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Karakterisasi Gen KIF12 (Kinesin Familly 12) serta Hubungannya dengan Komposisi Asam Lemak pada Domba Asep Gunawan; Sarah Tazkya; Kasita Listyarini; Mohamad Yamin; Ismeth Inounu; Cece Sumantri
Jurnal Ilmu dan Teknologi Peternakan Tropis Vol 5, No 3 (2018): JITRO, September
Publisher : Universitas Halu Oleo

ABSTRAKKinesin Family 12 (KIF12) merupakan gen yang terlibat dalam mediasi kaskade antioksidan dalam sel beta sebagai sebuah target intraselular dari kelebihan asupan lemak atau lipotoksit. Penelitian ini bertujuan untuk mengidentifikasi karakterisasai gen KIF12 melalui identifikasi keragaman dan asosiasi gen KIF12 terhadap komposisi asam lemak pada domba. Sampel domba yang digunakan sebanyak 35 ekor yang terdiri dari Domba ekor Gemuk (DEG) dan Domba Ekor Tipis (DET) masing-masing 20 dan 15 ekor. Titik mutasi gen KIF12 berada pada posisi g.9617965 C>T. Identifikasi keragaman gen KIF12 dianalisis menggunakan Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) dengan menggunakan enzim BfaI. Hasil keragaman gen KIF12 bersifat polimorfik dengan ditemukan tiga genotipe yaitu CC, CT, dan TT. Hasil Uji chi square menunjukkan bahwa lokus KIF12 berada pada keseimbangan Hardy-Weinberg (HWE) pada pada DET, hal berbeda ditunjukakan pada DEG. Titik mutasi gen KIF12 berasosiasi secara signifikan (P <0.05) terhadap asam lemak jenuh (SFA) asam laurik (C12:0), asam miristik (C14: 0) and asam heptadenoik (C17: 0) juga asam lemak jenuh tunggal (MUFA), asam miristoleinik (C14: 1) and asam oleik (C18: 1n9c). Gen KIF12 memiliki potensi untuk digunakan sebagai penanda seleksi terhadap komposisi asam lemak.Kata kunci: domba, asam lemak, KIF12, PCR RFLPABSTRACTKinesin Family 12 (KIF12) is one of gene which involved in mediates an antioxidant cascade in beta cells as an intracellular target of excess fat intake or lipotoxicitys. This study was aimed to identify the polymorphism and association of KIF12 gene as candidate gene for fatty acid composition in Indonesian sheep including fat-tailed sheep and thin-tailed sheep. The sample of sheeps used 35 heads consist fat-tailed sheep and thin-tailed sheep as many as each 20 and 15 samples. Identification of polymorphism of KIF12|BfaI gene were analyzed using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP). The results of polymorphism of KIF12 gene were polymorphic for three kind of genotypes of CC, CT, and TT. The chi square revealed that the locus of KIF12 was deviated in Hardy-Weinberg equilibrium (HWE) in fat-tailed sheep, but was in HWE in thin-tailed sheep. A SNP of KIF12 was associated (P <0.05) with saturated fatty acids (SFA) including lauric acid (C12:0), myristic acid (C14: 0) and heptadecanoic acid (C17: 0) as well as monounsaturated fatty acids (MUFA), namely miristoleinic acid (C14: 1) and oleic acid (C18: 1n9c).The KIF12 gene was the potential to be used as a marker of selection for fatty acid compositions. Keywords : sheep, fatty acids, KIF12, PCR-RFLP

Identifikasi Keragaman Gen DGAT1 serta Asosiasinya terhadap Karakteristik Karkas dan Sifat Perlemakan Domba Asep Gunawan; Ratna Sholatia Harahap; Kasita Listyarini; Cece Sumantri
Jurnal Ilmu dan Teknologi Peternakan Tropis Vol 6, No 2 (2019): JITRO, Mei
Publisher : Universitas Halu Oleo

