Judul: Characterization of Candidate Genes for Meat Quality of Indonesian Sheep using RNA Sequencing
Abstrak: Lamb tenderness is a very important characteristic in determining the quality and level of public acceptance in consuming meat. Genetic improvement of the tenderness of the meat needs to be done in an effort to produce lamb with a high level of tenderness. Genetic improvement through the RNA sequencing technology can be used to understand the mechanism of the relationship between tenderness traits and its relation to good quality lamb meat. This study aims to identify the candidate genes for meat quality including tenderness of lamb meat, study polymorphism of candidate genes, association and expression of candidate genes related to meat quality. Analysis of RNA sequencing profiling of 5 samples with high tenderness and 5 samples with low tenderness from 140 sheep that have value of tenderness were analyzed using the Illumina Hiseq 2500. The analysis was continued with gene grouping based was carried out using the Illumina Hiseq 2500. The analysis was continued with gene grouping based on function and pathway related to meat tenderness using DAVID software. Quantitative Real Time PCR (qRT-PCR) was used to validate differences in gene expression with RNA sequencing. Further validation using PCR-RFLP and mRNA expression to confirm the effect of the genetic markers that have been obtained. A total of 328 genes could be detected differences in gene expression (DEG), namely 110 genes with high expression and 218 genes with low expression. Gene grouping based on gene ontology obtained cellular and molecularly resulted in the dominant gene clusters, each of which was extracellular exosome and calcium banding. Pathway analysis showed steroid hormone biosynthesis as the dominant pathway for differences in the tenderness level of lamb meat. Gene expression analysis identified candidate genes TP53INP1, CYP2E1, HSD17B13, ADH1C, and LPIN1 showed high expression in influencing meat quality, while the top genes that showed low expression included ANGPTL2, IGFBP7, FABP5, OLFML3, and THOC5. In the liver sample, 334 SNPs from 328 DEG were found. Multiple SNPs (more than one SNP) were found in the OLFML3, THOC5, and ANGPTL2 genes. Several candidate genes that were selected for further validation are OLFML3, THOC5, and ANGPTL2 genes. The results of PCR-RFLP analysis showed that the OLFML3, THOC5, and ANGPTL2 genes were polymorphic. The OLFML3, THOC5, and ANGPTL2 genes were found to have three genotypes, CC, CT, and TT; CC, CT, and TT; GG, GA, and AA. The association results showed that the OLFML3 gene (g.90317673 C>T) (P<0.05) was significantly associated with meat quality traits including tenderness and cooking loss; fatty acid composition such as tridecanoic acid (C13:0), palmitoleic acid (C16:1), heptadecanoic acid (C17:0), ginkgolic acid (C17:1), linolenic acid (C18:3n3), arachidic acid (C20:0), eicosenoic acid (C20:1), arachidonic acid (C20:4n6), heneicosylic acid (C21:0), and nervonic acid (C24:1); carcass characteristics including carcass length; and the retail meat cut including intermuscular fat on the loin, muscle on the flank and shank. The TT genotype showed a higher level of meat quality, carcass characteristics, retail meatcut, and some fatty acid composition. The association results showed that the THOC5 gene (g.68234589 C>T) was significantly (P<0.05) associated with meat quality traits including tenderness; fatty acid composition such as
Keyword: gene, meat quality, RNA sequencing, sheep, tenderness

Judul: Characterization of CYP2E1 and HSD17β13 Gene as Candidate Marker for Improvement of Indonesian Lamb Quality
