Boar taint is an unpleasant smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone (5α-androst-16-en-3-one) and skatole (3-methylindole). It is crucial to understand the genetic mechanism of boar taint to select pigs for lower androstenone levels and thus reduce boar taint. The aim of the present study was to investigate transcriptome differences in boar testis and liver tissues with divergent androstenone levels using RNA deep sequencing (RNA-Seq). The total number of reads produced for each testis and liver sample ranged from 13,221,550 to 33,206,723 and 12,755,487 to 46,050,468, respectively. In testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver. The fold change values ranged from −4.68 to 2.90 in testis samples and −2.86 to 3.89 in liver samples. Differentially regulated genes in high androstenone testis and liver samples were enriched in metabolic processes such as lipid metabolism, small molecule biochemistry and molecular transport. This study provides evidence for transcriptome profile and gene polymorphisms of boars with divergent androstenone level using RNA-Seq technology. Digital gene expression analysis identified candidate genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family. Moreover, polymorphism and association analysis revealed mutation in IRG6, MX1, IFIT2, CYP7A1, FMO5 and KRT18 genes could be potential candidate markers for androstenone levels in boars. Further studies are required for proving the role of candidate genes to be used in genomic selection against boar taint in pig breeding programs.

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Boar taint is the unpleasant odour of meat derived from non-castrated male pigs, caused by the accumulation of androstenone and skatole in fat. Skatole is a tryptophan metabolite produced by intestinal bacteria in gut and catabolised in liver. Since boar taint affects consumer’s preference, the aim of this study was to perform transcriptome profiling in liver of boars with divergent skatole levels in backfat by using RNA-Seq. The total number of reads produced for each liver sample ranged from 11.8 to 39.0 million. Approximately 448 genes were differentially regulated (p-adjusted <0.05). Among them, 383 genes were up-regulated in higher skatole group and 65 were down-regulated (p<0.01, FC>1.5). Differentially regulated genes in the high skatole liver samples were enriched in metabolic processes such as small molecule biochemistry, protein synthesis, lipid and amino acid metabolism. Pathway analysis identified the remodeling of epithelial adherens junction and TCA cycle as the most dominant pathways which may play important roles in skatole metabolism. Differential gene expression analysis identified candidate genes in ATP synthesis, cytochrome P450, keratin, phosphoglucomutase, isocitrate dehydrogenase and solute carrier family. Additionally, polymorphism and association analysis revealed that mutations in ATP5B, KRT8, PGM1, SLC22A7 and IDH1 genes could be potential markers for skatole levels in boars. Furthermore, expression analysis of exon usage of three genes (ATP5B, KRT8 and PGM1) revealed significant differential expression of exons of these genes in different skatole levels. These polymorphisms and exon expression differences may have impacts on the gene activity ultimately leading to skatole variation and could be used as genetic marker for boar taint related traits. However, further validation is required to confirm the effect of these genetic markers in other pig populations in order to be used in genomic selection against boar taint in pig breeding programs.

ABSTRAK Penelitian ini bertujuan untuk mempelajari pengaruh genetik dan nongenetik sifat pertumbuhan bobot lahir, bobot sapih, dan bobot setahun sapi Bali. Analisis general linier model (GLM) digunakan untuk mengkaji pengaruh nongenetik. Selanjutnya untuk mempelajari pengaruh genetik, pendugaan nilai heritabilitas dihitung melalui analisis mixed models dengan memasukkan induk dan pejantan sebagai faktor acak dan jenis kelamin, paritas, tahun kelahiran serta musim sebagai pengaruh tetap. Hasil penelitian ini menunjukkan bahwa jenis kelamin tidak berpengaruh terhadap bobot lahir dan bobot sapih, tetapi berpengaruh (P<0,05) terhadap bobot setahun. Paritas hanya berpengaruh terhadap bobot sapih. Tahun kelahiran dan musim sangat berpengaruh (P<0,01) terhadap ketiga sifat pertumbuhan. Pendugaan nilai heritabilitas bobot lahir, bobot sapih, dan bobot setahun berturut-turut adalah 0,09+0,07; 0,33+0,09; dan 0,43+0,10. Nilai heritabilitas bobot sapih dan bobot setahun sapi Bali dikategorikan sedang sampai tinggi yang berarti seleksi terhadap kedua sifat tersebut akan efektif dalam meningkatkan kemajuan genetik sapi Bali.