ABSTRAK Karakteristik karkas dan sifat perlemakan pada daging domba dikontrol oleh banyak gen salah satunya gen DGAT1 (Diacylglycerol Acyltransferasel 1). Penelitian ini bertujuan mengidentifikasi SNP (Single Nucleotide Polymorphism) gen DGAT1 pada titik mutasi g.8539 C>T dan asosiasinya terhadap karakteristik karkas dan sifat perlemakan pada domba Indonesia. Total sampel domba yang digunakan sebanyak 150 buah terdiri dari 35 sampel domba compass agrinak (DCA), 36 sampel domba barbados cross (DBC), 41 sampel domba komposit garut (DKG), 20 sampel domba ekor gemuk (DEG), dan 18 sampel domba ekor tipis (DET). Karakteristik karkas dan sifat perlemakan diukur dari domba jantan berumur 10-12 bulan. Identifikasi keragaman DGAT1|ALuI dianalisis dengan metode PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). Hasil keragaman gen DGAT1 bersifat polimorfik dalam DET dan DEG, sedangkan DCA, DBC, dan DKG bersifat monomorfik. Dua genotipe disebut CC dan CT ditemukan dalam DET dan DEG. Titik mutasi gen DGAT1 berasosiasi (P<0.05) dengan karakteristik karkas, yaitu bobot dan panjang karkas. Selain itu, keragaman gen DGAT1 juga berasosiasi signifikan (P<0.05) dengan asam lemak jenuh, yaitu asam stearat (C18:0) dan asam arakidat (C20:0) dan asam lemak tak jenuh tunggal, yaitu asam oleat (C18:1n9c). Gen DGAT1 memiliki kontribusi dalam karakteristik karkas dan komposisi asam lemak pada domba.Kata Kunci: domba, gen DGAT1, karakteristik karkas, PCR-RFLP, sifat perlemakan ABSTRACT Characteristic of carcass and fatness traits of sheep is regulated by many genes such as DGAT1 (Diacylglycerol Acyltransferasel 1) gene. The research was aimed to investigate SNP (Single Nucleotide Polymorphism) of DGAT1 and its association with characteristic of carcass and fatness traits in Indonesian sheep. A total sample of sheeps used 150 rams of 10–12 months consisted 35 samples of compas agrinak sheep (CAS), 36 of barbados cross (BCS), 41 of garut composite (GCS), 20 of javanese fat tailed (JFT), and 18 of javanese thin tailed (JTT). Identification variant of DGAT1|ALuI were performed by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The results of polymorphism of DGAT1 were found in JTT and JFT. However, SNP of DGAT1 in CAS, BCS and GCS were monomorfic. Two genotype namely CC and CT were found in JTT and JFT populations. A SNP of the DGAT1 was associated (P<0.05) with characteristic of carcass, including weight and length of carcass. The variant of DGAT1 was associated too with saturated fatty acids (SFA) including stearic acid (C18:0) and arachidic acid (C20:0), and mono unsaturated fatty acid (MUFA) including oleic acid (C18:1n9c). The DGAT1 gene was contribute to characteristic carcass and fatty acid composition in sheep.Keywords: DGAT1 gene, characteristic carcass, fatness traits, PCR-RFLP, sheep

SNP Discovery of Chicken Liver with Divergent Unsaturated Fatty Acid using Next Generation RNA Sequencing Asep Gunawan; Mutasem Ali M. Abuzahra; Kasita Listyarini; Jakaria Jakaria; Cece Sumantri
Jurnal Ilmu dan Teknologi Peternakan Tropis Vol 6, No 1 (2019): JITRO, Januari
Publisher : Universitas Halu Oleo

ABSTRAKRNA sequencing memberikan peluang baru untuk mendeteksi variasi SNP (Single Nucleotide Polymorphism) pada perbedaan jaringan dengan perbedaan fenotipe. Tujuan dari penelitian ini adalah untuk mengkarakterisisasi penemuan SNP terbaru terkait perbedaan asam lemak tak jenuh pada ayam dengan menggunakan RNA sequencing. Sebanyak 6 sampel dipilih dari 62 sampel masing-masing 3 sampel tinggi dan 3 sampel rendah yang merepresentasikan perbedaan fenotip yang kontras terkait asam lemak tak jenuh dianalisis dengan menggunakan RNA Sequensing. Hasil identifikasi SNP memperlihatkan sebanyak 1208 SNP pada sampel tinggi dan rendah setelah disejajarkan dengan genom ayam Gallus gallus (GGA) v4.0. Sekitar 91% dari total SNP yang ditemukan memiliki tingkat polimorfisme yang tinggi pada 5 gen yang ditemukan terkait asam lemak yaitu gen SCD, COL6A2, CYP2J2L4, HSD17B4, dan SLC23A3. Gen SCD, HSD17B4, dan SLC23A3 memiliki jumlah titik mutasi dengan jumlah yang paling tinggi masing-masing berturut-turut 18, 13, dan 12 SNP. Tingkat level signifikan yang tinggi dan peranan dari ketiga gen tersebut yang sangat penting terkait komposisi asam lemak mengindikasikan bahwa gen SCD, HSD17B4, dan SLC23A3 merupakan tiga gen baru dan potensial untuk digunakan sebagai penanda seleksi kandungan asam lemak tak jenuh tinggi. Namun, hasil penelitian ini perlu divalidasi dan dikonfirmasi sebagai potensial kandidat gen dalam jumlah ayam yang lebih besar dan breed yang berbeda.Kata kunci: asam lemak, ayam, RNA-Seq, variasi transkriptomikABSTRACTRNA sequencing (RNA-Seq) reveals new opportunity for identification SNP discovery in different tissues with divergent phenotype. The objective of this study was to characterize SNP profile from divergent unsaturated fatty acids using RNA-Seq. Six liver samples were selected from 62 chicken which classified 3 high and 3 low unsaturated fatty acids were analyzed using RNA-Seq. The SNP identification showed 1208 SNPs in chicken samples and a large number of those corresponded to differences between high and low chicken genome assembly Gallus gallus (GGA) v4.0. Among them, about 91% of genes had multiple polymorphisms within 5 genes (SCD, COL6A2, CYP2J2L4, HSD17B4, and SLC23A3). The SCD, HSD17B4, and SLC23A3 contained the largest number of mutations with 18, 13, and 12 SNPs respectively. Combining the significant level of SNPs and gene function related with fatty acid composition allow us to suggest SCD, SLC23A3, HSD17B4 as the three novel and promising candidate genes for selecting unsaturated fatty acids. However, further validation is required to confirm the effect of these candidate genes in larger chicken populations.Keywords: chicken, fatty acids, RNA-Seq, transcriptome variants

