Polymorphisms in the bovine leptin promoter associated with serum leptin concentration, growth, feed intake, feeding behavior, and measures of carcass merit

Leptin in farm animals: where are we and where can we go?

Fat affects meat quality, value and production efficiency as well as providing energy reserves for pregnancy and lactation in farm livestock. Leptin, the adipocyte product of the obese (ob) gene, was quickly seen as a predictor of body fat content in animals approaching slaughter and an aid to assessing reproductive readiness in females. Its participation in inflammation and immune responses that help animals survive infection and trauma has clear additional relevance to meat and milk production. Furthermore, almost a decade of discoveries of nucleotide polymorphisms in the leptin and leptin receptor genes has suggested useful applications relating to feed intake regulation, the efficiency of feed use, the composition of growth, the timing of puberty, mammogenesis and mammary gland function and fertility in cattle, pigs and poultry. The current review attempts to summarise where research has taken us in each of these aspects and speculates on where future research might lead.

PCR-SSCP analysis of leptin gene and its association with milk production traits in river buffalo (Bubalus bubalis)

Leptin gene has been found to be associated with various economic traits including milk production and fat quality in dairy animals. In the present study, we investigated genetic variations in intron 1 region of leptin gene in riverine buffaloes (Bubalus bubalis) using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing methods and associated them with milk traits. The study revealed three SSCP variants A, B and C among a total of 301 buffaloes from nine breeds. The frequency of variant C was found invariably high among all the breeds except in Marathwada buffalo. Variant A was found to be absent in Chilika, Nili-Ravi, Nagpuri and Pandharpuri breeds and also had the lowest frequencies in Mehsana, Jaffarabadi, Murrah and Toda breeds. Sequencing of SSCP variants revealed a total of five polymorphic sites, with three haplotypes. Statistical analysis revealed significantly high fat percentage at 150 days in SSCP variant B in Mehsana buffaloes. However, the associations of SSCP variants of leptin gene with total milk yield, 305 days milk yield and total fat yield were found to be non-significant. The present study is the first report on association analysis of leptin gene polymorphisms with milk production and milk quality traits in river buffalo.

Nonsynonymous natural genetic polymorphisms in the bovine leptin gene affect biochemical and biological characteristics of the mature hormone

Leptin (LEP) is a cytokine-like hormone proven to be involved in diverse biological processes. In livestock, it regulates feed intake, BW homeostasis, and energy balance, among other traits. Natural nonsynonymous genetic polymorphisms in the ovine leptin (oLEP) alter the biochemical and physiological characteristics of its gene products. Here we studied in vitro and in vivo the biochemical and physiological characteristics of recombinant hormones representing the oLEP and bovine leptin (bLEP) reference sequences of wild-type (WT) leptins (GenBank accession No. U84247 and U50365, respectively), oLEP and bLEP recombinant muteins carrying the R4C mutation, and oLEP recombinant hormones carrying the A59V and Q62R mutations, which were detected in bLEP. All proteins were purified to homogeneity as monomers and formed 1:1 molar ratio complexes with the chicken leptin-binding domain (LBD). Surface plasmon resonance experiments revealed that all protein variants exhibit reduced (P < 0.05) affinity to chicken (ch) and human (h) LBD compared with the WT oLEP and bLEP recombinant proteins. The ovine and bovine R4C muteins exhibited significantly (P < 0.05) greater induction of cell proliferation in a Baf/3 cell line bioassay, despite lower affinity toward both hLBD and chLBD. Intra-third cerebral ventricle infusion of oLEP and its 3 muteins in sheep resulted in reduced feed intake. However, the 3 tested muteins had a decreased (P < 0.05) inhibitory effect than the WT LEP. It was concluded that natural genetic polymorphisms in the bLEP are associated with variation in the biochemical and physiological properties of the protein.

Leptin gene haplotypes are associated with change in immunological and hematological variables in dairy cow during the peripartum period