Cytochrome P450, family 2, subfamily A, polypeptide 6 (CYP2A6) and kinesin-like protein KIF12 (KIF12) genes are predicted as candidate genes which play important roles in lamb flavour and odour. The aim of this study was to analyse the genotype polymorphism of CYP2A6 and KIF12 genes, to study association and expression of these genes with lamb flavour and odour. Identification of genes polymorphism and associations of CYP2A6 and KIF12 genes were performed using PCR-RFLP method and GLM analysis. The PCR-RFLP products of CYP2A6 and KIF12 were digested by restriction enzyme BsmAI and BfaI, respectively. The expression of CYP2A6 gene was performed using qRT-PCR. The results showed that the CYP2A6 and KIF12 genes were polymorphics. The CYP2A6 gene found to have two genotypes (TT and GT), whereas the KIF12 gene found to have three genotypes (CC, CT, and TT). The CYP2A6 and KIF12 genes were in Hardy Weinberg Equilibrium (HWE). Association analysis showed that CYP2A6 (g.49170107 G>T) was significantly (P<0.05) associated with 3-methylindole (MI) or skatole, while KIF12 (g.9617965 C>T) was not significantly associated with lamb flavour and odour. The GT genotype exhibited a greater 3-methylindole (MI) or skatole than the TT genotype (P<0.05). The mRNA expression analysis showed that CYP2A6 mRNA expression was higher (P<0.01) in animals with the TT genotype. These results will improve the understanding of the functions of the CYP2A6 in lamb flavour and odour, especially in term of 3-methylindole (MI) or skatole compound within the liver and will shed light on CYP2A6 as a candidate in the selection of sheep with low lamb flavour and odour.

The aim of this study was to evaluate effect of non genetic factors on reproductive performance of Bali cattle. Data on reproduction performance were collected from Breeding Centre of Bali Cattle in Denpasar-Bali. Reproductive traits studied were age at first calving (AFC), calving interval (CI) and pregnancy rate (PR). To observe the effect of non genetic factors on the reproductive traits, a mixed model was used because all of the traits studied were measured repeatedly in individuals. The overall means for AFC, CI, PR and preweaning mortality were 43.86±0.70 months, 360.93±4.47 days, 88.44±1.91% and 7.58±1.07%, respectively. The results showed that AFC and PR were significantly (P<0.01) influenced by dam year of birth but mating system had no significant (P>0.05) effect. With regard to CI, dam year of birth and parity affected CI while mating system had no significantly affect (P>0.05) on CI. The preweaning mortality was only affected by the age of dam significantly (P<0.01). The average of reproductive performance and preweaning mortality in Bali Cattle were not depended remarkably on the mating system being practiced. It might be concluded that an improvement in Bali cattle reproductive traits is possible through improving management systems and utilisation of controlled breeding techniques.

Myostatin (MSTN) gene plays a key role in skletal muscle homeostasis such as inducing muscle athrophy, poliferation of myoblast, increasing ubiquitin-proteasomal, downregulating IGF pathway, and glucolysis. Myostatin gene expression is controled by CpG island located in promoter region. The objectives of this research were to identify polymorphism of MSTN promoter gene and to associate the polymorphism of SNP with growth and muscling traits in Bali cattle. A total of 48 Bali cattle from BPTU-HMT Bali island was screened to identify genetic polymorphisms in MSTN promoter region using sequencing method. The growth and muscling traits were measured at 12 months of age. The muscling traits were evaluated using ultrasound console with linear transducer having frequency 6.5 Hz and scaning we conducted at 130 mm in deep. Analysis of polymorphism was conducted by using PopGen 1.32 software. The association of MSTN with growth and muscling traits were analyzed by using General Linear Model (GLM) procedure. This result showed that a total of 20 polymorphic SNPs (seven SNPs in CpG island) were detected in this region. Although, only 3 SNPs (g.-8078C>T, g.-7996G>C, and g.-7930A>G) had equilibrium condition in Hardy-Weinberg analysis. The association result showed that 2 SNPs (g.-7799T>C and g.-7941C>T) were significantly associated with intramuscular fat percentage (P≤0.05) in Bali cattle. Although the 2 SNPs were nominally significant at nominal P≤0.05 threshold, they were not significant after Bonferroni correction for multiple testing. It could be concluded that MSTN promoter gene was polymorphic in Bali cattle and there were 2 SNPs associated with carcass quality.

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