Association of Cytochrome P450 2A6 (CYP2A6) Gene Polymorphisms with Fatty Acid Traits in Indonesian Native Sheep Gilang Kurnia Abdillah; Kasita Listyarini; Ratna Sholatia Harahap; Asep Gunawan; Cece Sumantri
Buletin Peternakan Vol 45, No 3 (2021): BULETIN PETERNAKAN VOL. 45 (3) AUGUST 2021
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v45i3.65604

A member of the cytochrome P450 superfamily enzyme that play a role in microsomal fatty acids oxidation process encoded by cytochrome P450 2A6 (CYP2A6). This study aimed to examined the CYP2A6 gene polymorphisms and their association on fatty acid traits in Indonesian native sheep. A total of 299 rams aged 10-12 months with body weights between 20-30 kg used to identify the CYP2A6 gene polymorphism are consisted of 36 samples of barbados cross sheep (BCS), 35 samples of compass agrinak sheep (CAS), 20 samples of javanese fat tailed sheep (JFT), 36 javanese thin tailed sheep (JTT), 20 samples of garut sheep (GS), 45 samples of garut composite sheep (GCS), meanwhile for the fatty acid analysis was carried out by using 107 of loin samples from the total sheep. Identification of the CYP2A6 gene polymorphisms were performed using PCR-RFLP (Polymorphism Chain Reaction-Restriction Fragment Length Polymorphism) with the BSmAI restriction enzymes. The amplification product was 286 bp. Polymorphism were found in JFT, JTT, GCS and JS with GG and GT genotypes, while BCS, CAS, and GS were monomorphic with TT genotype. The CYP2A6 BSmAI polymorphism was in Hardy-Weinberg Equilibrium for JFT, JTT and JS, while BCS, CAS, GS, GCS, and combined was deviated based on chi square. A SNP g.49170107 G>T of the CYP2A6 gene polymorphism was significantly associated (P <0.05) with only erucic acid (C22:1n9). The GT genotypes had a higher value than GG genotypes The CYP2A6 gene could be used as a selection marker to improve fatty acid traits in Indonesian native sheep.

Polymorphisms KIF12 GENE|BfaI and its Association on Carcass Characteristics and Lamb Meat Quality Raudah Putri Ekawati; Ratna Sholatia Harahap; Kasita Listyarini; Cece Sumantri; Asep Gunawan
Buletin Peternakan Vol 46, No 4 (2022): BULETIN PETERNAKAN VOL. 46 (4) NOVEMBER 2022
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v46i4.77029

One of gene which involves on mediation an antioxidant cascade in beta cells as an intracellular target of excess fat intake is Kinesin Family 12 (KIF12). This study aims to identify the diversity of SNP g. 9617965 C>T KIF12 and association with carcass characteristic and meat quality. The total sample used were 102 ram DNA samples consisted of 10 barbados cross sheep (BCS), 52 javanese thin tail (JTT), 15 jonggol sheep (JS), 15 garut sheep (GS), and 10 compass agrinak sheep (CAS). Identification of the diversity of KIF12|BfaI was conducted using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. The results showed that the amplification product was 696 bp. The diversity of the KIF12 gene was found three genotypes namely CC, CT, and TT. The allele frequency in all types of sheep was in Hardy-Weinberg equilibrium. A SNP of the KIF12 was associated (P<0.05) with characteristic of carcass, including length of carcass. The association of KIF12 with meat quality was significant (P<0.05) too associated with pH and water holding capasity (WHC). It could be concluded that KIF12 gene is a potential candidate gene for carcass characteristic and meat quality traits in sheep

