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Background and Aim: Milk physicochemical properties play essential role in the milk processing industry, which are moderately to highly affected by genetic factors. This study aimed to evaluate the association between single nucleotide polymorphisms in POU class 1 homeobox 1 ( POU1F1 ) and the physicochemical properties of milk in high-producing Holstein Friesian (HF) cows., Materials and Methods: A total of 149 high-producing dairy cows from PT Ultra Peternakan Bandung Selatan was included in this study. The physicochemical properties of milk, including density, freezing point, pH, lactose, solid non-fat, protein, and ash content, were determined. Moreover, three polymorphisms within the exon regions of POU1F1 (c.195G>A, c.300G>T, and c.828G>A) were analyzed using polymerase chain reaction-restriction fragment length polymorphism. The association between these polymorphisms and the physicochemical properties of milk was determined using a mixed-effects model analysis, in which the lactation period was used as a covariate., Results: This study found that two polymorphisms, c.195G>A and c.828G>A, significantly affected the pH of fresh milk. Cows with both the GG genotypes c.195G>A and c.828G>A had lower milk pH values than those with the other genotypes. In addition, a non-significant effect of POU1F1 was observed on the other physicochemical properties of milk., Conclusion: Two POU1F1 polymorphisms determined the pH of fresh milk in the Indonesian HF population. These are potential marker candidates for milk pH that directly affect the development of dairy products in the milk processing industry., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Cahyadi, et al.)

Background and Aim: Pleomorphic adenoma gene 1 ( PLAG1 ) encodes a multifunctional transcription factor that controls many genes and pathways and is associated with cattle body weight and measurements. This study aimed to evaluate the association between PLAG1 polymorphisms with body weight and measurements in Bali cattle., Materials and Methods: A total of 87 Bali cattle, consisting of 48 bulls and 39 heifers at the Breeding Center for Bali Cattle, were used as the population in this study. Cattle were 2 years old and kept semi-intensively in the pasture. Phenotype data consisting of body weight, withers height, body length, chest girth, waist height, and chest depth were measured. Birth weight data were obtained from birth records, and weight gain, adjusted weaning weight, and yearling weight were calculated using formulas. Blood samples were taken from the jugular vein as much as 5 mL, and genomic DNA was isolated using the salting-out method. Polymerase chain reaction (PCR) was performed to amplify three target polymorphisms, namely, g.48308 C>T, g.32212 (19 bp indel), and g.45233 T>C. The presence of a 19 bp indel was determined by direct observation of the PCR product on a 2% agarose gel. Two other polymorphisms were detected by PCR-restriction fragment length polymorphism using the restriction endonuclease enzymes Sac II and Bcl I. PLAG1 genotype and phenotype associations were analyzed using a general linear model., Results: The results showed that two of the target polymorphisms in PLAG1 did not vary. The DD genotype indicated by 123 bp of PCR product was the only genotype identified for g.32212 19 bp indel, and TT genotype was the only genotype found for g.45233 T>C single-nucleotide polymorphism (SNP). Conversely, g.48308 C>T SNP was found to be polymorphic. In addition, the g.48308 C>T polymorphism of PLAG1 was significantly associated with body length of Bali cattle. Cattle with the CC genotype had a greater body length than the other two genotypes., Conclusion: The g.48308 C>T SNP in PLAG1 was associated with Bali cattle body length characteristics. This finding could be used as a basis for selecting Bali cattle based on body length characteristics., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Cahyadi, et al.)

Background and Aim: Bali Cattle ( Bos j. javanicus ) is a local breed originating in Indonesia, accounting for 32.3% of the total cattle population. To date, no studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. Therefore, a study that used molecular breeding technologies to characterize the demography of Bali cattle would be timely. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size ( N e ) values in the cattle population., Materials and Methods: In this study, we explored the population structure and genetic diversity of Bali cattle using genomic-level analyses. Our study primarily studied cattle that had been bred in livestock breeding centers since these breeds had subsequently spread throughout Indonesia. We focused on characterizing the genetic structure, determining the level of LD present, and estimating the N e of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data., Results: We found that the LD values of Bali cattle from the breeding center and those raised elsewhere were 0.48±0.43 and 0.39±0.40, respectively. Subsequently, the N e value of Bali cattle from the breeding center and farmers was 151 and 96, respectively., Conclusion: Our results suggest that the selection program of the breeding center is beneficial for maintaining the genetic diversity of Bali cattle., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Sudrajad, et al.)