Single Nucleotide Polymorphisms (SNPs) in Exon 6 of Lecithin Cholesterol Acyltransferase (LCAT) Gene in Indonesian Local Sheep

Abstract

Lecithin cholesterol acyltransferase (LCAT) is a soluble enzyme that converts cholesterol and lecithin to cholesteryl esters and lysolecithins on the surface of high density lipoprotein and plays an important role in lipoprotein metabolism. The research was aimed to explore single nucleotide polymorphisms of LCAT gene in Indonesian local sheep. A total of 118 genomic DNA of Indonesian local sheep were used in this research, consisted of Sumatera Thin Tail (43 heads), Garut (19 heads), Javanese Thin Tail (17 heads), Javanese Fat Tail (6 heads), Rote Island (7 heads), Kissar (7 heads), Sumbawa (10 heads), and Lembah Palu (9 heads). Polymerase chain reaction was used to amplify genomic DNA for exon 6 (250 bp) and direct sequencing method was used to identify polymorphism sequences. The sequences were analyzed with BioEdit and MEGA 5.2 software. The BLAST sequence was obtained from Gene Bank GQ 150556.1. The results showed three novel SNPs, i.e. c.742C>T, c.770 T>A and c.882C>T. Substitution of cytosine to thymine c.742 is a synonymous mutation; thymine to adenine c.770 and cytosine to thymine c.882 are non-synonymous mutations. Polymorphisms of LCAT gene exon 6 was found in Sumatera Thin Tail, Javanese Thin Tail, Javanese Fat Tail, Garut, Lembah Palu, and Rote Island

Lecithin cholesterol acyltransferase (LCAT) adalah soluble enzyme yang mampu mengonversi kolesterol dan lesitin menjadi ester kolesterol dan lisolesitin pada permukaan high density lipoprotein dan berperan dalam metabolisme lipoprotein. Penelitian ini bertujuan untuk mengeksplorasi single nucleotide polymorphisms (SNPs) gen LCAT domba lokal Indonesia. Total 118 DNA genom domba lokal Indonesia yang terdiri atas: Ekor Tipis Sumatera (43 ekor), Garut (19 ekor), Ekor Tipis Jawa (17 ekor), Ekor Gemuk Jawa (6 ekor), Pulau Rote (7 ekor), Kissar (7 ekor), Sumbawa (10 ekor), dan Lembah Palu (9 ekor) digunakan dalam penelitian ini. Amplifikasi DNA genome menggunakan polymerase chain reaction pada fragmen ekson 6 gen LCAT (250 bp) dan metode direct sequencing digunakan untuk mengidentifikasi keragaman sekuens. Hasil sekuens dianalisis menggunakan software Bioedit dan MEGA 5.2. Sekuens kemudian disejajarkan dengan metode Clustal W dan selanjutnya urutan BLAST diperoleh dari gene bank GQ150556.1. Hasil penelitian menunjukkan bahwa ditemukan tiga SNPs baru, yaitu pada posisi basa c.742C>T, c.770 T>A, dan c.882C>T. Substitusi sitosin menjadi timin c.742 merupakan synonymous mutation; timin menjadi adenin c.770 dan sitosin menjadi timin c.883 merupakan non synonymous mutation. Keragaman gen LCAT ekson 6 ditemukan pada populasi Ekor Tipis Sumatera, Ekor Tipis Jawa, Ekor Gemuk Jawa, Garut, Lembah Palu, dan Pulau Rote.