Identification of Single Nucleotide Polymorphisms on Cattle Breeds in Indonesia Using Bovine 50k

Abstract

Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmentation, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.[ 3, 4, 5, 7, 13, 17, dan

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

“…5 Linkage disequilibrium as estimated using the r 2 method. 6 Effective population size. 7 Data sources: Decker et al [5], Hartati et al [7], and Sudrajad [13] considered together, our results suggest that the selection program of the Bali cattle breeding center is successful.…”

“…In Indonesia, genomic-level analyses have become an important part of research programs designed to support the improvement of livestock genetic quality. For example, such analyses have been utilized to evaluate Indonesian beef and dairy cattle genomes [4,6], as well as the relationship between PLAG1 (a gene on chromosome 14 of the cattle genome) with Ongole cattle birth weight [7].…”