The bovine 5' AMPK gene family: mapping and single nucleotide polymorphism detection

Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs

In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G>T, exonic g.4564T>C, exonic g.6378G>A, exonic g.6386C>T, intronic g.8643G>A, and intronic g.8857A>G. Association analysis revealed that g.42101G>T, g.60146A>T, g.61455G>A, g.4374G>T, g.4564T>C, g.6378G>A, g.6386C>T, g.8643G>A, and g.8857A>G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding.

Expression of genes involved in BMP and estrogen signaling and AMPK production can be important factors affecting total number of antral follicles in ewes

Follicular growth and ovulation of healthy oocytes is a complicated process which is regulated by several endocrine and paracrine factors as well as cross-talk between the oocyte and its surrounding somatic cells. This study compared the expression profile of some candidate genes involved in BMP signaling as well as estrogen and AMPK production in cumulus-oocyte complex (COC) of small and large antral follicles and their associated somatic cell layers in ovaries from ewes with high- and low-antral follicle count (AFC). Expression of GDF9 was increased by increasing the size of antral follicles, while BMP15 expression was decreased by follicular size. It should be noteworthy that transcription of both GDF9 and BMP15 was also detected in the adjacent cellular layers under the follicles. There was a very strong positive correlation between BMP15 and BMPR2 in ovary tissues. Expression of GDF9 was highly correlated with BMP15, BMPR1B, and BMPR2 in large antral follicles. Expression of BMP7 in small antral follicles and BMPR2 in ovary tissues was significantly increased in the high-AFC group. Expression of ESR1 and ESR2 involved in estrogen production as well as PRKAA1 which involved in AMPK production were significantly greater in large antral follicles of high-AFC. There was a very high correlation between Cyp19 and ESR1 in large antral follicles and ovary tissues. Expression of Cyp19 and PRKAA1 were positively correlated with GDF9, BMP15, and BMP7 in large follicles. In conclusion, this study suggests that apart from the BMP signaling, genes involved in AMPK and estrogen production can be pivotal players in ewe's follicular development process. In addition, a strong cross-talk can exist among AMPK, BMP signaling, and estrogen synthesis systems in ewe ovary.

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing

Background

Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics have led to the identification of several genetic markers associated with genes affecting economic traits. Until recently, the identification of the causative genetic variants involved in the phenotypes of interest has remained a difficult task. The advent of novel sequencing technologies now offers a new opportunity for the identification of such variants. Despite sequencing costs plummeting, sequencing whole-genomes or large targeted regions is still too expensive for most laboratories. A transcriptomic-based sequencing approach offers a cheaper alternative to identify a large number of polymorphisms and possibly to discover causative variants. In the present study, we performed a gene-based single nucleotide polymorphism (SNP) discovery analysis in bovine Longissimus thoraci, using RNA-Seq. To our knowledge, this represents the first study done in bovine muscle.

Results

Messenger RNAs from Longissimus thoraci from three Limousin bull calves were subjected to high-throughput sequencing. Approximately 36–46 million paired-end reads were obtained per library. A total of 19,752 transcripts were identified and 34,376 different SNPs were detected. Fifty-five percent of the SNPs were found in coding regions and ~22% resulted in an amino acid change. Applying a very stringent SNP quality threshold, we detected 8,407 different high-confidence SNPs, 18% of which are non synonymous coding SNPs. To analyse the accuracy of RNA-Seq technology for SNP detection, 48 SNPs were selected for validation by genotyping. No discrepancies were observed when using the highest SNP probability threshold. To test the usefulness of the identified SNPs, the 48 selected SNPs were assessed by genotyping 93 bovine samples, representing mostly the nine major breeds used in France. Principal component analysis indicates a clear separation between the nine populations.

Conclusions

The RNA-Seq data and the collection of newly discovered coding SNPs improve the genomic resources available for cattle, especially for beef breeds. The large amount of variation present in genes expressed in Limousin Longissimus thoracis, especially the large number of non synonymous coding SNPs, may prove useful to study the mechanisms underlying the genetic variability of meat quality traits.

A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations

BACKGROUND

Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci.

METHODS

We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection.

RESULTS

No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol's modified frequentist test and the Bayesian FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRtheta' statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium.

CONCLUSION

Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.

Association of polymorphisms in candidate genes with colour, water-holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus

The objective of this study was to determine the association of single nucleotide polymorphisms (SNP) in selected candidate genes with sensory and technological meat quality traits in commercial cattle. SNP in seven candidate genes were genotyped in 130 crossbred Bos taurus cattle using PCR-RFLP. Reported associations between calpastatin (CAST) and Warner-Bratzler shear force and carboxypeptidase E (CPE) and intra-muscular fat were not confirmed. However, SNP in CAST, amp-activated protein kinase, gamma-3 subunit (PRKAG3), growth hormone receptor (GHR) and stearoyl coA desaturase (SCD) genes were significantly associated with colour traits (p<0.05). The PRKAG3 SNP was additionally associated with cook loss in M. longissimus thoracis et lumborum (p<0.05) and tended towards association in M. semimembranosus (p<0.1). An association with pH was identified for the SCD SNP (p<0.001). The GHR polymorphism was influential on moisture and intra-muscular fat in M. semimembranosus and protein content in both muscles (p<0.05). Only CPE was associated with sensory traits (flavour in M. longissimus, p<0.01).