In this study, the effect of polymorphisms in the leptin gene on the hematological variables in periparturient dairy cows was investigated. The hematological profile of 67 Holstein cows was assessed for 6 wk around calving. The DNA of the cows was genotyped at 6 polymorphic loci within the leptin gene, and 7 haplotypes were reconstructed. Significant haplotype substitution effects were found, for haplotype 1, on total white blood cell count for 2 wk around calving (+0.70 10(3)/μL, P = 0.05; +1.38 10(3)/μL, P = 0.0001); on neutrophil cell count in the first week after calving (+0.94 10(3)/μL, P = 0.001); on lymphocyte count during the 3 wk before and the first week after calving (+0.32 10(3)/μL, P = 0.05; +0.27 10(3)/μL, P = 0.03; +0.26 10(3)/μL, P = 0.04; +0.34 10(3)/μL, P = 0.01); on red blood cell count during the last week before calving and wk 1 and 2 after calving (+0.21 10(6)/μL, P = 0.02; +0.23 10(6)/μL, P = 0.01; +0.20 10(6)/μL, P = 0.03); on mean corpuscular volume (-1.35 fL, P = 0.01; -1.29 fL, P = 0.002; -1.18 fL, P = 0.004; -1.09 fL, P = 0.008; -1.23 fL, P = 0.003; -1.31 fL, P = 0.003); and on mean corpuscular hemoglobin (-0.37 pg, P = 0.05; -0.38 pg, P = 0.02; -0.39 pg, P = 0.01; -0.34 pg, P = 0.03; -0.40 pg, P = 0.01; -0.40 pg, P = 0.01) during all 6 wk analyzed. Significant haplotype substitution effects, but opposite those of haplotype-1, were found for haplotype-2 on white blood cell count (-1.10 10(3)/μL, P = 0.01; -1.30 10(3)/μL, P = 0.002; -1.09 10(3)/μL, P = 0.01) and neutrophil count (-0.82 10(3)/μL, P = 0.02; -0.95 10(3)/μL, P = 0.005; -0.92 10(3)/μL, P = 0.01). Haplotype-3 influenced red blood cell count (-0.23 10(6)/μL, P = 0.03; -0.28 10(6)/μL, P = 0.01; -0.34 10(6)/μL, P = 0.002) during the last 2 wk before and the first week after calving, and also, with effects evident only in wk 3 and 2 before calving, mean corpuscular volume (+1.38 fL, P = 0.03; +0.97 fL, P = 0.05; +1.08 fL, P = 0.05), mean corpuscular hemoglobin (+0.58 pg, P = 0.02; +0.38 pg, P = 0.04; 0.51 pg, P = 0.01), and red blood cell distribution width (-0.56% P = 0.02; -0.47%, P = 0.05). The current study provided evidence that several polymorphisms in the leptin gene play a role in the variability of hematological variables during the peripartum period, and might be used as genetic markers for improving the immunological conditions of dairy cows in critical productive periods.

A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.

Evaluating markers in selected genes for association with functional longevity of dairy cattle

Background

Longevity expressed as the number of days between birth and death is a trait of great importance for both human and animal populations. In our analysis we use dairy cattle to demonstrate how the association of Single Nucleotide Polymorphisms (SNPs) located within selected genes with longevity can be modeled. Such an approach can be extended to any genotyped population with time to endpoint information available. Our study is focused on selected genes in order to answer the question whether genes, known to be involved into the physiological determination of milk production, also influence individual's survival.

Results

Generally, the highest risk differences among animals with different genotypes are observed for polymorphisms located within the leptin gene. The polymorphism with a highest effect on functional longevity is LEP-R25C, for which the relative risk of culling for cows with genotype CC is 3.14 times higher than for the heterozygous animals. Apart from LEP-R25C, also FF homozygotes at the LEP-Y7F substitution attribute 3.64 times higher risk of culling than the YY homozygotes and VV homozygotes at LEP-A80V have 1.83 times higher risk of culling than AA homozygotes. Differences in risks between genotypes of polymorphisms within the other genes (the butyrophilin subfamily 1 member A1 gene, BTN1A1; the acyl-CoA:diacylglycerol acyltransferase 1 gene, DGAT1; the leptin receptor gene, LEPR; the ATP-binding cassette sub-family G member 2, ABCG2) are much smaller.

Conclusions

Our results indicate association between LEP and longevity and are very well supported by results of other studies related to dairy cattle. In view of the growing importance of functional traits in dairy cattle, LEP polymorphisms should be considered as markers supporting selection decisions. Furthermore, since the relationship between both LEP polymorphism and its protein product with longevity in humans is well documented, with our result we were able to demonstrate that livestock with its detailed records of family structure, genetic, and environmental factors as well as extensive trait recording can be a good model organism for research aspects related to humans.

Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi

Background

Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations are conserved in this cattle breed.

Results

In this study, we evaluated genetic features of this breed, including single nucleotide polymorphism (SNP) information, by whole-genome sequencing using a Genome Analyzer II. A total of 64.2 Gb of sequence was generated, of which 86% of the obtained reads were successfully mapped to the reference sequence (Btau 4.0) with BWA. On an average, 93% of the genome was covered by the reads and the number of mapped reads corresponded to 15.8-fold coverage across the covered region. From these data, we identified 6.3 million SNPs, of which more than 5.5 million (87%) were found to be new. Out of the SNPs annotated in the bovine sequence assembly, 20,432 were found in protein-coding regions containing 11,713 nonsynonymous SNPs in 4,643 genes. Furthermore, phylogenetic analysis using sequence data from 10 genes (more than 10 kbp) showed that Kuchinoshima-Ushi is clearly distinct from European domestic breeds of cattle.

