Genetic variants affecting meat and milk production traits appear to have effects on reproduction traits in cattle

Polymorphisms located in the genes ABCG2, DGAT1, LEP, PRLR, RORC, CAPN1 and CAST previously have been associated with milk or meat production traits. In this study, these polymorphisms were examined for significant effects on reproductive traits [age at puberty (AGECL), post-partum anoestrus interval (PPAI) and the ability ovulate prior to weaning (PW)] and on a panel of correlated traits such as weight, growth and serum concentration of insulin-like growth factor I. The effects of the polymorphisms were examined in two samples of tropically adapted beef cattle: Brahman (N = 932) and Tropical Composites (N = 1097). A polymorphism in the gene DGAT1 was associated with age at puberty in the combined sample (P = 0.042), and two polymorphisms in CAPN1 were associated with PPAI (P = 0.033) and with the ability ovulate PW (P = 0.017). The favourable allele for reproductive traits was not always the favourable allele associated with production traits. The effects of these polymorphisms on reproductive traits were small compared to their effects on the traits for which they were originally discovered.     

Effects of a single nucleotide polymorphism in the leptin gene on the productive traits of dairy buffaloes (Bubalus bubalis)

The gene responsible for coding the leptin hormone has been associated with productive and reproductive traits in cattle. In dairy cattle, different polymorphisms found in the leptin gene have been associated with several traits of economic interest, such as energy balance, milk yield and composition, live weight, fertility and dry matter consumption. The aim of this study was to detect genetic variability in the leptin gene of buffaloes and to test possible associations with milk yield, fat and protein percentages, age at first calving and first calving interval. Three genotypes (AA, AG and GG) were identified by polymerase chain reaction–restriction fragment length polymorphism, which presented genotypic frequencies of 0.30, 0.54 and 0.16, respectively. The allele frequencies were 0.57 for the A allele and 0.43 for the G allele. No significant effects were found in the present study, but there is an indicative that leptin gene affects lipid metabolism.     

Effects of DGAT1 and GHR on milk yield and milk composition in the Chinese dairy population

Previous studies have demonstrated that the p.Lys232Ala substitution in the acylCoA: diacylglycerol acyltransferase ( DGAT1 ) gene and the p.Phe279Tyr mutation in the growth hormone receptor ( GHR ) gene are the causative quantitative trait loci underlying milk yield and composition on BTA14 and BTA20 respectively. To examine their applications in the genetic improvement of Chinese dairy cattle productivity, we herein investigated the effects of the DGAT1 p.Lys232Ala and GHR p.Phe279Tyr mutations on milk, fat and protein yield, as well as fat and protein percentage in the milk of 1222 Holstein cows. Genotyping was performed using PCR-RFLP for DGAT1 or primer-introduced restriction analysis (PCR-PIRA) for GHR . With a mixed animal model, the significant associations of the DGAT1 p.Lys232Ala substitution with 305-day milk, fat and protein yield were identified ( P  =   0.0001). The DGAT1 allele that encode lysine at position 232 was associated with increased 305-day milk fat yield, but with decreased 305-day milk and protein yield, whereas the GHR p.Phe279Tyr mutation was found to be significantly associated with protein percentage ( P  =   0.0014). The allele substitution effect of p.279Phe by p.279Tyr may lead to a significant increase in protein percentage. Our findings indicate that DGAT1 p.232Ala and GHR p.279Phe could be used to increase milk yield and protein yield of Chinese Holstein cows.     

Do established SNPs affecting bovine milk traits exist in other dairy ruminants?

To assess whether established single nucleotide polymorphisms (SNPs) affecting bovine milk traits are present in small ruminants, we genotyped samples from Chios and Cyprus fat-tailed sheep, as well as Damascus and Machaeras goats for the presence of the acylCoA:diacylglycerol acyltransferase 1 (DGAT1) K232A and the growth hormone receptor (GHR) F279Y SNPs. Both of these SNPs have been previously well documented in cattle as having strong effects on milk yield and composition and have been postulated as being the causative mutations to partially explain QTLs identified on bovine chromosomes 14 and 20. Although we were able to confirm the presence of both of these mutations in bovine sample controls by both allele specific PCR reactions and direct DNA sequencing, we were unable to detect them in any of the four major pure breeds of sheep and goats supporting the dairy industry of Cyprus.     

