A missense mutation in the bovine leptin receptor gene is associated with leptin concentrations during late pregnancy

Genetic structure of some candidate genes of repeat breeder syndrome in Egyptian buffaloes

Background

This study aimed to explore the association between polymorphisms in three genes: leptin (LEP), leptin receptor (LEPR), and BMP4, and incidence of repeat breeding in Egyptian buffaloes.

Methods

DNA was extracted from 160 female buffaloes, involving 108 fertile and 52 repeat breeders. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Sequence analysis and alignment were performed by employing NCBI/BLAST/blastn suite, to identify SNPs among different patterns and alleles. We utilized PredictSNP software to predict the non-synonymous SNPs influences on protein function. Moreover, the conservation score of the amino acids within the target proteins was computed by ConSurf server.

Results

The genotyping results showed that LEP and BMP4 genes were monomorphic (CC, GG) in all tested fertile and repeat breeder buffaloes. Leptin gene sequencing showed a non-synonymous C73T SNP, replacing R to C at position 25 within the leptin polypeptide (position 4 in the mature form; R4C) which is a neutral mutation, not affecting function or structure of LEP protein. For LEPR, one synonymous SNP (T102C) and two non-synonymous SNPs (A106G and C146A), triggering V967A and G954C replacements, respectively in LEPR protein. Moreover, they are neutral mutations. Sequencing results of BMP4 showed HinfI restriction site indicate fixed GG genotype (CC genotype in the anti-sense strand) in all sequenced samples. No SNPs were observed within the amplified region.

Conclusion

Genotyping and sequencing results of the surveyed three genes revealed that there is no association between these genes mutations and the incidence of repeat breeding in Egyptian buffaloes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00397-2.

The LEPR Gene Is Associated with Reproductive Seasonality Traits in Rasa Aragonesa Sheep

The aim of this study was to characterize and identify causative polymorphisms in the leptin receptor (LEPR) gene responsible for the seasonal variation of reproductive traits in sheep. Three reproductive seasonality traits were studied: the total days of anoestrous (TDA), the progesterone cycling months (P4CM) and the oestrous cycling months (OCM). In total, 18 SNPs were detected in 33 ewes with extreme values for TDA and OCM. Six SNPs were non-synonymous substitutions and two of them were predicted in silico as deleterious: rs596133197 and rs403578195. These polymorphisms were then validated in 239 ewes. The SNP rs403578195, located in exon 8 and leading to a change of alanine to glycine (Ala284Gly) in the extracellular domain of the protein, was associated with the OCM trait, being the G allele associated with a decrease of 12 percent of the OCM trait. Haplotype analyses also suggested the involvement of other non-synonymous SNP located in exon 20 (rs405459906). This SNP also produces an amino acid change (Lys1069Glu) in the intracellular domain of the protein and segregates independently of rs403578195. These results confirm for the first time the role of the LEPR gene in sheep reproductive seasonality.

Single-step genome-wide association studies (GWAS) and post-GWAS analyses to identify genomic regions and candidate genes for milk yield in Brazilian Girolando cattle

Milk production is economically important to the Brazilian agribusiness, and the majority of the country's milk production derives from Girolando (Gir × Holstein) cows. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with 305-d milk yield (305MY) in Girolando cattle. In addition, we investigated the SNP-specific variances for Holstein and Gir breeds of origin within the sequence of candidate genes. A single-step genomic BLUP procedure was used to identify QTL associated with 305MY, and the most likely candidate genes were identified through follow-up analyses. Genomic breeding values specific for Holstein and Gir were estimated in the Girolando animals using a model that uses breed-specific partial relationship matrices, which were converted to breed of origin SNP effects. Differences between breed of origin were evaluated by comparing estimated SNP variances between breeds. From 10 genome regions explaining most additive genetic variance for 305MY in Girolando cattle, 7 candidate genes were identified on chromosomes 1, 4, 6, and 26. Within the sequence of these 7 candidate genes, Gir breed of origin SNP alleles showed the highest genetic variance. These results indicated QTL regions that could be further explored in genomic selection panels and which may also help in understanding the gene mechanisms involved in milk production in the Girolando breed.