Conclusions

These results provide a framework for further genetic studies in the Kuchinoshima-Ushi population and research on functions of SNP-containing genes, which would aid in understanding the molecular basis underlying phenotypic variation of economically important traits in cattle and in improving intrinsic defects in domestic cattle breeds.

Relationships between fed cattle traits and Igenity panel scores

Although several previous studies have identified associations between cattle carcass characteristics and various SNP, comparatively little work has sought to validate the marker panels currently sold and marketed by commercial genotyping companies. Panels typically use a handful of SNP, but these range from as few as 2 to more than 100. Data from 764 commercially fed steers and heifers were used to assess the relationships of growth and carcass traits and Igenity panel scores for ADG, marbling (or percentage of USDA Choice), rib-eye area (REA), tenderness, fat thickness, and USDA Yield grade (YG). Results revealed statistically significant, but low, correlations between carcass measurements and corresponding Igenity panel scores. Genetic correlations were computed among the various Igenity panels and demonstrated either that several common markers existed across the panels or that markers across panels were in high linkage disequilibrium. Across all breeds, the genotypic correlations between the Igenity panel scores for ADG, REA, marbling, and YG with observed ADG, REA, USDA Quality grade, and YG at slaughter were 0.51, 0.38, 0.63, and 0.59 (P < 0.01), respectively. The partial effects of the Igenity marbling panel persisted in a multivariate regression model. Net return was significantly affected only by marbling panel score; a 1-unit increase in marbling panel score increased the net return by an estimated $7.53 per animal.

Ruminant enteric methane mitigation: a review

In Australia, agriculture is responsible for ~17% of total greenhouse gas emissions with ruminants being the largest single source. However, agriculture is likely to be shielded from the full impact of any future price on carbon. In this review, strategies for reducing ruminant methane output are considered in relation to rumen ecology and biochemistry, animal breeding and management options at an animal, farm, or national level. Nutritional management strategies have the greatest short-term impact. Methanogenic microorganisms remove H2 produced during fermentation of organic matter in the rumen and hind gut. Cost-effective ways to change the microbial ecology to reduce H2 production, to re-partition H2 into products other than methane, or to promote methanotrophic microbes with the ability to oxidise methane still need to be found. Methods of inhibiting methanogens include: use of antibiotics; promoting viruses/bacteriophages; use of feed additives such as fats and oils, or nitrate salts, or dicarboxylic acids; defaunation; and vaccination against methanogens. Methods of enhancing alternative H2 using microbial species include: inoculating with acetogenic species; feeding highly digestible feed components favouring ‘propionate fermentations’; and modifying rumen conditions. Conditions that sustain acetogen populations in kangaroos and termites, for example, are poorly understood but might be extended to ruminants. Mitigation strategies are not in common use in extensive grazing systems but dietary management or use of growth promotants can reduce methane output per unit of product. New, natural compounds that reduce rumen methane output may yet be found. Smaller but more permanent benefits are possible using genetic approaches. The indirect selection criterion, residual feed intake, when measured on ad libitum grain diets, has limited relevance for grazing cattle. There are few published estimates of genetic parameters for feed intake and methane production. Methane-related single nucleotide polymorphisms have yet to be used commercially. As a breeding objective, the use of methane/kg product rather than methane/head is recommended. Indirect selection via feed intake may be more cost-effective than via direct measurement of methane emissions. Life cycle analyses indicate that intensification is likely to reduce total greenhouse gas output but emissions and sequestration from vegetation and soil need to be addressed. Bio-economic modelling suggests most mitigation options are currently not cost-effective.

Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

Background

Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire.

Results

All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05).

Conclusions

Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.

Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattle

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2-11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.

Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers

This study examined the relationship of feed efficiency and performance with feeding behavior, blood metabolic variables, and various body composition measurements in growing beef heifers. Individual DMI and growth were measured in yearling Limousin x Holstein-Friesian heifers [n = 86; initial BW = 191.8 (SD = 37) kg] fed a TMR diet comprising 70:30 concentrate:corn silage on a DM basis (ME of 2.65 Mcal/kg of DM; DM of 580 g/kg) for 82 d. Meal duration (min/d) and meal frequency (events/d) were calculated for each animal on a daily basis using an Insentec computerized feeding system. Physical measurements as well as ultrasonic fat and muscle depths were recorded on 3 equally spaced occasions during the experimental period. Blood samples were collected by jugular venipuncture on 4 equally spaced occasions and analyzed for plasma concentrations of IGF-I, insulin, leptin, and various metabolites. Phenotypic residual feed intake (RFI) was calculated for all animals as the residuals from a multiple regression model regressing DMI on ADG and midtest BW(0.75). Overall, ADG, DMI, feed conversion ratio (FCR), and RFI were 1.51 (SD = 0.13), 6.74 (SD = 0.99), 4.48 (SD = 0.65), and 0.00 (SD = 0.48) kg/d, respectively. Residual feed intake was positively correlated with DMI (r = 0.47) and FCR (r = 0.46), but not with ADG or midtest BW. Positive correlations (ranging from r = 0.27 to r = 0.63) were estimated between ultrasonic measures of final lumbar fat and lumbar fat accretion over the test period and DMI, FCR, and RFI. The inclusion of gain in lumbar fat to the base RFI model increased R(2) (0.77 vs. 0.80) value for the degree of variation in DMI not explained by midtest BW and ADG alone. The Pearson rank correlation between RFI and carcass-adjusted RFI (RFI(c)) was high (r = 0.93). From the plasma analytes measured, NEFA (r = -0.21; P < 0.05) and beta-hydroxybutyrate (r = 0.37; P < 0.05) concentrations were correlated with RFI. Plasma leptin (r = 0.48), glucose:insulin (r = -0.23), NEFA (r = -0.32), and beta-hydroxybutyrate (r = 0.25) were associated with FCR. However, systemic IGF-I and insulin were unrelated (P > 0.05) to any measure of feed efficiency. The feeding behavior traits of eating rate, daily feeding events, and nonfeeding events were positively correlated (P < 0.05) with RFI and RFI(c). This multifactorial study provides new information on some of the biological processes responsible for variation in feed efficiency in beef cattle.

Comparison of skeletal muscle transcriptional profiles in dairy and beef breeds bulls

A cDNA microarray (18 263 probes) was used for transcriptome analysis of bovine skeletal muscle (m. semitendinosus) in 12-month-old bulls of the beef breed Limousin (LIM) and the typical dairy breed Holstein-Friesian (HF, used as a reference). We aimed to identify the genes whose expression may reflect the muscle phenotype of beef bulls. A comparison of muscle transcriptional profiles revealed significant differences in expression of 393 genes between HF and LIM. We classified biological functions of 117 genes with over 2-fold differences in expression between the examined breeds. Among them, 72 genes were up-regulated and 45 genes were down-regulated in LIM vs. HF. The genes were involved in protein metabolism and modifications (22 genes), signal transduction (15), nucleoside, nucleotide and nucleic acid metabolism (13), cell cycle (9), cell structure and motility (9), developmental processes (9), intracellular protein traffic (7), cell proliferation and differentiation (6), cell adhesion (6), lipid, fatty acid and steroid metabolism (5), transport (5), and other processes. For the purpose of microarray data validation, we randomly selected 4 genes: trip12, mrps30, pycrl, and c-erbb3. Real-time RT-PCR results showed similar trends in gene expression changes as those observed in microarray studies. Basing on results of the present study, we proposed a model of the regulation of skeletal muscle growth and differentiation, with a principal role of the somatotropic pathway. It may explain at least in part the development of muscle phenotype in LIM bulls. We assume that the growth hormone directly or indirectly (through IGF-1) activates the calcium-signaling pathway with calcineurin, which stimulates myogenic regulatory factors (MRFs) and inhibits early growth response gene. The inhibition results in indirect activation of MRFs and impaired activation of TGF-beta1 and myostatin, which finally facilitates terminal muscle differentiation.

Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle

BACKGROUND

The purpose of this study was to evaluate the effects of eight single nucleotide polymorphisms (SNP), previously associated with meat and milk quality traits in cattle, in a population of 443 commercial Aberdeen Angus-cross beef cattle. The eight SNP, which were located within five genes: mu-calpain (CAPN1), calpastatin (CAST), leptin (LEP), growth hormone receptor (GHR) and acylCoA:diacylglycerol acyltransferase 1 (DGAT1), are included in various commercial tests for tenderness, fatness, carcass composition and milk yield/quality.

METHODS

A total of 27 traits were examined, 19 relating to carcass quality, such as carcass weight and fatness, one mechanical measure of tenderness, and the remaining seven were sensory traits, such as flavour and tenderness, assessed by a taste panel.

RESULTS

An SNP in the CAPN1 gene, CAPN316, was significantly associated with tenderness measured by both the tenderometer and the taste panel as well as the weight of the hindquarter, where animals inheriting the CC genotype had more tender meat and heavier hindquarters. An SNP in the leptin gene, UASMS2, significantly affected overall liking, where animals with the TT genotype were assigned higher scores by the panellists. The SNP in the GHR gene was significantly associated with odour, where animals inheriting the AA genotype produced steaks with an intense odour when compared with the other genotypes. Finally, the SNP in the DGAT1 gene was associated with sirloin weight after maturation and fat depth surrounding the sirloin, with animals inheriting the AA genotype having heavier sirloins and more fat.