<Emphasis Type="Italic">IGF-1</Emphasis> and <Emphasis Type="Italic">IGF-1R</Emphasis> gene polymorphisms in East Anatolian Red and South Anatolian Red cattle breeds

The aim of this study was to determine the allele and genotype frequencies of the Insulin like growth factor 1 gene (IGF-1) and Insulin like growth factor 1 receptor gene (IGF-1R) polymorphisms in East Anatolian (EAR) and South Anatolian Red cattle (SAR). Polymorphisms in both genes are claimed to affect economic parameters like body weight and subcutaneous back fat. For the study, blood samples were collected from 50 SAR and 50 EAR cattle. In both breeds, high frequencies of allele B of IGF-1, which was supposed to have positive effect on carcass traits and allele A of IGF-1R, related to milk traits, were observed. Therefore, no relationship of the polymorphisms studied with economic traits was observed, as both breeds have respectively low carcass and milk parameters. However, distribution of allele frequencies of IGF-1 and IGF-1R in SAR and EAR cattle was similar with Zebu cattle that support Bos indicus introgression to Anatolian breeds.     

Associations Between Milk Performance Traits in Holstein Cows and 16 Candidate SNPs Identified by Arrayed Primer Extension (APEX) Microarray

An oligonucleotide microarray—which allows for parallel genotyping of many SNPs in genes involved in cow milk protein biosynthesis—was used to identify which of the 16 candidate SNPs are associated with milk performance traits in Holstein cows. Four hundred cows were genotyped by the developed and validated microarray. Significant associations were found between four single SNPs, namely DGAT1 (acyloCoA:diacylglycerol acyltransferase), LTF (lactoferrin), CSN3 (kappa-casein), and GHR (growth hormone receptor) and with fat and protein yield and percentage. Many significant associations between combined genotypes (two SNPs) and milk performance traits were found. The associations between the combined genotypes DGAT1/LTF and DGAT1/LEPTIN analyzed traits are presented as examples.

The microarray based on APEX (Arrayed Primer Extension) is a fast and reliable method for multiple SNP analysis of potential application in marker-assisted selection. After further development, the chip may prospectively be used for dairy cattle paternity analysis and evolutionary studies.     

Single-nucleotide polymorphisms in the promoter of the growth hormone-releasing hormone receptor gene are associated with growth and reproduction traits in chickens

Growth hormone‐releasing hormone receptor (GHRHR) plays a critical role in growth hormone (GH) synthesis, release and regulation in animals. The objective of this study was to investigate variations of the chicken GHRHR gene and their associations with growth and reproduction traits in 768 Beijing You chickens. Results revealed three single nucleotide polymorphisms (SNPs) in the promoter region of the gene (g.‐1654A>G, g.‐1411A>G and g.‐142T>C). Association analysis revealed that the novel SNP g.‐1654A>G had significant effects on chicken body weight at 7, 9, 11, 13, 17 weeks of age and the age of first egg as well as egg number at 32, 36 and 40 weeks. Significant association was also observed between g.‐1411A>G and g.‐142T>C with EN24. Moreover, the age of first egg was distinctly related with g.‐142T>C (P < 0.05). Although significant statistical difference was not detected in GHRHR mRNA levels among genotypes of the SNPs (P > 0.05), strong expression variations of the gene were found between the ages 17 and 20 weeks in the population (P < 0.05). These results suggest that the three SNPs in the GHRHR promoter could be used as potential genetic markers to improve the growth and reproductive traits in chickens.     

Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP

Diacylglycerol O-acyltransferase 1 (DGAT1) is a microsomal enzyme that catalyzes the final step of triglyceride synthesis. The DGAT1 gene is a strong functional candidate for determining milk fat content in cattle. In this work, we used PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing to examine polymorphism in the region spanning exon 7 to exon 9 of the DGAT1 gene in Murrah and Pandharpuri buffaloes. Three alleles (A, B and C) and four novel single-nucleotide polymorphisms were identified in the buffalo DGAT1 gene. The frequencies of the alleles differed between the two buffalo breeds, with allele C being present in Murrah but not in Pandharpuri buffalo. The allele variation detected in this work may influence DGAT1 expression and function. The results described here could be useful in examining the association between the DGAT1 gene and milk traits in buffalo.     

郏县红牛DGAT2基因多态性与生长性状的相关性分析

利用PCR-RFLP技术对随机抽取的92头郏县红牛的DGAT2基因进行多态性分析。结果表明, DGAT2基因第6内含子的PCR扩增产物被限制性酶TaqⅠ酶切消化后表现多态性。经电泳检测后, 显出AA、AB两种不同基因型。该基因座处于Hardy-Weinberg平衡状态, 通过对郏县红牛DGAT2基因多态性与体重及体尺指标的方差分析显示：郏县红牛DGAT2基因不同基因型对郏县红牛体重和体长有显著影响(P<0.05), 而对其他体尺指标在统计学上无显著影响(P>0.05), 且初步认为AB基因型对选择有正向效应。     

Associations between milk performance traits in Holstein cows and 16 candidate SNPs identified by arrayed primer extension (APEX) microarray