Prediction of lactation persistency in crossbred cattle using genotype profile of lactation curve traits

The objective of the present study was to identify the best fit lactation model in relation to bovine leptin gene and to assess lactation persistency based on lactation curve traits in crossbred Karan Fires cattle. Incomplete gamma (Wood) function and exponential (Wilmink) function tests were used to describe the characteristics of lactation curve in first lactation. Woods model showed a comparatively better fit. Different types of lactation curves depicted by these cattle using data spread over a period of 15 years (1994 to 2009) were grouped into desired and nondesired type of lactation curve. Subsequently, genotype profiling was done using PCR-RFLP. A single nucleotide polymorphism identified in exon-2 region of bovine leptin gene, was associated with desired type of lactation curve and animals having TT genotype showed better persistency of milk yield. The results validated in test population had shown positive relationship between leptin genotypes and lactation curve traits. The inference from work has a potential application in breeding program of the country, where it may give support to existing expected producingability (EPA) based selection methodology followed for selection of dairy animals, by adding leptin genotype as one additional selection criterion for early selection in crossbred dairy bulls and cattle.

Candidate gene association analysis for milk yield, composition, urea nitrogen and somatic cell scores in Brown Swiss cows

The aim of this study was to investigate 96 single-nucleotide polymorphisms (SNPs) from 54 candidate genes, and test the associations of the polymorphic SNPs with milk yield, composition, milk urea nitrogen (MUN) content and somatic cell score (SCS) in individual milk samples from Italian Brown Swiss cows. Milk and blood samples were collected from 1271 cows sampled once from 85 herds. Milk production, quality traits (i.e. protein, casein, fat and lactose percentages), MUN and SCS were measured for each milk sample. Genotyping was performed using a custom Illumina VeraCode GoldenGate approach. A Bayesian linear animal model that considered the effects of herd, days in milk, parity, SNP genotype and additive polygenic effect was used for the association analysis. Our results showed that 14 of the 51 polymorphic SNPs had relevant additive effects on at least one of the aforementioned traits. Polymorphisms in the glucocorticoid receptor DNA-binding factor 1 (GRLF1), prolactin receptor (PRLR) and chemokine ligand 2 (CCL2) were associated with milk yield; an SNP in the stearoyl-CoA desaturase (SCD-1) was related to fat content; SNPs in the caspase recruitment domain 15 protein (CARD15) and lipin 1 (LPIN1) affected the protein and casein contents; SNPs in growth hormone 1 (GH1), lactotransferrin (LTF) and SCD-1 were relevant for casein number; variants in beta casein (CSN2), GH1, GRLF1 and LTF affected lactose content; SNPs in beta-2 adrenergic receptor (ADRB2), serpin peptidase inhibitor (PI) and SCD-1 were associated with MUN; and SNPs in acetyl-CoA carboxylase alpha (ACACA) and signal transducer and activator of transcription 5A (STAT5A) were relevant in explaining the variation of SCS. Although further research is needed to validate these SNPs in other populations and breeds, the association between these markers and milk yield, composition, MUN and SCS could be exploited in gene-assisted selection programs for genetic improvement purposes.

Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle

Given the important role of leptin in metabolism, we looked for a possible association of leptin and leptin receptor polymorphisms with carcass and growth traits in Nellore cattle. We examined associations of leptin and leptin receptor SNPs with ultrasound carcass (longissimus dorsi muscle area (ribeye area), backfat thickness and rump fat thickness and growth traits (weaning weight adjusted to 210 days of age, yearling weight adjusted to 550 days of age, weight gain of weaning to yearling and scrotal circumference adjusted to 550 days of age) of 2162 Bos primigenius indicus (Nellore) animals. Allele and genotypic frequencies were calculated for each marker. Allele substitution, additive and dominance effects of the polymorphisms were also evaluated. Some alleles of the molecular markers had low frequencies, lower than 1%, in the sample analyzed, although the same polymorphisms described for B. p. taurus cattle were found. Due to very low allelic frequencies, the E2JW, A59V and UASMS2 markers were not included in the analysis, because they were almost fixed. E2FB was found to be significantly associated with weight gain, ribeye area and backfat thickness. The promoter region markers, C963T and UASMS1, were also found to be significantly associated with ribeye area. T945M was significantly associated with weight gain. We conclude that the leptin and receptor gene markers would be useful for marker-assisted selection.

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.