Abstrak: Gen CYP2E1 dan HSD17β13 merupakan salah satu kandidat gen yang diduga berperan dalam mengontrol kualitas daging domba. Penelitian ini bertujuan melakukan karakterisasi gen CYP2E1 dan HSD17β13 dengan tujuan untuk perbaikan kualitas daging tujuh jenis domba Indonesia, yaitu domba compass agrinak (DCA), domba barbados cross (DBC), domba komposit garut (DKG), domba garut (DG), domba ekor gemuk (DEG), domba ekor tipis (DET), dan domba jonggol (DJ). Karakterisasi gen dilakukan dengan tiga tahapan, yaitu melakukan identifikasi keragaman gen CYP2E1 (g 50.657.948 T>G) dan HSD17β13 (g 101.689.913 C>T) dengan menggunakan metode Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP), melakukan asosiasi gen CYP2E1 dan HSD17β13 dengan kualitas daging menggunakan uji T-test, serta menganalisis ekspresi gen CYP2E1 dan HSD17β13 dengan menggunakan Quantitative Real Time PCR (qRT-PCR). Hasil penelitian menunjukkan bahwa gen CYP2E1 dan HSD17β13 bersifat polimorfik yang ditandai dengan adanya tiga macam genotipe pada gen CYP2E1 (GG, GT, dan TT) dan HSD17β13 (CC, CT, dan TT). Keragaman genotipe gen CYP2E1 dan HSD17β13 tidak berada dalam kesetimbangan Hardy-Weinberg. Hasil analisis menunjukkan bahwa gen CYP2E1 (g 50.657.948 T>G) secara nyata berasosiasi (P<0,05) dengan kualitas daging seperti pH, keempukan daging, komposisi asam lemak (asam lemak tak jenuh tunggal seperti asam elaidik (C18:1n9t) dan asam lemak tak jenuh ganda seperti asam linoleat (C18:2n6c)), serta kandungan flavor dan odor, yaitu 3-methylindole (skatole). Domba dengan genotipe GG memiliki nilai kualitas daging yang lebih baik dibandingkan genotipe GT dan TT untuk sifat fisik daging dan komposisi asam lemak. Gen HSD17β13 (g 101.689.913 C>T) berasosiasi (P<0,05) dengan komposisi asam lemak, seperti asam lemak jenuh (asam arakidat (C20:0), asam henekosanoat (C21:0)), asam lemak tak jenuh, yaitu asam lemak tak jenuh tunggal (MUFA) seperti asam lemak ginkgoleat (C17:1) dan asam lemak tak jenuh ganda (PUFA) yaitu asam eikosedienoat (C20:2). Daging domba dengan genotipe CT memiliki nilai asam lemak tak jenuh yang lebih tinggi dibandingkan genotipe lainnya. Analisis ekspresi gen CYP2E1 menunjukkan adanya perbedaan yang nyata (P<0,05) antar genotipe. Genotipe GG memiliki tingkat ekspresi tertinggi di antara genotipe lainnya. Di lain pihak gen HSD17β13 tidak menunjukkan level ekspresi yang berbeda (P>0,05) antar genotipenya. Hasil penelitian ini menunjukkan bahwa gen CYP2E1 dan HSD17β13 dapat dijadikan sebagai kandidat marker dalam program seleksi domba untuk memperbaiki kualitas daging., CYP2E1 and HSD17β13 genes are candidate genes that play important role in controlling the lamb quality. This study aims to characterize the CYP2E1 and HSD17β13 genes in order to improve the quality of lamb of seven Indonesian sheep, namely compass agrinak sheep (DCA), barbados cross sheep (DBC), garut composite sheep (DKG), garut sheep (DG), fat tailed sheep (DEG), thin-tailed sheep (DET), and jonggol sheep (DJ). Gene characterization was carried out in three stages, namely identifying the diversity of CYP2E1 (g 50.657.948 T>G) and HSD17β13 (g 101.689.913 C>T) genes using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method, associated CYP2E1 and HSD17β13 genes with meat quality using the T-test, and analyzed the expression of CYP2E1 and HSD17β13 genes using Quantitative Real Time PCR (qRT-PCR). The results showed that the CYP2E1 and HSD17β13 genes were polymorphic which was indicated by the presence of three genotypes in the CYP2E1 (GG, GT, and TT) and HSD17β13 (CC,
Keyword: CYP2E1 gene, HSD17β13 gene, meat quality, PCR-RFLP, sheep

Judul: Closed Knight’s Tour pada Papan Catur Berbentuk Persegi Panjang dengan Ukuran Maksimal 8 × 8
Abstrak: Closed Knight’s Tour merupakan langkah kuda yang mengunjungi setiap kotak pada papan catur tepat satu kali dengan langkah kuda berawal dan berakhir pada kotak yang sama. Graf yang terbentuk dari closed knight’s tour dinotasikan sebagai graf G(m,n), dengan m adalah banyaknya baris dan n adalah banyaknya kolom. Graf tersebut memuat Hamiltonian cycle. Sebuah graf terhubung G adalah graf bipartite jika dan hanya jika graf tersebut tidak memiliki cycle dengan panjang ganjil. Papan catur yang memenuhi syarat cukup untuk memiliki closed knight’s tour adalah papan catur berukuran 5 × 6, 5 × 8, 6 × 6, 6 × 7, 6 × 8, 7 × 8, dan 8 × 8.
Keyword: bipartite, closed knight’s tour, hamiltonian cycle, knight’s tour, teori graf