Kajian Genomik dan Transkriptomik Gen Penentu Karakteristik Karkas, Kualitas, dan Kandungan Gizi Daging Domba Lokal Indonesia

Abstract

Domba merupakan salah satu ternak penting di Indonesia. Domba telah lama dipelihara oleh rumah tangga petani, berperan penting pada aspek kehidupan ekonomi, sosial, budaya dan religi masyarakat serta berkontribusi terhadap pemenuhan permintaan daging merah nasional. Permintaan daging merah nasional menunjukkan tren yang terus meningkat pada lima tahun terakhir, namun disisi lain, permintaan daging domba menunjukkan tren yang relatif menurun. Lebih lanjut, konsumsi daging merah, termasuk daging domba, masih menemui tantangan dari aspek kesehatan, khususnya terkait dengan tingginya kandungan asam lemak yang berpotensi meningkatkan risiko penyakit metabolik. Peningkatan kesadaran konsumen terhadap kesehatan juga mendorong meningkatnya permintaan daging yang berkualitas tinggi dan memiliki kandungan gizi yang lebih baik. Sejauh ini, produksi daging domba nasional masih didominasi oleh produksi daging domba lokal, sehingga peningkatan kualitas daging domba lokal sangat diperlukan untuk lebih meningkatkan minat konsumen terhadap daging domba. Sifat kualitas daging memiliki nilai heritabilitas yang sedang (moderat), sehingga peningkatan mutu genetik melalui seleksi berpeluang besar dapat meningkatkan kualitas daging domba yang dihasilkan. Peningkatan kualitas daging melalui peningkatan genetik ternak akan memberikan hasil yang lebih permanen dibandingkan peningkatan berbasis manajemen. Penelitian transkriptomik terbaru pada domba lokal komposit mengidentifikasi gen insulin-like growth factor-binding protein 7 (IGFBP7) dan monoglyceride lipase (MGLL) sebagai gen-gen yang berhubungan dengan kualitas daging domba. Hubungan antara kedua gen tersebut dengan sifat kualitas daging juga dilaporkan teridentifikasi pada berbagai bangsa domba yang berbeda dan jenis ternak lain dalam berbagai penelitian sebelumnya di mancanegara. Penelitian ini bertujuan untuk menganalisis keragaman gen IGFBP7 dan MGLL pada domba lokal Indonesia dan mengevaluasi asosiasinya terhadap karakteristik karkas, kualitas daging, dan kandungan gizi daging. Penelitian ini juga bertujuan menganalisis ekspresi gen IGFBP7. Sebanyak 191 domba lokal jantan digunakan dalam penelitian ini, terdiri atas 125 domba ekor tipis (DET), 20 domba Garut (DG), 20 domba ekor gemuk (DEG), 10 domba Bahtera Agrinak (DBA), 9 domba Compass Agrinak (DCA), dan 7 domba Komposit Garut (DKG). Variabel karakteristik karkas yang diamati meliputi bobot karkas hangat, persentase karkas, dan panjang karkas. Variabel kualitas daging yang diamati meliputi pH akhir, keempukan, susut masak, dan daya ikat air (DMA), sedangkan variabel kandungan gizi daging meliputi kandungan asam lemak, kolesterol, dan mineral (Fe, Zn, K, dan Se). DNA diekstraksi dari sampel otot longissimus dorsi. Analisis ekspresi gen dilakukan dengan menggunakan sampel dari hati. Metode Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) digunakan untuk mengidentifikasi genotipe domba pada gen IGFPB7. Metode sanger sequencing digunakan untuk mengidentifikasi genotipe domba pada gen MGLL. Analisis sidik ragam digunakan untuk mengevaluasi asosiasi keragaman gen IGFBP7 dan MGLL dengan variabel yang diamati. Analisis sidik ragam juga digunakan untuk mengevaluasi pengaruh bangsa domba terhadap variabel yang diamati pada genotipe yang sama. Uji Tukey digunakan sebagai uji lanjut untuk mengindentifikasi perbedaan antar kelompok genotipe. Hasil penelitian menunjukkan bahwa gen IGFBP7 (g.72351183 A>C) polimorfik pada semua populasi lokal Indonesia yang diamati. Frekuensi alel A (87%) ditemukan lebih tinggi dibandingkan alel C (13%). Keragaman gen IGFBP7 berasosiasi nyata (P<0,05) dengan kandungan asam lemak daging. DET dengan genotipe CC memiliki kandungan asam linoleat (C18:2n6c), asam eikosapentanoat (C20:5n3), dan total asam lemak tak jenuh ganda (PUFA) daging yang lebih tinggi (P<0,05) dibandingkan DET dengan genotipe AA dan AC. Ekspresi gen IGFBP7 yang dinormalisasi dengan gen referensi glyceraldehyde 3-phosphate dehydrogenase (GAPDH) dan ß-Actin menunjukkan bahwa genotipe CC memiliki nilai ekspresi gen yang lebih rendah (P<0,05) dibandingkan genotipe AC dan lebih rendah secara deskriptif dibandingkan genotipe AA. Hasil sekuensing parsial pada gen MGLL ditemukan dua SNP, yaitu SNP g.59596702 G>A dan g.59596749 C>T pada ekson kelima. Kombinasi kedua SNP menghasilkan empat jenis haplotipe, yaitu Haplotipe 1 (H1) (G-C; 88,77%), H2 (G-T; 0,36%), H3 (A-C; 6,26%), dan H4 (A-T; 4,71%). Sebanyak empat jenis diplotipe ditemukan pada populasi domba yang diamati, yaitu H1H1 (86,61%), H1H3 (11,59%), H2H3 (2,11%), dan H4H4 (4,35%). Gen MGLL polimorfik pada populasi DET, DEG, dan DCA. Keragaman gen MGLL berasosiasi nyata (P<0,05) dengan bobot hidup, karkas hangat, keempukan, DMA, kadar lemak, dan kandungan asam lemak daging. Secara umum, DET dengan diplotipe H4H4 memiliki bobot hidup, karkas hangat, keempukan, DMA, asam cis-11-eikosanoat (C20:1), total MUFA, asam dokosadienoat (C22:2), total PUFA, dan total asam lemak tidak jenuh yang lebih baik dibandingkan jenis diplotipe yang lain. Hasil penelitian ini mengindikasikan bahwa gen IGFBP7 dan MGLL berpotensi dapat dijadikan sebagai kandidat penanda genetik untuk meningkatkan kualitas daging lokal Indonesia melalui seleksi.