Mapping QTL for fat area ratios and serum leptin concentrations in a Duroc purebred population

The reduction of extra subcutaneous, intermuscular and abdominal fat is important to increase the carcass lean percentage of pigs. Image analyses of fat area ratios were effective for estimation of separated fat in pig carcasses. Serum concentrations of leptin are useful as physiological predictors of fat accumulation in pigs. The objectives of the present study were to perform a quantitative trait locus (QTL) analysis for fat area ratios and serum leptin concentrations in a Duroc purebred population. Pigs (n = 226 to 538) were measured for fat area ratios of carcass cross-sections at the fifth to sixth thoracic vertebrae, half body length and last thoracic vertebra using an image analysis system, and serum leptin concentration. In total, animals were genotyped for 129 markers and used for QTL analysis. For fat area ratios, four significant and 12 suggestive QTLs were detected on chromosomes 1, 6, 7, 8, 9, 12 and 13. Significant QTLs were detected on the same region of chromosome 6, which was located near a leptin receptor gene. For serum leptin concentrations, two significant and two suggestive QTLs were detected on chromosomes 6, 9, and 16, and the QTLs on chromosome 6 were also in the same region for fat area ratios.

Effect of polymorphisms in the leptin, leptin receptor and acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) genes and genetic polymorphism of milk proteins on bovine milk composition

The relations between cow genetics and milk composition have gained a lot of attention during the past years, however, generally only a few compositional traits have been examined. The aim of this study was to determine if polymorphisms in the leptin (LEP), leptin receptor (LEPR) and acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) genes as well as genetic polymorphism of β-casein (β-CN), κ-CN and β-lactoglobulin (β-LG) impact several bovine milk composition traits. Individual milk samples from the Swedish Red and Swedish Holstein breeds were analyzed for components in the protein, lipid, carbohydrate and mineral profiles. Cow alleles were determined on the following SNP: A1457G, A252T, A59V and C963T on the LEP gene, T945M on the LEPR gene and Nt984+8(A-G) on the DGAT1 gene. Additionally, genetic variants of β-CN, κ-CN and β-LG were determined. For both the breeds, the same tendency of minor allele frequency was found for all SNPs and protein genes, except on LEPA1457G and LEPC963T. This study indicated significant (P<0·05) associations between the studied SNPs and several compositional parameters. Protein content was influenced by LEPA1457G (G>A) and LEPC963T (T>C), whereas total Ca, ionic Ca concentration and milk pH were affected by LEPA1457G, LEPA59V, LEPC963T and LEPRT945M. However, yields of milk, protein, CN, lactose, total Ca and P were mainly affected by β-CN (A2>A1) and κ-CN (A>B>E). β-LG was mainly associated with whey protein yield and ionic Ca concentration (A>B). Thus, this study shows possibilities of using these polymorphisms as markers within genetic selection programs to improve and adjust several compositional parameters.

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.

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.

Testing candidate gene effects on milk production traits in dairy cattle under various parameterizations and modes of inheritance

The major objectives of this study were 1) to assess the statistical properties of models commonly used for the estimation of single nucleotide polymorphism (SNP) effects under the assumption of various modes of inheritance and various parameterizations of SNP genotypes using simulated data, and 2) to compare effects of the selected polymorphisms located within butyrophilin (BTN1A1), diacylglycerol acyltransferase 1 (DGAT1), leptin (LEP), and leptin receptor (LEPR) candidate genes on milk production traits using data from 2 dairy cattle breeds (190 Jersey cows and 475 Polish Holstein-Friesian cows). Simulation results showed that type I error and power were not dependent on the assumed parameterization, but differences were observed regarding confidence intervals of estimated SNP effects. In the presence of epistasis, correct confidence intervals for all (epistatic and nonepistatic) SNP and all modes of inheritance were provided only by the parameterization proposed by C. H. Kao and Z. B. Zeng in 2002. However, if no dominance effect was included in the model, confidence intervals for SNP effects were correct for all parameterizations. Results based on real data showed that for both breeds the additive effects of polymorphisms were generally similar, except for LEPR, which had a different allele associated with increased fat content in Holstein-Friesians than in Jerseys. In both breeds, DGAT1 had the largest additive effect of the polymorphisms considered, but its effect on most milk traits was more pronounced in Jerseys than in Holstein-Friesians. Evidence of epistasis was found between LEPR and DGAT1, as well as between LEPR and BTN1A1, but only for milk content traits and only in the Holstein-Friesian breed. There was also more evidence for dominance in the Holstein-Friesian breed than in the Jersey breed.

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.

