were collected from Lombok and Sumbawa islands, West Nusa Tenggara Province. Research showed the average of BW in Bali calves were 15.69±1.70 kg (Lombok) and 13.49±1.89 (Sumbawa). The average of CI in Bali cows at both islands were about 385 days. In addition, the heritability (h2) values of BW in both islands was about 0.90. The repeatability (r) values of BW in both islands were about 0.30. Meanwhile, the r value of CI in Sumbawa island was 0.39. The highest of EBVBW for sire was +4.25 kg by bull’s ID: 0838 (Sumbawa). Meanwhile, the highest of EBVBW for calves was +6.07 kg by calf’s ID: 0917 (Sumbawa). The highest of MPPABW was +2.67 kg by cow’s ID: 0872 (Sumbawa). The lowest of MPPACI was -25.70 days by cow’s ID: 02076 (Lombok).

The F94L mutation of the MSTN gene (MSTN-F94L) is considered not to cause disrupted the function of the myostatin gene drastically. Interestingly, this mutation has a very significant effect on muscle mass, carcass, or meat yield and meat quality without any associated severe negative problems. This study aimed to confirm the MSTN-F94L mutation in four local cattle breeds in Indonesia. A total of 518 individuals (140 of Bali, 107 of Sumbawa, 168 of Pasundan, and 103 of Holstein-Friesian (H-F) cattle) were used in this study. Genotype identification was performed by PCR-RFLP method. In the present study showed that the wild-type C allele was fixed (1.000) in Bali, Sumbawa, and HF cattle. However, the wild-type C allele and the mutant A allele were found in Pasundan cattle, even though the frequency of the mutant A allele was very low (0.012). Therefore, in conclusion, the mutation of the MSTN-F94L was detected in Pasundan cattle but no in all three cattle breeds. However, the presence of the mutant A allele in Pasundan cattle allegedly derived from Limousin bulls. The further investigation in other local and exotic breeds and its crossing will answer the status of the MSTN-F94L mutation in local cattle breeds in Indonesia.

Breed characterization in the livestock is important for the breeding program in the future. This research aimed to characterize Thin-tail sheep in the highland and lowland areas of Jambi Province based on 7 body measurements and body indices using multivariate analysis. Data were collected from 160 sheep consisted of 80 rams and 80 ewes from each area (320 sheep in total with 1-2 years old). The research showed that the principal component analysis (PCA) in this study was explained 65.84%-72.30% by body measurements and 78.23%-84.99% by body indices of the total phenotypic variance of animals. The body measurement of cannon circumference (CC) and body indices of area index (AI), relative cannon index (RCI), dactyl thorax index (DTI), conformation index (CI), and index of body weight (IBW) were selected as the discriminating variable for Thin-tail sheep in different areas. However, this study’s canonical correlation (rc) values were 0.44 for body measurements and 0.47 for body indices. Therefore, about 67.5% of Thin-tail sheep from the lowland area and 57.5% of Thin-tail sheep from the highland area can be characterized with body measurements. Hence, about 61.2% of Thin-tail sheep from the lowland area and 65.6% of Thin-tail sheep from the highland area can be characterized with body indices. Temperature, humidity, rainfall, and length of radiation in the highland areas are lower than in the lowland areas. The cluster analysis in four Thin-tail sheep populations revealed two clusters, i.e., cluster 1 consisted of Kerinci and Sungai Penuh and cluster 2 consisted of Muaro Jambi and Batanghari. It was concluded that about 60% of Thin-tail sheep could be characterized through their body indices.

Bovine Pituitary specific transcription factor 1 (bPit-1) is one of amino acid that controling pituitary gland in mammals. The pituitary gland is important for secretion of growth hormone from growth genes. This study was carried out to detect polymorphism in the exon 6 of bPit-1 (g.1256G>A) in Pasundan cattle using PCR-RFLP method and its association with body weight. Total of 69 heads (15 males and 54 females) of Pasundan cattle from breeding station (BPPIBT-SP Ciamis, West Java) were used in this study. Research showed that two genotypes of bPit-1/HinfI gene were identified in this study i.e GG (0.90) and AG (0.10) with allele frequencies of 0.05 (A) and 0.95 (G). The polymorphic informative content (PIC) and number of effective allele (ne) values were 0.09 (low) and 1.11. respectively. The Chi-square (χ2) value in the population studied was 0.20 and in Hardy-Weinberg equilibrium (χ2

A study was conducted to identify the polymorphism in the intron 3 of the Growth Hormone (GH) gene and also to evaluate the association of the GH gene polymorphism with growth parameters and dressing percentage in the Sumba Ongole (SO) cattle. A total of 267 individual DNA samples were used in the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The SO cattle growth parameters data (n=44) including birth weight (BW), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365) and also dressing percentage (DP) (n=122) were investigated in this study. There were three genotypes (AA, AB, and BB) of the GH gene based on the PCR-RFLP analysis with allele frequency was 0.87 and 0.13 for A allele and B allele respectively. The highest genotype frequency in the SO cattle is AA (0.76) and the lowest is BB (0.02). The Heterozygosity Observed (Ho) value in the SO cattle population is 0.23 and Polymorphism Information Content (PIC) value is 0.20. Therefore, the genetic diversity in the SO cattle based on the GH gene polymorphism is quite low. There is no association (P>0.05) in BW, WW205, YW365, and DP with genotypes of the GH gene. As the result, the GH gene in this study cannot be used as a genetic marker in the SO cattle breeding program.

