Analisis Keragaman Daerah 5' dan 3' UTR Gen Calpain serta Hubungannya dengan Pertumbuhan dan Sifat Kualitas Daging pada Sapi Pedaging

Abstract

Bali cattle (Bos javanicus) are native cattle that originally specified from domestication of banteng (Bibos banteng). Bali cattle have the potential to be developed as a premium beef producer. Genes that have important role in meat quality are calpain genes (CAPN). Calpains are classified as Ca2+ dependent intracellular cysteine proteases, including the ubiquitously expressed μ-calpain (CAPN1) and m-calpain (CAPN2). The objective of this study was to analyze 5’ and 3’UTR region polymorphism of calpain gene in beef cattle and its association with growth traits, meat quality in bali cattle using ultrasound. The blood samples of beef cattle used was 113 cattle consist of bali cattle (n=52 cattle) obtained from obtained from BPTU-HMT Denpasar Bali Province, Belgian Blue (n=30 cattle), Limousine (n=14 cattle) from BPTU Padang Mangatas, Wagyu (n=7 cattle), and PO (n=10 cattle) from BET Cipelang Bogor, West Java Province. Carcass include longissimus dorsi thickness (LDT), backfat thickness (BFT) and meat include marbling score (MS), intramuscular fat percentage (PIMF) characteristics were measured using ultrasound images and the USG result data was performed by Image-J NIH software. Polymorphism of 5’UTR and 3’UTR regions in CAPN1 gene were analyzed by PCR-RFLP and DNA direct sequencing respectively. Frequencies of genotype and allele, heterozygosity, and HardyWeinberg equilibrium (ꭓ2) were analyzed using PopGen 1.32 program. The association SNPs polymorphism in CAPN1 gene with growth traits namely weaning weight, body weight at 365 days, body weight at 730 days, and body weight gain, carcass and meat characteristics were performed by General Linier Model (GLM) procedure using SAS 9.4 software. The result shows that CAPN1 g.232 G>T SNP at 5’UTR region was polymorphic in bali cattle and PO, however monomorphic in Belgian Blue, Limousine, and Wagyu. The total of six SNPs at 3’UTR region which were g.15284 C>T, g.15347 T>G, g.15525 G>A, g.15853 G>A, g.15905 G>A, and g.15915 G>A were polymorphic in bali cattle, however monomorphic in Belgian Blue, Limousine, Wagyu and PO. The 3’UTR region was also found indel mutation g.15795–g.15802DelCTCCCTCC which was polymorphic in bali cattle and PO, Belgian Blue, and Limousine, however monomorphic in Wagyu. The polymorphism of g.232 G>T SNP in 5’UTR was associated with body weight at 730 days, however in 3’UTR region were not associated with growth traits in bali cattle. The g.232 G>T SNP in 5'UTR in bali cattle was associated (P <00.5) with marbling score and intramuscular fat percentage. The 3’UTR of g.15525 G>A SNP was associated with back fat thickness. These results further suggest that CAPN1 is a strong candidate gene influencing body weight at 730 days , marbling score, and intramuscular fat percentage in bali cattle.

Sapi bali (Bos javanicus) merupakan salah satu ternak asli hasil domestikasi banteng (Bibos banteng). Sapi bali berpotensi untuk dikembangkan sebagai penghasil daging sapi premium. Salah satu gen yang berperan penting dalam kualitas daging adalah gen calpains (CAPN). Calpains diklasifikasikan sebagai protease sistein intraseluler yang diaktivasi oleh Ca2+, termasuk μ-calpain (CAPN1) dan m-calpain (CAPN2). Tujuan dari penelitian ini adalah menganalisis keragaman daerah 5’ dan 3’UTR gen CAPN1 pada sapi pedaging dan asosiasinya dengan sifat pertumbuhan, kualitas daging khususnya pada sapi bali menggunakan citra ultrasonografi. Sampel darah sapi pedaging yang digunakan sebanyak 113 ekor terdiri atas sapi Bali (n=52 ekor) diperoleh dari BPTU-HMT Provinsi Bali, sapi Belgian Blue (n=30 ekor) dan Limousine (n=14 ekor) dari BPTU Padang Mangatas, Wagyu (n=7 ekor) dan PO (n=10 ekor) dari BET Cipelang, Bogor, Jawa Barat. Karakteristik karkas meliputi tebal longissimus dorsi (TLD), tebal lemak punggung (TLP) dan daging meliputi skor marbling (SM), presentase lemak intramuskular (PLIM) diukur menggunakan citra ultrasonografi dan hasil gambar dianalisis menggunakan perangkat lunak Image-J NIH. Keragaman gen CAPN1 daerah 5’UTR dan 3’UTR masing-masing diidentifikasi dengan PCR-RFLP dan direct DNA sequencing. Frekuensi alel dan genotipe, heterozigositas serta uji keseimbangan HardyWeinberg (ꭓ2) dianalisis menggunakan program PopGen 1.32. Asosiasi keragaman (SNP) gen CAPN1 dengan sifat pertumbuhan meliputi bobot sapih, bobot badan 365 hari, bobot badan 730 hari, dan pertambahan bobot badan serta karakteristik karkas dan daging dianalisis menggunakan metode General Linier Model (GLM) dengan program SAS. Hasil penelitian menunjukkan bahwa SNP g.232 G>T daerah 5’UTR gen CAPN1 bersifat polimorfik pada sapi bali dan PO. Total 6 SNP daerah 3’UTR gen CAPN1 pada sapi bali diantarnya adalah g.15284 C>T, g.15347 T>G, g.15525 G>A, g.15905 G>A, dan g.15915 G>A bersifat polimorfik di sapi bali, namun monomorfik di Belgian Blue, Limousine, Wagyu, dan PO. Mutasi indel g.15795–g.15802DelCTCCCTCC bersifat polimorfik pada sapi bali, PO, Belgian Blue, dan Limousine namun pada sapi Wagyu bersifat monomorfik. Keragaman SNP g.232 G>T daerah 5’UTR memiliki asosiasi dengan bobot badan 730 hari, sedangkan daerah 3’UTR tidak berasosiasi dengan sifat pertumbuhan pada sapi bali.

Keragaman SNP g.232 G>T pada sapi bali juga berasosiasi (P<0.05) dengan skor marbling (SM) dan presentase lemak intramuskular (PLIM). Adapun keragaman SNP 3’UTR g.15525 G>A berasosiasi dengan tebal lemak puunggung (TLP). Hasil ini lebih lanjut menunjukkan bahwa CAPN1 merupakan gen kandidat kuat yang mempengaruhi bobot badan 730 hari serta skor marbling dan presentase lemak intramuskular pada sapi bali.