Characterization of exon 2 and intron 2 of leptin gene in Indian goats

Leptin, the hormonal product of the leptin (obese) gene (LEP), has multiple physiological effects and plays a pivotal role in the control of body growth, immune function, and reproduction. LEP gene polymorphism has been analyzed in cattle, buffalo, and pigs, and the polymorphic pattern has been associated with energy balance, milk production, and live weight and fertility trait in different livestock species. The present study has been designed to analyze polymorphism in exon 2 and intron 2 region of leptin gene in Indian goats. Genotyping was carried out in 111 kids including 70 samples from Barbari and 41 samples from Jamunapari breeds. The amplified product of exon 2 and intron 2 region of leptin gene was 152 bp and 400 bp, respectively, in both breeds. Sequencing of the exon 2 and intron 2 region of leptin gene and restriction analysis were carried out to analyze the polymorphism in goats. Five major haplotypes were observed in exon 2 region and six major haplotypes observed in intron 2 region in both breeds. Restriction fragment analysis and sequence analysis confirmed the mutation at 60 bp position of exon 2 and 100 bp position in intron 2 in all the analyzed samples. Sequences of exon 2 region of goats were unique as compared to other livestock species in BLAST analysis.

Genetic relationships of body composition, serum leptin, and age at puberty in gilts

Leptin produced by adipocytes acts through leptin receptors in the hypothalamus to control appetite and food intake and thus communicates information about degree of fatness. It is thought that a degree of body fat is required for initiation of puberty and maintenance of reproductive function in mammals. The objective of this study was to determine whether polymorphisms in the leptin (LEP), leptin receptor (LEPR), paired box 5 (PAX5), aldo-keto reductase (AKR), and pro-opiomelanocortin (POMC) genes were associated with age, leptin concentration, backfat as an indicator of body condition, or BW at puberty in 3 lines of gilts and to characterize genetic relationships among these traits. The first 2 lines, born in 2001, were formed by crossing maternal White Cross (Yorkshire x Maternal Landrace) gilts to Duroc (n = 210) or (lean) Landrace (n = 207) boars. The remaining line (n = 507), born in 2002, was formed by crossing progeny of the Duroc- and Landrace-sired lines. At first estrus, age, BW (BWP), and backfat (BFP) at puberty were recorded and blood was collected for leptin assays. Nine SNP were detected in candidate genes/regions: 1 in LEP, 3 in LEPR, 1 in PAX5, 2 in AKR, and 2 in POMC. Animals were genotyped for each of the SNP; genotypes were validated using GenoProb. The association model included fixed effects of farrowing group, covariates of SNP genotypic probabilities (from GenoProb), and random additive polygenic effects to account for genetic similarities between animals not explained by SNP. Variance components for polygenic effects and error were estimated using MTDFREML. Leptin concentrations were logarithmically transformed for data analysis. All 4 traits were moderately to highly heritable (0.38 to 0.48). Age and leptin at puberty had a significant (P < 0.01) genetic correlation at -0.63 +/- 0.097, and the genetic correlation between BWP and age at puberty was 0.65 +/- 0.083 (P < 0.01). Significant additive associations (a; P < 0.05) were detected at PAX5 for age at puberty (a = 3.2 d) and for BFP (a = 0.61 mm). One SNP in LEPR was associated with leptin concentration (a = 0.31 log units; P < 0.05). The associations from PAX5 correspond to a QTL peak for age at puberty detected on SSC1. Although not necessarily the causative mutation, this result implies that a QTL that can decrease age at puberty without increasing BFP and BWP at puberty may exist in this region in commercial pigs.

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.

Statistical modeling of candidate gene effects on milk production traits in dairy cattle