CONCLUSION

The results of this study confirm some previously documented associations. Furthermore, novel associations have been identified which, following validation in other populations, could be incorporated into breeding programmes to improve meat quality.

Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle

BACKGROUND

Marbling defined by the amount and distribution of intramuscular fat is an economically important trait of beef cattle in Japan. We have recently reported that single nucleotide polymorphisms (SNPs) in the endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene were associated with marbling in Japanese Black beef cattle. As well as EDG1, the titin (TTN) gene, involved in myofibrillogenesis, has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus TTN was considered as a positional functional candidate for the gene responsible for marbling. In this study, we explored SNP in TTN and analyzed association of the SNP with marbling.

FINDINGS

A SNP in the promoter region of TTN, referred to as g.231054C>T, was the only difference detected between high- and low-marbled steer groups. The SNP was associated with marbling in 3 experiments using 101 sires (P = 0.004), 848 paternal half-sib progeny steers from 5 sires heterozygous for the g.231054C>T (P = 0.046), and 820 paternal half-sib progeny steers from 3 sires homozygous for C allele at the g.231054C>T (P = 0.051), in Japanese Black beef cattle. The effect of genotypes of the SNP on subcutaneous fat thickness was not statistically significant (P > 0.05).

CONCLUSION

These findings suggest that in addition to the EDG1 SNPs, the TTN SNP polymorphism is associated with marbling and may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. Further replicate studies will be needed to confirm the allelic association observed here, and to expand the results to evaluate all possible genotypic combinations of alleles.

Association of single nucleotide polymorphisms in the endothelial differentiation sphingolipid G-protein-coupled receptor 1 gene with marbling in Japanese Black beef cattle

Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. The endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene, involved in blood vessel formation, has been previously shown to be expressed at different levels in musculus longissimus muscle between low-marbled and high-marbled steer groups. It is located within the genomic region of a quantitative trait locus for marbling, and thus was considered as a positionally functional candidate for the gene responsible for marbling. In this study, two single nucleotide polymorphisms (SNPs) in the 5' untranslated region (UTR) and the 3' UTR of EDG1, referred to as c.-312A>G and c.*446G>A, respectively, were detected between the two steer groups. The two SNPs were associated with the predicted breeding value for beef marbling standard number by analyses using a population of Japanese Black beef cattle. The effect of genotypes at each of the SNPs on the predicted breeding value for subcutaneous fat thickness was not statistically significant (P > 0.05). Reporter gene assays revealed no significant differences in gene expression between alleles at each of the SNPs. These findings suggest that EDG1 SNPs, although they may not be regarded as a causal mutation, may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.

Lack of an association between single nucleotide polymorphisms in the bovine leptin gene and intramuscular fat in Bos taurus cattle

Leptin contributes to the regulation of adiposity and metabolism, and single nucleotide polymorphisms (SNPs) in the leptin gene have been associated with intramuscular fat (IMF) levels in beef. Our objectives were to estimate the frequency of four SNPs in the leptin gene in nine purebred cattle (n=430), to test for linkage disequilibrium and infer haplotypes, and to determine if individual genotypes or estimated haplotypes were associated with IMF values in crossbred cattle (n=244). The four SNP loci were found to be in linkage disequilibrium and thus, the frequencies of each of the 16 possible haplotypes were inferred by maximum likelihood. No significant association between any individual SNP and haplotype was found with the divergent IMF values. Our results suggest that these SNPs are not influential on the divergent IMF levels in the crossbred population tested.

A critical analysis of production-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig

Increasing productivity is one of the main objectives in animal production. Traditional breeding methods have led to increased gains in some traits but gains are not easily attainable in traits with low heritabilities. Exploiting the genetic variations underlying desired phenotypes is the goal of today's animal producers. Such positive genetic variants must, however, be known before possible application. Consequently, candidate genes of traits of interest have been searched for possible relationships with such traits or to explain reported quantitative trait loci (QTL) for such traits. DNA variants or polymorphisms have been identified in many such genes and their relationships with production traits determined. However, only a few genes have been evaluated, given the wealth of information on reported QTL for production traits, and in most cases genes are only partially investigated. This review presents available information on DNA variants for production traits and discusses steps that are required for effective utilization of this information for successful marker-assisted selection programs.

