Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

Abstract

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 (Ne) 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 Ne 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 Ne 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.

Genome-wide Association Study of Birth Weight in Bali Cattle (Bos javanicus)

“…To ensure the samples variability, the genomic structure of the Bali cattle population in the breeding center have been previously explained by Sudrajad et al (2022), i.e., observed heterozygosity (H o ) 0.30, expected heterozygosity (H e ) 0.26, and negative inbreeding coefficient (-0.19). The quality control process yielded 49.439 cleaned variants, accounting for 93% of the total SNPs.…”

“…Furthermore, heterozygosity is a useful metric that must be checked prior to GWAS (Gondro et al, 2013). Despite our small sample size, the heterozygosity value of the Bali cattle population in the breeding center is higher than that of the Bali cattle population in the farmer with low inbreeding coefficients (Sudrajad et al, 2022) so that we can be certain of the sample's variability. Moreover, the value of H o was not too high when compared to H e , indicating that there was no DNA contamination or samples deviated from the population (Gondro et al, 2013).…”

Genome-Wide Association Study for Body Weight and Carcass Weight in Sumba Ongole Bulls (Bos indicus)

“…Otherwise, STXBP6 and TERT have been identified as the candidate genes for birth weight in Bali cattle, according to a different study by Sudrajad et al (2023). Additionally, Indonesian Bali cattle (Bos javanicus) have had their genetic structure and effective population size evaluated by Sudrajad et al (2022) using GWAS. Presently, the GWAS in productivity traits of SO cattle has not been reported.…”

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

“…Since livestock producers in Indonesia rely heavily on cattle for their revenue, cattle are one of the most essential livestock products (Dakhlan et al, 2022;Kuswati et al, 2022;Pakpahan et al, 2022;Prihandini et al, 2022;Sudrajad et al, 2022). The productivity of Indonesian livestock, especially local cattle, is still relatively low and is a major problem that must be resolved immediately (Mayulu et al, 2010).…”