Sheep are one of the important livestock species in Indonesia. They have long been raised by smallholder farmers and play a vital role in the economic, social, cultural, and religious aspects of rural communities, while also contributing to the national red meat supply. National demand for red meat has shown a steadily increasing trend over the past five years, however, the demand for sheep has exhibited a relatively declining trend. Furthermore, the consumption of red meat, including lamb, remains a health concern due to its high content of fatty acids, which has been associated with an increased risk of metabolic disorders. Additionally, increased health awareness among customers is likely to further boost demand for high-quality and nutritious meat. Currently, national sheep production relies primarily on local sheep breeds. Therefore, enhancing the meat quality of these local sheep breeds is critically needed in order to increase customer preference for sheep meat. Genetic improvement via selection programs holds significant probability for enhancing meat quality, particularly given their moderate heritability. Such improvements are likely to yield more permanent results compared to improvements through management practices. A recent transcriptomic study on local composite sheep identified insulin-like growth factor-binding protein 7 (IGFBP7) and monoglyceride lipase (MGLL) as genes related to meat quality. Previously, similar association results between these genes and meat quality traits have also been identified and reported in other sheep breeds and livestock species in international studies. The objectives of this study were to analyze the polymorphisms of the IGFBP7 and MGLL genes in Indonesian local sheep and to evaluate their associations with carcass characteristics, meat quality, and the nutritional composition of meat. In addition, this study aimed to analyze the expression of IGFBP7 and MGLL genes. A total of 191 local rams were used in this study, consisting of 125 thin-tailed sheep (DET), 20 Garut sheep (DG), 20 fat-tailed sheep (DEG), 10 Bahtera Agrinak sheep (DBA), 9 Compass Agrinak sheep (DCA), and 7 Composite Garut sheep (DKG). Carcass characteristics were assessed by measuring hot carcass weight, carcass percentage, and carcass length. Meat quality traits assessed included ultimate pH, tenderness, cooking loss, and water-holding capacity (WHC). The nutritional composition included fatty acid profiles, cholesterol, and minerals content (Fe, Zn, K, and Se). DNA was extracted and amplified from the Longissimus dorsi muscle samples. The gene expression analysis was performed using liver tissue samples. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) was conducted for IGFBP7 gene genotyping, whereas Sanger sequencing was employed for MGLL gene genotyping. Analysis of variance (ANOVA) was conducted to evaluate the associations between polymorphisms in the IGFBP7 and MGLL genes and the observed variables. ANOVA was also used to assess the effect of sheep breed on the observed variables within the same genotype. Tukey’s test was applied as a post hoc analysis to identify specific group differences. The results revealed that the IGFBP7 gene (g.72351183 A>C) was polymorphic across all sheep breeds in this study. The frequency of the A allele (87%) was notably higher than that of the C allele (13%). Polymorphisms in the IGFBP7 gene were significantly associated (P<0.05) with meat fatty acid composition. Sheep with the CC genotype exhibited significantly higher (P<0.05) concentrations of linoleic acid (C18:2n6c), eicosapentaenoic acid (C20:5n3), and the total polyunsaturated fatty acid (PUFA) compared to those with AA and AC genotypes. The expression of the IGFBP7 gene, normalized to the reference genes glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and ß-Actin, showed that sheep with the CC genotype exhibited significantly lower gene expression (P<0.05) compared to the AC genotype and was also descriptively lower than the AA genotype. Partial sequencing of the MGLL gene revealed that two single nucleotide polymorphisms (SNPs) in exon 5: g.59596702 G>A and g.59596749 C>T. These SNPs formed four types of haplotypes: Haplotype 1 (H1) (G-C; 88.77%), H2 (G-T; 0.36%), H3 (A-C; 6.26%), and H4 (A-T; 4.71%). Four diplotypes were identified in the studied sheep population: H1H1 (86.61%), H1H3 (11.59%), H2H3 (2.11%), and H4H4 (4.35%). The MGLL gene was found to be polymorphic in DET, DEG, and DCA populations. Significant associations (P<0.05) were detected between MGLL gene polymorphisms with live weight, hot carcass weight, tenderness, WHC, fat content, and meat fatty acid composition. Overall, sheep with the H4H4 diplotype exhibited superior live weight, hot carcass weight, tenderness, WHC, levels of paullinic acid (C20:1), total MUFA, docosadienoic acid (C22:2), total PUFA, and total unsaturated fatty acid compared to other diplotypes. These findings indicate that the IGFBP7 and MGLL genes are promising candidate genetic markers for the selection programs aimed at improving meat quality traits in Indonesian local sheep.