Leptin genotype is associated with lactation performance and health of Holstein cows

The objectives were to evaluate the associations among single nucleotide polymorphisms (SNP) in the R4C locus in exon 2 of the leptin gene and the lactational performance and health of Holstein cows. Eight hundred and fourteen lactating dairy cows had their DNA sequenced in exon 2 of the leptin gene to determine the presence of SNP in the R4C locus. Cows were milked 3 times daily, and yields of milk and milk components were recorded monthly individually during the first 305 d of lactation. Cows were examined daily by herd personnel for diagnosis of health events such as retained fetal membranes, displacement of abomasum, lameness, and mastitis. Resulting genotypes were CC (34.6%), CT (48.2%), and TT (17.2%). Cows bearing the CT genotype had lower body condition (2.98 +/- 0.02) during the first 62 d in milk (DIM) than cows homozygous for the C (3.02 +/- 0.02) and T (3.04 +/- 0.03) alleles. Leptin genotype was associated with yields of milk and milk components, and cows homozygous for the C allele were less productive than those carrying the CT and TT genotypes. The 305-d yields of 3.5% fat-corrected milk, milk fat, and milk true protein were less in CC compared with CT cows by 258, 12, and 10.7 kg, respectively. Cows carrying the TT genotype had increased incidence of displacement of abomasum (4.3%), but genotype did not affect the incidence of retained fetal membranes, clinical and subclinical mastitis, or lameness. Risk of developing at least one clinical health disorder was influenced by leptin genotype, and cows carrying the CT genotype had the lowest risk for developing any disease (19.6%). Mating decisions to increase the frequency of cows heterozygous in the R4C locus may improve productivity and health.

Impact of single nucleotide polymorphisms in leptin, leptin receptor, growth hormone receptor, and diacylglycerol acyltransferase (DGAT1) gene loci on milk production, feed, and body energy traits of UK dairy cows

The impact of 9 single nucleotide polymorphisms (SNP) in the leptin (LEP), leptin receptor (LEPR), growth hormone receptor (GHR), and diacylglycerol acyltransferase (DGAT1) gene loci on daily milk production, feed intake, and feed conversion, and weekly measures of live weight, BCS, and body energy traits was evaluated using genetic and phenotypic data on 571 Holstein cows raised at the Langhill Dairy Cattle Research Center in Scotland. Six SNP were typed on the LEP gene and 1 on each of the other 3 loci. Of the 6 LEP SNP, 3 were in very high linkage disequilibrium, meaning there is little gain in typing all of them in the future. Seven LEP haplotypes were identified by parsimony-based analyses. Random-regression allele-substitution models were used to assess the impact of each SNP allele or haplotype on the traits of interest. Diacylglycerol acyltransferase had a significant effect on milk yield, whereas GHR significantly affected feed intake, feed conversion, and body energy traits. There was also evidence of dominance in allelic effects on milk yield and BCS. The LEP haplotype CCGTTT (corresponding to leptin SNP C207T, C528T, A1457G, C963T, A252T, and C305T, respectively) significantly affected milk yield and feed and dry matter intake. Animals carrying this haplotype produced 3.13 kg more milk daily and consumed 4.64 kg more feed. Furthermore, they tended to preserve more energy than average. Such results may be used to facilitate genetic selection in animal breeding programs.

Genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit of feedlot cattle1

Leptin is the hormone product of the obese gene that is synthesized and predominantly expressed by adipocytes. This study estimated the genetic variation in serum leptin concentration and evaluated the genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit. There were 464 steers with records for serum leptin concentration, performance, and efficiency of gain and 381 steers with records for carcass traits. The analyses included a total of 813 steers, including those without phenotypic records. Phenotypic and genetic parameter estimates were obtained using SAS and ASREML, respectively. Serum leptin concentration was moderately heritable (h2 = 0.34 +/- 0.13) and averaged 13.91 (SD = 5.74) ng/mL. Sire breed differences in serum leptin concentration correlated well with breed differences in body composition. Specifically, the serum leptin concentration was 20% greater in Angus-sired steers compared with Charolais-sired steers (P < 0.001). Consequently, ultrasound backfat (27%), carcass 12th-rib fat (31%), ultrasound marbling (14%), and carcass marbling (15%) were less in Charolais- than Angus-sired steers (P < 0.001). Conversely, carcass LM area (P = 0.05) and carcass lean meat yield (P < 0.001) were greater in Charolais- compared with Angus-sired steers. Steers with greater serum leptin concentration also had greater DMI (P < 0.001), greater residual feed intake (P = 0.04), and partial efficiency of growth (P = 0.01), but did not differ in feed conversion ratio (P > 0.10). Serum leptin concentration was correlated phenotypically with ultrasound backfat (r = 0.41; P < 0.001), carcass 12th-rib fat (r = 0.42; P < 0.001), ultrasound marbling (r = 0.25; P < 0.01), carcass marbling (r = 0.28; P < 0.01), ultrasound LM area (r = -0.19; P < 0.01), carcass LM area (r = -0.17; P < 0.05), lean meat yield (r = -0.38; P < 0.001), and yield grade (r = 0.32; P < 0.001). The corresponding genetic correlations were generally greater than the phenotypic correlations and included ultrasound backfat (r = 0.76 +/- 0.19), carcass 12th-rib fat (r = 0.54 +/- 0.23), ultrasound marbling (r = 0.27 +/- 0.22), carcass marbling (r = 0.76 +/- 0.21), ultrasound LM area (r = -0.71 +/- 0.19), carcass LM area (r = -0.75 +/- 0.20), lean meat yield (r = -0.59 +/- 0.22), and yield grade (r = 0.39 +/- 0.26). Serum leptin concentration can be a valuable tool that can be incorporated into appropriate selection programs to favorably improve the carcass merit of cattle.

