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Applied Animal Reproduction

As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease Therefore, the objective of this study was to determine the extent to which molecular markers could account for variation in fatty acid composition of skeletal muscle and identify genomic regions that harbor genetic variation Subsets of markers on the Illumina 54K bovine SNPchip were able to account for up to 57% of the variance observed in fatty acid composition In addition, these markers could be used to calculate a direct genomic breeding values (DGV) for a given fatty acids with an accuracy (measured as simple correlations between DGV and phenotype) ranging from -006 to 057 Furthermore, 57 1-Mb regions were identified that were associated with at least one fatty acid with a posterior probability of inclusion greater than 090 1-Mb regions on BTA19, BTA26 and BTA29, which harbored fatty acid synthase, Sterol-CoA desaturase and thyroid hormone responsive candidate genes, respectively, explained a high percentage of genetic variance in more than one fatty acid It was also observed that the correlation between DGV for different fatty acids at a given 1-Mb window ranged from almost 1 to -1 Further investigations are needed to identify the causal variants harbored within the identified 1-Mb windows For the first time, Angus breeders have a tool whereby they could select for altered fatty acid composition Furthermore, these reported results could improve our understanding of the biology of fatty acid metabolism and deposition

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Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattlea

Background: Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian x Landrace backcross with extreme phenotypes according to FA profile. Results: We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with lipid metabolism. Moreover, 18 of the differentially-expressed genes were located in genomic regions associated with IMF composition in an independent GWAS study in the same genetic background. Thus, our results indicate that the lipid metabolism of FAs is differently modulated when the FA composition in muscle differs. For instance, a high content of PUFA may reduce FA and glucose uptake resulting in an inhibition of the lipogenesis. These results are consistent with previous studies of our group analysing the liver and the adipose tissue transcriptomes providing a view of each of the main organs involved in lipid metabolism. Conclusions: The results obtained in the muscle transcriptome analysis increase the knowledge of the gene regulation of IMF deposition, FA profile and meat quality, in terms of taste and nutritional value. Besides, our results may be important in terms of human health.

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Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition

There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.

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A functional variant in the Stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork

Veterinary endocrinology and reproduction

Fatty acid composition of meat is becoming more important due to consumer demand for high quality and healthy foods. The present study evaluated the associations of five candidate genes (FABP4, FASN, NR1H3, GH and SCD) with fatty acid composition in Korean cattle (Hanwoo). The g.3691G > A single nucleotide polymorphism (SNP) in the FABP4 gene had significant effects on high myristic acid (C14:0; P   A was also significantly associated with myristic acid (P < 0.01). In case of the SCD gene, a significant effect was only observed in myristoleic acid (C14:1; P < 0.01). However, SNPs in GH and NR1H3 genes showed no effects on fatty acid composition. The results indicate that SNPs in three candidate genes, FABP4, FASN and SCD, may be influential in breeding design for fatty acid composition in Hanwoo.

Association of five candidate genes with fatty acid composition in Korean cattle

Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F2 intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.−353T>C, g.−233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3′ UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F2 animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F2 intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P  C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10−3). No significant association of FA composition traits with SNP g.−353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10−10). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.

Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs

OBJECTIVE At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. METHODS In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. RESULTS The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations (FIT = 0.237), was partly due to the heterozygote deficiency within populations (FIS = 0.114) and moderate level of genetic differentiation among populations (FST = 0.137). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. CONCLUSION The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.

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Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations.

BACKGROUND AND OBJECTIVE Repeat breeding is a major problem in beef cows. The objective of the present study was to determine the blood biochemical levels in repeat breeder and fertile Ongole cross breed cows. MATERIALS AND METHODS This study compared the blood biochemical profiles from 30 repeat breeders and 30 fertile Ongole cross breed cows. Plasma glucose, total cholesterol, total protein and urea nitrogen concentrations were examined in repeat breeder cows and compared with those of fertile cows. Blood samples were collected from the caudal vein into anticoagulant-coated tubes. Cells were removed from plasma by centrifugation and blood glucose, total cholesterol and urea nitrogen concentrations were measured using commercially available kits; a non-commercial kit was used to determine total protein content. RESULTS Significantly different blood profiles between repeat breeder and fertile cows were reported. Specifically, repeat breeder cows had lower levels of glucose, total cholesterol and total protein, but higher levels of urea nitrogen than fertile cows. CONCLUSION Finally, a low level of total protein, total cholesterol and glucose, accompanied by a high level of urea nitrogen, may cause reproductive problems in repeat breeders. Additionally, present findings indicated that biochemical blood profiling could be used as a diagnostic tool for repeat breeding.

Blood Biochemical Profile in Fertile and Repeat Breeder Ongole Cross Breed Cows.

MC4R gene is known as an important candidate gene for the growth trait. The purpose of this research was to identify the MC4R gene in Kebumen Ongole grade cattle and examine its association with growth traits. D ata of birth weight (BW) , weaning weight (WW), birth body length (BBL), birth chest circumference (BCC), birth shoulder height (BSH), weaning body length (WBL), weaning chest circumference (WCC), weaning shoulder height (WSH) and average daily gain (ADG) were collected and used for analysis of MC4R gene. Sixty blood samples were collected for DNA isolation and PCR amplification. The single nucleotide polymorphisms (SNP) g.1133 C>G was used for genotyping by using PCR-RFLP methods. The frequenciy of G allele (0.59) was greater than C allele (0.41). The highest genotype frequencies have been detected in CG heterozygote animals (0.52) followed by GG (0.33) and CC (0.15) in homozygote animals. The results of Pearson ‘s Chi-square test indicated that the population was not deviate (P>0.05) from the Hardy-Weinberg equilibrium (HWE). The SNP g. 1133 C>G of MC4R gene indicated affecting high birth body length with GG genotype (P G may can be a marker for birth body length of calf selection.

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Dyah Maharani

Papers

Association of five candidate genes with fatty acid composition in Korean cattle

Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs

Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations.

Blood Biochemical Profile in Fertile and Repeat Breeder Ongole Cross Breed Cows.

Identification of MC4R gene and its association with body weight and body size in Kebumen Ongole Grade cattle