Effects of metformin on bovine granulosa cells steroidogenesis: possible involvement of adenosine 5' monophosphate-activated protein kinase (AMPK)

In mammals, IGFs are important for the proliferation and steroidogenesis of ovarian cells. Metformin is an insulin sensitizer molecule used for the treatment of the infertility of women with polycystic ovary syndrome. It is, however, unclear whether metformin acts on ovarian cells. Adenosine 5' monophosphate-activated protein kinase (AMPK) is involved in metformin action in various cell types. We investigated the effects of metformin on bovine granulosa cell steroidogenesis in response to IGF1 and FSH, and studied AMPK in bovine ovaries. In granulosa cells from small follicles, metformin (10 mM) reduced production of both progesterone and estradiol and decreased the abundance of HSD3B, CYP11A1, and STAR proteins in presence or absence of FSH (10(-8) M) and IGF1 (10(-8) M). In cows, the different subunits of AMPK are expressed in various ovarian cells including granulosa and theca cells, corpus luteum, and oocytes. In bovine granulosa cells from small follicles, metformin, like AICAR (1 mM) a pharmaceutical activator of AMPK, increased phosphorylation of both Thr172 of AMPK alpha and Ser 79 of ACACA (Acetyl-CoA Carboxylase). Both metformin and AICAR treatment reduced progesterone and estradiol secretion in presence or absence of FSH and IGF1. Metformin decreased phosphorylation levels of MAPK3/MAPK1 and MAPK14 in a dose- and time-dependent manner. The adenovirus-mediated production of dominant negative AMPK abolished the effects of metformin on secretion of progesterone and estradiol and on MAPK3/MAPK1 phosphorylation but not on MAPK14 phosphorylation. Thus, in bovine granulosa cells, metformin decreases steroidogenesis and MAPK3/MAPK1 phosphorylation through AMPK activation.

Identification of single-nucleotide polymorphisms in 5' end and exons of the PRKAG3 gene in Hubbard White broiler, Leghorn layer, and three Chinese indigenous chicken breeds

5'-AMP-activated protein kinase plays an important role in regulating the level of ATP in the presence of metabolic stress. Previous studies revealed that polymorphisms in 5'-AMP-activated protein kinase gamma 3 subunit (PRKAG3) gene are associated with meat quality in pigs. In the present study, single-nucleotide polymorphisms (SNPs) in the 5'-end and exons of chicken PRKAG3 gene were identified with the method of single-strand conformation polymorphism in Hubbard ISA White broiler, Leghorn layer, and three Chinese indigenous chicken breeds, Tibet Chicken, Shouguang Chicken and Beijing Yellow Chicken. Two SNPs in the 5'-end of the gene and 10 SNPs in exons 3, 4, 9 and 11, of which three caused amino acid substitutions, were identified in the PRKAG3 gene of the five chicken breeds. The results will facilitate further study on the association between the mutations of PRKAG3 and chicken meat quality.

Molecular cloning and characterization of bovine PRKAG3 gene: structure, expression and single nucleotide polymorphism detection

The protein kinase adenosine monophosphate-activated gamma3-subunit (PRKAG3) gene encodes a muscle-specific isoform of the regulatory gamma-subunit of adenosine monophosphate-activated protein kinase, which plays a key role in regulating energy homeostasis in eucaryotes. It is well known that mutations in the PRKAG3 gene affect high glycogen content in the porcine skeletal muscle and, consequently, meat quality. The genomic structure and sequence of the bovine PRKAG3 were analysed from a Korean cattle BAC clone. The bovine PRKAG3 gene comprises 13 exons and spans approximately 6.8 kb on BTA2. From 5' and 3'-rapid amplification of cDNA ends experiments, the full-length cDNA of bovine PRKAG3 has been identified, encoding a deduced protein of 465 amino acids. Two splice isoforms, generated by the alternative splicing of exon 2, were also identified. Northern blot analysis demonstrated that, similar to other species, the bovine PRKAG3 transcript was only expressed in skeletal muscle. Seven single nucleotide polymorphisms, including two previously identified variants, were detected in four Bos taurus cattle breeds. The bovine PRKAG3 gene described in this study may be involved in muscle-related genetic diseases or meat quality traits in cattle.

Characterization of the bovine PRKAG3 gene: structure, polymorphism, and alternative transcripts

The bovine PRKAG3 gene encodes the AMPK gamma3 subunit, one isoform of the regulatory gamma subunit of the AMP-activated protein kinase (AMPK). The AMPK plays a major role in the regulation of energy metabolism and mutations affecting the genes encoding the gamma subunits have been shown to influence AMPK activity. The gamma3 subunit is involved in the regulation of AMPK activity in skeletal muscle and strongly influences glycogen metabolism. Glycogen content in muscle is correlated to meat quality in livestock because it influences postmortem maturation process and ultimate pH. Naturally occurring mutations in the porcine PRKAG3 gene highly affect meat quality by influencing glycogen content before slaughter. We present the characterization of the bovine PRKAG3 gene and a polymorphism analysis in three cattle breeds. Thirty-two SNPs were identified among which 13 are in the coding region, one is in the 3' UTR, and 18 are in the introns. Five of them change an amino acid in the PRKAG3 protein sequence. Allelic frequencies were determined in the three breeds considered, and mutant alleles affecting the coding sequence are found at a very low frequency. Alternative splicing sites were identified at two positions of the gene, introducing heterogeneity in the population of proteins translated from the gene.