Association of single nucleotide polymorphisms in the leptin gene with body weight and backfat growth curve parameters for beef cattle1

Previous research has identified differences in carcass characteristics across SNP in the bovine leptin gene at slaughter, but before feedlot operators implement selection and sorting strategies, more information is needed to determine how carcass characteristics change over time. The objective of this study was to investigate the effect of 2 leptin SNP on growth curve parameters for BW and backfat. Two SNP (UASMS2 and R25C) were genotyped on 1,653 cross-bred steers and heifers in a commercial feedlot. Up to 4 serial measures of BW and ultrasound estimates of backfat thickness were taken for each animal from the time of placement on feed to slaughter. The measures were used to estimate growth models that describe changes in BW and backfat thickness as a function of days on feed. Data analysis was carried out by estimating nonlinear mixed models to determine the individual and joint effect of each SNP on growth curve parameters. Brody growth curves were fit to the BW data. Variations in the R25C SNP did not significantly affect growth parameters individually or in combination with the UASMS2 SNP. Variations in the UASMS2 SNP were significant in Brody growth curve parameters for BW growth (P < 0.001). The genotype UASMS2-CC was the heaviest at the beginning of the feeding period and exhibited the largest asymptotic mature BW, but UASMS2-TT cattle exhibited the fastest rate of BW growth. A modified power function was fit to the serial ultrasound backfat measures. Models that included the combined effect of the R25C and UASMS2 SNP provided the best fit to the data. Genotypes differed significantly in power function parameters for backfat growth (P < 0.001). The R25C-CC/UASMS2-TT cattle had the smallest backfat thickness at placement. The genotype R25C-CC/UASMS2-TT exhibited the fastest backfat growth rate, whereas backfat in R25C-CC/UASMS2-CC cattle grew at the slowest rate. The association between leptin genotype and growth in BW and backfat presents opportunities to identify genetically distinct cattle and to differentially optimize feeding times accordingly.

Effect of polymorphisms linked to LEP gene on its expression on adipose tissues in beef cattle

In cattle, genetic markers at the leptin (LEP) gene and at those linked to the gene have been described as affecting calving interval (markers LEPSau3AI and IDVGA51), or daily weight gain (BMS1074 and BM1500). This work investigated the effect of these alleles on LEP mRNA levels in cattle subcutaneous and omental adipose tissues. A sample of 137 females of a Brangus-Ibage beef cattle herd was analysed to evaluate the distribution of the polymorphisms; then, animals having at least one of the IDVGA51*181 (allele 181 at marker IDVGA51; six animals), LEPSau3AI*2 (four), BMS1074*151 (13), BM1500*135 (six) alleles and a control group composed of animals without any of these alleles (four animals) were submitted to surgery to obtain omental and subcutaneous adipose tissues. Leptin mRNA expression was quantified by TaqMan RT-PCR, using 18S rRNA as internal control and adjusted for the effect of body condition score, through regression analysis. Omental fat had LEP gene expression 33% lower than the subcutaneous tissue. Carriers of IDVGA*181 and BMS1074*151 showed subcutaneous fat leptin mRNA levels higher than the controls. Leptin controls feed intake and coordinates reproduction; therefore, animals with higher LEP gene expression will probably have lower daily weight gain than others with similar forage offer and nutritional condition and probably will also have longer calving interval.

