Abstract
Background:
Bali cattle are native cattle to Indonesia. Bali cattle are kept for meat production. In general, Bali cattle have various horn characteristics, including scurs and polled patterns, with very few frequencies. However, horn characteristics can influence the behavior and economic value of Bali cattle.

Aim:
This study aimed to identify the functional genes for horn development in Bali cattle using single nucleotide polymorphism (SNP) array analysis.

Methods:
As the first investigation, 48 heads of Bali cattle (unsexed) with polled (19 heads), scurred (7 heads), and horned (22 heads) horn status were used for the investigation. The cattle were collected from farmers in Barru Regency, South Sulawesi Province, Indonesia. The SNP array analysis was performed using the Bovine SNP50K BeadChip and the Illumina i-Scan machine. Filtering was conducted by selecting SNPs with a minimum allele frequency (MAF) of less than 0.50 and removing SNPs outside the chromosome region. SNP markers with the highest Bonferroni threshold value were selected as potential genetic markers. The TASSEL 5 program was used to analyze the SNP array output in PED and MAP formats. Furthermore, the STRING program was used to observe the interaction among the candidate genes.

Results:
Four SNP markers, ARS-BFGL-NGS-29467 (SNP1), ARS-BFGL-NGS-43990 (SNP2), ARS-BFGLNGS-102231 (SNP3), and ARS-BFGL-NGS-80175 (SNP4), were identified as potential genetic markers for horn development in Bali cattle. These SNP markers are located in the intronic regions of the ERBB4 (SNP1), SEZ6L (SNP3), and LOC104976682 (SNP4) genes. The PIC values of ERBB4, SEZ6L, and LOC104976682 were 0.32, 0.20, and 0.13, respectively. The haplotyping with the three observed genes revealed that AG/GG/AA and AA/GG/AA were the most frequent haplotypes in each horn status group. However, four specific haplotypes were detected in polled animals (GG/GG/AC, AG/AG/AC, AA/AG/AA, and GG/AG/AC), and one specific haplotype was found in horned animals (AA/GG/AC).

Conclusion:
SNP array analysis detected the specific genetic marker for each horn status trait in Bali cattle. However, two horn development genes (ERBB4 and SEZ6L) had a relationship with the SYNJ1, IFNAR1, and IFNAR2 genes, which control cattle horn development. Unfortunately, the LOC104976682 gene was not characterized in the STRING database and thus could not be investigated in this study. In the future, an in-depth study of gene expression and transcriptomics will be important for obtaining accurate genetic markers of horn development in Bali cattle.

Key words: Bali cattle; Bovine SNP50K BeadChip; Genetic markers; Horn development; SNP array.