Genetic variation in the first intron and exon of the myostatin gene in several Indonesian cattle populations

Biodiversity of Indonesian indigenous buffalo: First review of the status, challenges, and development opportunities

In Indonesia, the buffalo is important for small and marginal farmers' livelihood and economic development as a source of food, working animal, and tourist attraction. Therefore, an in-depth study is needed to examine challenges and opportunities for buffalo development in Indonesia. In Indonesia, the buffalo is divided into two types: swamp buffalo and river buffalo. The buffalo population in Indonesia has declined significantly. A decrease of approximately 39.35% was recorded from 2022 to 2017. The decline occurred due to low reproduction rate and suboptimal rearing management systems. There are three buffalo-rearing systems: Intensive, semi-intensive, and extensive. The productivity of buffalo is diverse and closely related to the characteristics of the regional agroecosystem, consistent with existing natural resources and rearing management systems. The diversity of buffalo productivity provides a good opportunity to improve productivity. Improvement of buffalo genetics is urgently needed, by improving mating management, etc., especially to reduce potential inbreeding. In recent years, genetic and molecular research on Indonesian buffalo has made progress, including use of molecular markers, such as microsatellites and single-nucleotide polymorphisms, to evaluate genetic diversity within and among buffalo populations across Indonesia. In addition, studies are being conducted on the relationship of genotype mutations that contribute to appearance and phenotypic performance (heat stress, reproduction, behavior, coat color, and production attributes) in buffaloes. Identification of genetic diversity in local buffaloes can be improved using various genetic and genomic techniques. These findings will form a basis for the targeted conservation of local buffaloes in Indonesia. This study aimed to collect information on the genetic resources of the local buffalo, particularly its status and production system and provide recommendations for developing buffalo production in Indonesia.

Polymorphism of Genes and Their Impact on Beef Quality

The single-nucleotide polymorphism (SNP) form of genes is a valuable source of information regarding their suitability for use as specific markers of desirable traits in beef cattle breeding. For several decades, breeding work focused on improving production efficiency through optimizing the feed conversion ratio and improving daily gains and meat quality. Many research teams previously undertook research work on single-nucleotide polymorphism in myostatin (MSTN), thyroglobulin (TG), calpain (CAPN), and calpastatin (CAST) proteins. The literature review focuses on the most frequently addressed issues concerning these genes in beef cattle production and points to a number of relevant studies on the genes' polymorphic forms. The four genes presented are worth considering during breeding work as a set of genes that can positively influence productivity and production quality.

Genetic polymorphism of myostatin gene in Sumba Ongole (Bos indicus) cattle and its association with growth traits

Objective

As one of the most valuable genetic resources of Ongole beef cattle globally, the Sumba Ongole (SO) cattle population is being studied in this investigation of myostatin (MSTN) gene polymorphism and its association with growth traits.

Materials and Methods

Blood samples from 161 SO cattle were collected and analyzed. Deoxyribonucleic acid (DNA) was isolated. The DNA was electrophoresed and extracted, and finally, the annealing temperature was optimized, followed by amplification and sequencing. Next, we used a Basic local alignment search tool to assess the sequencing data.

Results

The analysis revealed 22 single nucleotide polymorphisms (SNPs) in the MSTN gene in this region that showed genetic variation. Two SNPs, c.424 G > A, and c.467 G > C, were found to be significantly associated with SO cattle phenotypes of wither height, heart girth, and hip height (p < 0.05) but not with body weight or body length (p > 0.05).

Conclusion

As a result of our findings, the MSTN gene polymorphism and its correlation with growth traits in SO cattle may be employed as a candidate marker in SO cattle and other beef cattle breeds.

Genetic polymorphisms of the 5' untranslated regions of the HSP70 gene in Indonesian cattle populations

Background and Aim:

Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. HSP70 is a conserved, sensitive, and abundant gene associated with heat stress’s physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the HSP70 gene (5’ untranslated region [UTR]) in seven cattle populations in Indonesia.

Materials and Methods:

Polymerase chain reaction products (551 bp) of the HSP70 gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue x Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method.

Results:

Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy–Weinberg equilibrium (p>0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the HSP70 gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue x PO crossbred cattle were farther apart.

Conclusion:

The polymorphisms in the 5’ UTR of the HSP70 geneidentified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.