Involvement of leptin signaling in the survival and maturation of bone marrow-derived dendritic cells

Previous studies demonstrated that lymphocyte development is impaired in leptin receptor (Ob-R)-deficient db/db mice. However, it remains unclear whether or not leptin signaling plays a physiological role in dendritic cell (DC) development and function. In this study, we first detected Ob-R expression in murine DC. Using db/db mice at a pre-diabetic stage, we demonstrate that the total number of DC generated from bone marrow (BM) cultures is significantly lower than in WT controls. Similarly, selective blockade of leptin with a soluble mouse Ob-R chimera (Ob-R:Fc) inhibited DC generation in wild-type BM cultures. The reduced DC yield in db/db BM culture was attributed to significantly increased apoptosis, which was associated with dysregulated expression of Bcl-2 family genes. Moreover, db/db DC displayed markedly reduced expression of co-stimulatory molecules and a Th2-type cytokine profile, with a poor capacity to stimulate allogeneic T cell proliferation. Consistent with their impaired DC phenotype and function, db/db DC showed significantly down-regulated activities of the PI3K/Akt pathway as well as STAT-3 and IkappaB-alpha. In conclusion, our findings demonstrate the involvement of leptin signaling in DC survival and maturation.

The importance and identification of regulatory polymorphisms and their mechanisms of action

The search for the genetic variations underlying all human phenotypes is in its infancy but must be one of the long term goals of the scientific community. There is evidence that most, if not all human phenotypes, including illnesses are influenced by the genetic makeup of the individual. There are an estimated 11 million human genetic polymorphisms with a minor allele frequency >1% and possibly many times that number of rare sequence variants. The proportion of these sequence variants which have any functional effect is unknown but it is likely that the majority of those which influence illness lie outside of the amino acid coding regions of genes, and affect the regulation of gene expression--these are called rSNPs. Recent research suggests that about 50% of genes have one or more common rSNPs associated with them and probably most if not all genes have an rSNP within the human population. In the long term, determining which polymorphisms are potentially functional must be done bio-informatically using algorithms based upon experimental data. However, at the current time, the limited data that has been obtained does not allow the creation of such an algorithm. In vitro studies suggest that a large proportion of rSNPs lie within the core and proximal promoter regions of genes but it is not clear how the majority of these influence transcription, as they do not appear to be within any known transcription factor binding sites. However, promoter regions possess a number of sequence-dependent characteristics which make them distinct from the rest of the genome, namely stability, curvature and flexibility. Subtle changes to these features may underlie the mechanisms by which many polymorphisms exert their function.

Association of single nucleotide polymorphisms in the leptin gene with carcass and meat quality traits of beef cattle1

Studies with different populations are required to properly characterize the robustness of associations of polymorphisms in candidate genes with economically important traits across beef cattle populations before this sort of genetic information can be used efficiently in breeding and management decisions. The objective of this study was to evaluate the association of previously reported SNP in the bovine leptin gene with carcass and meat quality traits from a large sample of crossbred beef cattle. Five SNP (UASMS1, UASMS2, UASMS3, E2JW, and E2FB) were genotyped on 1,111 crossbred bulls, heifers, and steers. The measured traits included fat, lean, and bone yield (%) by partial rib dissection, grade fat, LM area, HCW, quality grade, LM i.m. fat, and tenderness evaluation of LM and semitendinosus muscle. Only four SNP were analyzed (UASMS1, UASMS2, E2JW, and E2FB), because UASMS1 and UASMS3 were completely linked. A uni-variate mixed-inheritance animal model was used to evaluate the association of either genotypes or haplo-types with the traits. The two leptin exon 2 SNP were associated with fat and lean yield and grade fat (E2JW, P < 0.01; E2FB, P < 0.05), and they interacted in their effect on LM tenderness (P < 0.01). The leptin promoter SNP were either not associated with any of the traits (UASMS2) or with fat yield only (UASMS1). Three haplotypes (TCAC, CCAT, TTAC) were at high frequency in the population (88%) and had similar effects on all the traits. Compared with the common haplotypes, one haplotype (CCTT) showed a significantly different effect on fat and lean yield and grade fat (P < 0.01), and one haplotype (TTTT) had a different effect on LM tenderness (P < 0.03). Therefore, important associations between SNP within the leptin gene with lean yield, fatness (fat yield and subcutaneous fat), and tenderness were detected. Results confirm some of the previously reported associations, but diverge with respect to others, showing that further efforts are required to validate some prospective associations.

Application and impact of new genetic technologies on beef cattle breeding: a 'real world' perspective

Molecular genetics is a maturing discipline with innovations that are finding application in animal breeding. Currently, DNA tests are available for parent identification or verification, and markers tests also exist for quantitative trait loci affecting important traits in beef cattle. The beef industry is, however, a particularly challenging industry in which to design breeding programs that fully capitalise on the potential of this technology. Hence, adoption within this industry to date has been below expectation. This paper examines several applications that are being investigated and will include discussion on issues constraining the transfer of DNA technology. An example of using DNA parentage testing for expanding the reach of selection programs into the commercial sector of the beef industry is explored in some depth, as it represents a potential high impact application. Use of molecular information in selection programs and in genetic evaluations is also discussed.