Polymorphism and Association of the Novel KCTD2 Gene with Flavor and Odor in Indonesian Local Sheeps Herpina Herpina; Kasita Listyarini; Cece Sumantri; Katrin Roosita; Asep Gunawan
Buletin Peternakan Vol 47, No 1 (2023): BULETIN PETERNAKAN VOL. 47 (1) FEBRUARY 2023
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v47i1.80711

A candidate marker that influences the flavor and odor of Indonesian sheep that is the Potassium Channel Tetramerization Domain Containing 2 (KCTD2) gene. This study aims to examine the polymorphism and association between the KCTD2 gene and lamb flavor and odor in Indonesian local sheeps. This study used DNA taken from the longissimus dorsi (LD) muscle of 100 rams including 75 Javanese Thin-Tail sheep (JTTS), 10 Javanese Fat-Tail Sheep (JFTS), and 15 Jonggol Sheep (JS), with ranged in weight from 20 to 35 kg and were 10 to 12 months old. The PCR-RFLP technique and GLM test analysis were used to identify polymorphisms and association of KCTD2 gene. The restriction enzyme BafI digests the PCR-RFLP product of the KCTD2 gene. The results showed that the KCTD2 gene was polymorphic (CC and CT). KCTD2 gene analysis showed a significant (P<0.05) association with 3-Methylphenol (MP). This research provide information regarding the role of the KCTD2 gene in lamb flavor and odor, especially in 3-Methylphenol (MP) compounds, and explain KCTD2 as a functional gene in the selection of premium sheep with low flavor and odor in lamb meat.

Association and Polymorphism of the APOA5 Gene Related to Carcass Characteristics and Lamb Quality in Sheep Novita Nur Anggraeni; Kasita Listyarini; Ratna Sholatia Harahap; Cece Sumantri; Asep Gunawan
Buletin Peternakan Vol 47, No 2 (2023): BULETIN PETERNAKAN VOL. 47 (2) MAY 2023
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v47i2.81956

The apolipoprotein A-V (APOA5) gene is a candidate gene that plays an important role in carcass characteristics and lamb quality. This study aimed to association and polymorphism of the APOA5 gene with carcass characteristics and lamb quality in sheep. The breed of sheep were used 100 sheep consisting of Thin Tailed Sheep (TTS) (n=55), Compass Agrinac Sheep (CAS) (n=10), Garut Sheep (GS) (n=18), Garut Composite Sheep (GCS) (n=8), and Barbados cross sheep (BCS) (n=9). Identification of APOA5 gene polymorphism was performed using PCR-RFLP method and association study was performed using GLM analysis. The results showed that the APOA5 (g.26929941 C>T) gene polymorphism was polymorphic in TTS, CAS, GS, and GCS, while BCS was monomorphic. The APOA5 gene has three genotypes (CC, CT, and TT). Association showed that the APOA5 was a significantly (P<0.05) associated with carcass percentage and carcass length. The polymorphism of the APOA5 (g.26929941 C>T) was also significant (P<0.05) associated with lamb quality of the pH dan tenderness. The TT genotype showed greater carcass length and pH than the CC and CT genotypes. The CT genotype showed a greater percentage of carcass and tenderness than the CC and TT genotypes. The APOA5 gene helps improve sheep carcass characteristics and lamb quality.

Characterization and Association of CFHR5 Gene Polymorphism with Fatty Acid Composition and Cholesterol in Sheep Akbanugra Yudhananda; Kasita Listyarini; Cece Sumantri; Asep Gunawan
Buletin Peternakan Vol 47, No 3 (2023): BULETIN PETERNAKAN VOL. 47 (3) AUGUST 2023
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v47i3.84177