A major objective of dairy cattle genomic research is to identify genes underlying the variability of milk production traits that could be useful in breeding programs. The candidate gene approach provides tools for searching for causative polymorphisms affecting quantitative traits. Genes with a possible effect on milk traits in cattle can be involved in different physiological pathways, such as triglyceride synthesis [acyl-CoA:diacylglycerol acyltransferase 1 gene (DGAT1)], fat secretion from the mammary epithelial tissue (butyrophilin), or entire-body energy homeostasis regulation (leptin and leptin receptor). In this study, based on data from 252 Black and White bulls from the active Polish dairy population, effects and potential interactions of 9 single nucleotide polymorphisms in the butyrophilin, DGAT1, leptin, and leptin receptor genes were investigated. Additionally, the effect of the number of additive, dominance, and epistatic genetic effects fitted into the model on the estimates of model parameters and model selection was illustrated. Phenotypic records were daughter yield deviations for milk, fat, and protein yields, obtained from a routine national genetic evaluation. Out of all the analyzed polymorphisms, DGAT1 K232A had a much larger effect on milk traits than the other single nucleotide polymorphisms considered. Estimates of the additive genetic effect of K232A expressed as half of the difference between Lys- and Ala-encoding variants were -107.4 kg of milk, 5.4 kg of fat, and -1.6 kg of protein at first parity, as well as -120 kg of milk and 6.8 kg of fat at second parity. In terms of model selection, it was demonstrated that the modified version of Bayesian information criterion selects models with the parameterization reflecting the genetic background of the analyzed trait, while the Bayesian information criterion chooses models that are too highly parameterized.

Genetics and physiology of leptin in periparturient dairy cows

In dairy cattle, the increase in milk yield has been accompanied by a more negative energy balance (EB) during early lactation and a decrease in fertility. As the hormone leptin is involved in regulation of nutritional status and reproductive function this hormone is an interesting protein to investigate during the periparturient period in dairy cattle. This study was performed to get insight into the function of leptin during the periparturient period and to perform an association study between polymorphisms in the bovine leptin gene and leptin receptor gene and fertility as well as production traits. Leptin concentrations in the periparturient cow undergo remarkable changes; leptin concentrations were high during late pregnancy and declined to a nadir at parturition. Genetic analysis of the leptin gene indicated that a combination of three polymorphisms located at a 135 bp region of the leptin promoter explained most of the variance in prepartum leptin concentrations. The two extreme genotype combinations could be used to investigate the function of leptin concentrations in pregnant cows. A polymorphism located on intron 2 of the leptin gene explained a significant part of the variation in milk yield. On the promoter region of the leptin gene an SNP was detected that was associated with first postpartum luteal activity (FPLA). This SNP could be a candidate marker for fertility in dairy cows. Another SNP on the leptin promoter was associated with energy balance and dry matter intake (DMI) where a higher dry matter intake occurred together with a higher energy balance. Two genotype combinations of the aforementioned three associated SNPs were defined which had a good milk yield together with a good energy balance and fertility. Calculations of an economical value per trait have to validate if one of these genotype combinations would be a possible candidate to be used in selection.

Missense mutations in exon 4 of the porcine LEPR gene encoding extracellular domain and their association with fatness traits

Three non-synonymous single nucleotide polymorphisms (T221C, T232A and C233T) were detected in exon 4 of the porcine leptin receptor (LEPR) gene. The T232A substitution could be identified as a (Tsp509I) restriction fragment length polymorphism. The frequency of genotype TT varied in six genetic groups from 0.62 (Duroc) to 0.99 (Polish Large White). Sequencing of exon 4, performed for 30 animals, revealed that only two intragenic haplotypes (TC and AT at nucleotide position 232-233) were present. The phenotypic effect of the Tsp509I polymorphism was tested for the Polish Landrace (n = 241) and a synthetic line 990 (n = 243). There was no statistical evidence for the direct effect of the LEPR polymorphisms on fatness traits. However, in Polish Landrace allele A at position 232 was associated with thicker backfat over shoulder.

Leptin promoter mutations affect leptin levels and performance traits in dairy cows

Leptin concentrations in body fluids and tissues undergo dynamic changes during the periparturient period. Polymorphisms in the leptin gene have been shown to be associated with differences in leptin concentration during late pregnancy but not during lactation. As the promoter of leptin regulates the expression of leptin, polymorphisms in this region could play an important role in the differences in leptin expression observed during the periparturient period. We sequenced the leptin promoter and discovered 20 SNP in a 1.6-kbp region of the bovine leptin promoter. Fourteen of these SNP were genotyped for all animals and these were found to be associated with leptin concentrations during late pregnancy but not during lactation. Three of these SNP are located in a 135-bp promoter region and together explained 14.3% of the variance in prepartum leptin concentrations which indicates that this region might be important for pregnancy-induced leptin synthesis. In the association study of the 14 SNP with dairy traits three were separately found to be associated with fertility, energy balance and protein yield. These might serve as markers for future breeding programmes for better fertility and energy balance without significantly influencing milk yield in dairy cattle.