Bovine growth hormone receptor (bGHR) gene was one of the growth hormone family genes that important for body growth and development of cattle. This research was carried out to identify the polymorphism in the exon 10 of bGHR gene from 142 heads of Pasundan cows at West Java and its association with body length (BL), withers height (WH), heart girth (HG), and body weight (BW). There are two mutation points in the bGHR gene based on the sequencing analysis i.e. g.3322del.A and g.3338A>G. The single nucleotide polymorphism (SNP) at g.3338A>G was detected using PCR-RFLP method with AluI restriction enzyme and showed three genotypes of AA (0.49), AG (0.37), and GG (0.14). The allelic frequencies were 0.67 (A) and 0.33 (G). The number of allele effective (ne) value was 1.79 and described that A allele was the higher allele in the bGHR gene in this study. The polymorphic informative content (PIC) value was 0.34 and categorized as a moderate category. The Chi-square (χ2) analysis showed that the population sample was in the Hardy-Weinberg equilibrium (χ2

Selection of livestock was purposed to increase productivity. A performance test was conducted using 25 males and 25 females of Sumba Ongole (SO) cattle. The performance test were conducted in three periods (2014, 2015 and 2016) for about 535 days. Descriptive statistics ws used to analyze data of body weight. Cattle with age between 300 to 600 days were used for evaluation. Result showed that heritability value of yearling weight (YW365) was 0.77+0.68 as a high category. The highest breeding value of YW365 were 66.05 kg (male) and 41.89 kg (female). The average of corrected final weight (CFW) weight were 172.55+34.22 kg (male) and 159.80+37.73 kg (female). The performance test in this study obtained six A class (1 bull and 5 cows) based on the standard minimum of body measurements for SO cattle.

An estimation of most probable producing ability (MPPA) value based on the calves performance is very important for the cow selection. The birth data record of 48 Sumba Ongole (SO) cows and record data from 52 callf birth’s performance were used to estimate the value of MPPA. High of r value (r > 0.30) was obtained at the body length (BL). Birth weight (BW), withers high (WH) and chest girth (CG) had a moderate value (0.10 < r < 0.30) of repeatability. The MPPA value of the cumulative calf birth’s performance of cows based on the highest birth records was 4.64 (cow number 3770) and the lowest was -4.64 (cow number 2283). Calf number B2076 (cow number 3586) had the highest ratio of WH (115.70); BL (124.26); CG (118.90), while the highest ratio of BW (168.35) was obtained in calf number B2095 (cow number 3731). It was concluded that the BW of birth had a moderate value of r (0.10) and could be used as a selection criteria accurately.

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Sumba Ongole (Bos indicus) is a native beef cattle that adapts well in Sumba Island of Indonesia. This study was carried out to perform a genome-wide association study for body weight (BW) and carcass weight (CW) in Sumba Ongole (SO) bulls. A total of forty-eight (n=48) SO bulls were used in this study. The data were collected from the slaughterhouse at Bogor City, West Java, Indonesia, and were analyzed using a genomic software of TASSEL 5.0 to obtain the best genetic marker. The result showed that the threshold Manhattan plot (-Log10P3) was used to select SNP markers for BW and CW in SO bulls. The two (2) SNP markers at BTA1, i.e., ARS-BFGL-NGS-3162 (CEP63 gene) and ARS-BFGL-NGS-78232 were significantly associated with BW and CW, respectively. Nonetheless, the genetic diversity in both SNP markers was low, with a PIC value of less than 0.30. In conclusion, the heterozygous TG bulls in CEP63 gene have higher CW than homozygous TT bulls.

Swamp buffalo (Bubalus bubalis) is one of the Indonesian germplasm that adapts well to Borneo Island. This study aimed to determine the genetic diversity, phylogenetic tree, and phylogeographic structure of Bornean swamp buffalo based on control region (D-loop) mitochondrial DNA sequences. A total of 120 animals were collected from three populations in Indonesia, i.e., the North, East, and South of Kalimantan Provinces. Along 1140 bp of D-loop mtDNA gene of Bornean swamp buffaloes was amplified with a design primer of F: 5'-CAA CAC CCA AAG CTG AAG TT-3’ and R: 5'-CGC TCC TCT TAG TCT CGT TG-3’. Therefore, the forward and reverse sequencing was performed to visualize the full length of D-loop mtDNA gene sequence (1140 bp). Results showed that a total of 47 haplotypes were detected in the animal study, with haplotype and nucleotide diversities of 0.936 and 0.005, respectively. Consequently, two haplogroups were observed in the animal study, i.e., Haplogroup A (North) and Haplogroup B (East and South). Based on structure analysis, Bornean swamp buffaloes were comparable to filing swamp buffaloes of China based on structure. According to the analysis of molecular (AMOVA), the geographical component contributed over 56.44% of the total mtDNA sequence variations. In conclusion, it was discovered that the haplogroups of buffalo from the East and South populations were identical.