The Complement Factor H Related 5 (CFHR5) gene is speculated to have an important role in regulating fatty acid composition in sheep. The aim of this study was to investigate the polymorphism of the CFHR5 gene and its association with fatty acid composition and cholesterol of sheep in Indonesia. A total of 172 rams from 83 priangan sheep (PS), 20 sapudi sheep (SS), 19 Garut sheep (GS), 20 jonggol sheep (JS), 10 Garut composite sheep (GCS), 10 compass agrinac sheep (CAS), and 10 Barbados cross sheep (BCS) were used for this study. Identification of CFHR5 gene polymorphism were performed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) using AciI restriction enzyme. The results showed that the CFHR5 gene in all sheep populations were polymorphic producing three genotypes, e.g. CC, CT and TT, respectively. The polymorphism had a significant effect (p<0.05) on fatty acid composition (miristoleic [C14:1], ginkgolic [C17:1], tridecanoic [C13:0], and heptadecanoic [C17:0] acids) and cholesterol. The breed and polymorphism had a significant effect (p<0.05) on fatty acid composition (JS with tridecanoic acid [C13:0] and BCS with miristoleic acid [C14:1]). The CC genotype is the preferred genotype and as it exhibits reduced levels of saturated fatty acids and cholesterol. The BCS sheep is the preferred genotype and as it exhibits high PUFA/SFA ratio. The CFHR5 gene (SNP c.1011C>T) has the potential to be used as a genetic marker for the selection of low saturated fatty acid composition and cholesterol in sheep

Evaluasi Keragaman Gen Selenoprotein W1 (SEPW1) dan Kaitannya Terhadap Komposisi Asam Lemak Pada Domba Yusuf, Salman; Harahap, Ratna Sholatia; Listyarini, Kasita; Rahayu, Sri; Sumantri, Cece; Gunawan, Asep
Jurnal Ilmu dan Teknologi Peternakan Tropis Vol 9, No 1 (2022): JITRO, January
Publisher : Universitas Halu Oleo

Kandungan asam lemak dipengaruhi oleh sejumlah gen dan di antaranya ialah selenoprotein W1 (SEPW1). Eksperimen ini bermaksud untuk mengetahui polimorfisme gen SEPW1 serta hubungannya terhadap kandungan asam lemak di domba. Sejumlah 102 ekor domba yang tersusun dari 20 domba ekor gemuk (DEG), 30 domba ekor tipis (DET), 9 domba komposit garut (DKG), 10 domba compass agrinak (DCA), 10 domba barbados cross (DBC), dan 23 domba jonggol (DJ) digunakan dalam penelitian ini. Analisis polimorfisme gen SEPW1 dicari dengan memanfaatkan Polymerase Chain Reaction-Restriction Fragment Lenght Polymorphism (PCR-RFLP), enzim BanI, serta produk amplifikasi berukuran 478 bp. Analisis Chi-square memberikan hasil bahwa populasi berada dalam keseimbangan Hardy-Weinberg, kecuali sampel domba jonggol. Polimorfisme gen SEPW1 teramati berada di semua sampel rumpun domba. Single nucleotide polymorphism (SNP) g.53617063 G>A gen SEPW1 berasosiasi (P<0,05) dengan asam laurat (C12:0), asam palmitat (C16:0), asam arakidat (C20:0), asam henekosilat (C21:0), asam miristoleinat (C14:1), asam oleat (C18:1n9c), asam linoelat (C18:2n6c) dan asam lemak total. Genotipe GG memiliki kandungan asam lemak tak jenuh yang paling tinggi dibandingkan genotipe lainnya. Gen SEPW1 memiliki kapasitas untuk dikembangkan sebagai penanda asam lemak di domba.

Polymorphism of PPM1K Gene and The Association Related to Retail Indonesian Sheep Meat Cuts Suhendra, Muhammad; Ratna Sholatia Harahap; Kasita Listyarini; Cece Sumantri; Cahyo Budiman; Katrin Roosita; Gunawan, Asep
ANIMAL PRODUCTION Vol. 26 No. 1 (2024)
Publisher : Faculty of Animal Science, Jenderal Soedirman University in associate with the Animal Scientist Society of Indonesia (ISPI) and the Indonesian Association of Nutrition and Feed Science (AINI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jap.2024.26.1.216-1

The PPM1K (Protein Phosphatase, Mg2+/Mn2+ Dependent 1K) gene is assumed to associate with retail meat cuts. This study aims to determine the association of the PPM1K gene polymorphisms with retail meat cuts among various breeds of Indonesian sheep. The Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) approach was used to determine the polymorphisms of the PPM1K gene in 130 Indonesian rams aged 10-12 months with body weights ranging from 20-25 kg. The association study between PPM1K and retail meat cuts was analyzed using General Linear Model (GLM). The research showed that the PPM1K gene was polymorphic, with three genotypes: AA (458 bp), GG (259 bp and 199 bp), and AG (458 bp, 259 bp, and 199 bp). The PPM1K gene polymorphisms were significantly (P<0.05) associated with breast cut, which is the breast muscle and bone. The GG genotype of the PPM1K gene had a higher value on breast lamb. This result implies that the PPM1K gene could be a potential candidate for marker-assisted selection for improving the lamb quality of Indonesian sheep.

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