Genetic polymorphism analysis of 5' untranslated region of thyroglobulin gene in Bali cattle (Bos javanicus) from three different regions of Indonesia

Abstract

ABSTRAKVariasi nukleotida g.422C>T pada gen thyroglobulin dibagian 5'untranslated region (5'UTR) (disebut TG5) telah dilaporkan mempunyai asosiasi dengan tingkat kandungan lemak intramuskuler atau marbling pada sapi potong. Penelitian ini ditujukan untuk mengkonfirmasi keragaman genetik gen TG5 pada sapi Bali dari tiga wilayah sumber bibit yang berbeda di Indonesia. Sebanyak 200 ekor sapi Bali telah dilakukan genotyping pada gen TG5 menggunakan metode polymerase chain reaction-restriction fragment lenght polymorphism (PCR-RFLP) dan analisis sekuen. Hasil penelitian menunjukkan bahwa TG5 terkonfirmasi monomorfik pada sapi Bali dimanapun wilayah asalnya. Selain itu, sebanyak sembilan kandidat SNP ditemukan di dalam gen TG bagian 5'UTR pada sapi Bali dibandingkan dengan sekuens Genbank, meskipun tidak ditemukan variasi SNP di dalam sampel sapi Bali yang diteliti. Marker genetik lain dari gen TG perlu dieksplorasi dan diverifikasi keragamannya pada sapi Bali. Sembilan kandidat SNP juga perlu diverifikasi dan divalidasi lebih lanjut dengan sampel yang lebih besar untuk dapat dikatakan sebagai SNP baru antara sapi Bali dengan referensi sekuen dari GenBank. Kata kunci : gen thyroglobulin, marbling, polimorfisme genetik, sapi Bali, 5'-untranslated region ABSTRACTThe g.422C>T nucleotide variations in the 5' untranslated region (5'UTR) of TG gene (called as TG5) has been reported to be associated with level in intramuscular fat (IMF) content or marbling in beef cattle. The objective of this study was to confirm genetic polymorphism of TG5 gene in Bali cattle populations from three different regions as the main resources of Bali cattle in Indonesia. A total of 200 head of Bali cattle have been performed genotyping on TG5 gene using polymerase chain reactionrestriction fragment lenght polymorphism (PCR-RFLP) method and sequence analysis. Results of the study confirmed that TG5 was monomorphic in Bali cattle wherever their origin regions. Moreover, nine candidate SNPs were detected within 5'UTR of TG gene in Bali cattle compared to Genbank reference sequences, although no SNP variations among Bali cattle sample studied. The new other genetic markers within an entire TG gene suggested to be explored and verified for their polymorphisms in Bali cattle. (S. Anwar et al.) 5'UTR of Thyroglobulin Gene Polymorphism in Bali Cattle 175The nine candidate SNPs were also required further verification and validation in a larger sample to be regarded as new SNPs between Bali cattle and Genbank reference sequences.

The The favorable alleles of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN:g.231054C>T as candidate markers for high-marbling are very low in Bali cattle

“…Exploration of specific genes that responsible for highmarbling is expected to be used for efficiency in MAS program to improve marbling level in Bali cattle. However, in a previous study, Anwar et al (2017) did not find the favorable T allele at 5'-untranslated region (5'UTR) of thyroglobulin gene (422T>C SNP) in pure breeding location of Bali cattle. The AKIRIN2, endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) and TITIN (TTN) genes are the three of the most promising positional functional candidate gene that can be used to achieve these purposes since they were detected to have different expression patterns in musculus longissimus muscle between low-and high-marbled steers groups (Sasaki et al 2006;Sasaki et al 2009;Yamada et al 2009a).…”

“…This presumption seems corroborated by several previous studies in Bali cattle. Anwar et al (2017) revealed that the T allele of thyroglobulin gene (TG5) as favorable allele for marbling was not found in three different regions of purebreeding of Bali cattle. In the study on marbling score using ultrasonic scanning method, Sri Rachma and Harada (2010) showed that the marbling score for Bali bulls at the age of 24 months was very low (0.17 to 0.20) (scale of 0 to 5 based on beef carcass grading standard of Japan).…”

“…A total of 125 genomic DNA samples of Bali cattle were used and prepared as a part of samples of the previous study (Anwar et al 2016;Anwar et al 2017). The animals were mostly raised under extensive management system that grazed freely in grasslands, plantations or postharvested paddy fields.…”

Polymorphism of ADIPOQ and EDG1 genes in Indonesian beef cattle

“…Other constraints were random matting, the absence of mutation, the absence of selection as well as the absence of migration. thyroglobulin (TG5) gene (Anwar et al, 2017), and 5'UTR of EDG1 gen (this study). Therefore, Bali beef cattle could be potential to be developed into premium beef cattle.…”

Associations between gene polymorphisms and selected meat traits in cattle — A review

“…The 5' flanking region of the TG gene plays a crucial role in transcriptional regulation, thus different mutations within its structure affect the different affinities of the transcriptional factors [29]. However, some studies have indicated that this particular SNP occurs in monomeric form among different populations, such as native Bali cattle, and Angus or Hereford [30,31]. The C422T SNP of the TG gene has been recognized…”