Quantitative or complex traits are determined by the combined effects of many loci, and are
affected by genetic networks or molecular pathways. In the present study, we genotyped a total
of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a
Wagyu x Limousin reference population. Two hundred forty six F2 animals were
measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280
single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW
analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed
from the analysis due to the small number of animals (≤ 9) in one genotype group or
absence of one genotype among three genotypes. The remaining 94 single-trait associations were
then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and
overdominant effects. All significant markers and their QTMs associated with each of these 19
traits were involved in a linear regression model analysis, which confirmed single-gene
associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks
for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high
correlations between predicted and actual values of performance, thus providing evidence that
the classical Mendelian principles of inheritance can be applied in understanding genetic
complexity of complex phenotypes. Our present study also indicated that carcass, eating quality
and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted
selection for improvement of one category of these traits would not interfere with improvement
of another.
Gene expression studies in humans and animals have shown that elevated stearoyl-CoA desaturase (SCD1) activity is associated with increased fat accumulation and monounsaturation of saturated fatty acids in skeletal muscle. However, results of the two reported association studies in humans are inconsistent. In the present study, we annotated the bovine SCD1 gene and identified 3 single nucleotide polymorphisms (SNPs) in its 3'untranslated region (UTR). Genotyping these SNPs on a Wagyu x Limousin reference population revealed that the SCD1 gene was significantly associated with six fat deposition and fatty acid composition traits in skeletal muscle, but not with subcutaneous fat depth and percent kidney-pelvic-heart fat. In particular, we confirmed that the high stearoyl-CoA desaturase activities/alleles were positively correlated with beef marbling score, amount of monounsaturated fatty acids and conjugated linoleic acid content, but negatively with amount of saturated fatty acids. The inconsistent associations between human studies might be caused by using different sets of markers because we observed that most associated markers are located near the end of 3'UTR. We found that the proximity of the polyadenylation signal site is highly conserved among human, cattle and pig, indicating that the region might contain functional elements involved in posttranscriptional control of SCD1 activity. In conclusion, our cross species study provided solid evidence to support SCD1 gene as a critical player in skeletal muscle fat metabolism.
Porcine reproductive and respiratory syndrome (PRRS) has devastated the pig industry worldwide for almost 25 years, and its virus (PRRSV) preferentially infects and replicates in pulmonary alveolar macrophages (PAMs). To discover cellular protein responses in PRRSV-infected PAMs, two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling was employed to quantitatively identify the differentially expressed proteins between the PRRSV-infected groups and the controls. A total of 160 cellular proteins in PAMs that were significantly altered post-infection were identified. These differentially expressed proteins are related to the biological processes of virus binding, cell structure, signal transduction, cell adhesion, etc., and their interactions. This is the first report that analyzed the cellular protein profile of PRRSV-infected PAMs using iTRAQ technology, and this data provides important information to help understand the host response to PRRSV and to define the cellular requirements for the underlying mechanism of PRRSV replication and pathogenesis.
Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 -10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb -73.84 Mb and 7.86 Mb -39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb -45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle.
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