An oligonucleotide microarray-which allows for parallel genotyping of many SNPs in genes involved in cow milk protein biosynthesis-was used to identify which of the 16 candidate SNPs are associated with milk performance traits in Holstein cows. Four hundred cows were genotyped by the developed and validated microarray. Significant associations were found between four single SNPs, namely DGAT1 (acyloCoA:diacylglycerol acyltransferase), LTF (lactoferrin), CSN3 (kappa-casein), and GHR (growth hormone receptor) and with fat and protein yield and percentage. Many significant associations between combined genotypes (two SNPs) and milk performance traits were found. The associations between the combined genotypes DGAT1/LTF and DGAT1/LEPTIN analyzed traits are presented as examples. The microarray based on APEX (Arrayed Primer Extension) is a fast and reliable method for multiple SNP analysis of potential application in marker-assisted selection. After further development, the chip may prospectively be used for dairy cattle paternity analysis and evolutionary studies.     

Metabolic variables and plasma leptin concentrations in dairy cows exhibiting reproductive cycle abnormalities identified through milk progesterone monitoring during the post partum period

We have used milk progesterone analysis to monitor reproductive function in lactating dairy cows and have then related this reproductive function to a variety of metabolic variables. Monitoring of cows (n = 41) during the period of onset of luteal function (first milk progesterone reading>5 ng/ml) revealed that delayed onset was associated with increased milk yield and greater loss of body weight and body condition but was not related to plasma metabolite or leptin concentrations. Further monitoring of reproductive function in these 41 cows and an additional 33 cows (total n = 74) during the mating period (from weeks 6 to 14 post partum) identified reproductive cycle abnormalities in 29 (39.2% of animals). The occurrence of cycle abnormalities was associated with increased milk yield (P < 0.05), elevated plasma beta hydroxybutyrate (P < 0.05) and reduced plasma leptin (P < 0.01) concentrations as well as a lower (P < 0.05) rate of gain of body weight and condition score but was not associated with plasma urea or glucose concentrations. Furthermore, cows exhibiting cycle abnormalities had a longer (P < 0.01) interval to first service and a smaller percentage had conceived by 100 days post partum (34.5% versus 66.7%; P < 0.01). These results provide further evidence that impaired reproductive function during the post partum period in dairy cows is caused by a poor energy status and not elevated urea concentrations. Reduced plasma leptin concentrations in animals suffering reproductive dysfunction further supports this view.     

Association between body energy content in the dry period and post-calving production disease status in dairy cattle

The transition from gestation to lactation is marked by significant physiological changes for the individual cow such that disease incidence is highest in early lactation. Around the time of calving, cows rely on mobilisation of body energy reserves to fill the energy deficit created by an increase in nutrient demands at a time of restricted feed intake. It is well established that monitoring of body energy reserves in lactation is an important component of herd health management. However, despite their influence on future health and productivity, monitoring of body energy reserves in the dry period is often sparse. Further, there is increasing concern that current dry off management is inappropriate for modern cattle and may influence future disease risk. This study aimed to identify candidate indicators of early lactation production disease from body energy data collected in the dry period and production data recorded at the time of dry off. Retrospective analysis was performed on 482 cow-lactations collected from a long-term Holstein-Friesian genetic and management systems project, the Langhill herd in Scotland. Cow-lactations were assigned to one of four health groups based on health status in the first 30 days of lactation. These four groups were as follows: healthy, reproductive tract disorders (retained placenta and metritis), subclinical mastitis and metabolic disorders (ketosis, hypocalcaemia, hypomagnesaemia and left displaced abomasum). ANOVA, employing a GLM was used to determine effects for the candidate indicator traits. Cows which were diagnosed with a reproductive tract disorder in the first 30 days of lactation experienced a significantly greater loss in body energy content, body condition score and weight in the preceding dry period than healthy cows. The rate of change in body energy content during the first 15 days of the dry period was −18.26 MJ/day for cows which developed reproductive tract disorder compared with +0.63 MJ/day for healthy cows. Cows diagnosed with subclinical mastitis in the first 30 days of lactation had significantly greater milk yield at dry off in the previous lactation than cows that developed a reproductive tract disorder or metabolic disease in addition to a significantly higher yield to body energy content ratio at dry off than healthy cows. Physiological and production traits recorded in the lactation and dry period preceding a disease event differed between cows which developed different diseases post-calving. Differences in these traits allow the development of new disease indicators for use in models for the prediction of disease risk in the transition period.     

徐淮白山羊DGAT2基因内含子3多态性与生长性状关联分析

目的：探讨DGAT2基因内含子3的遗传多态性及其与山羊生长性状的关联。方法：采用PCR-SSCP、DNA序列分析及生物信息学技术研究徐淮白山羊DGAT2基因内含子3的多态性及其与山羊生长性状的关联情况。结果：徐淮白山羊DGAT2基因内含子3存在A、B2个等位基因,其基因频率依次为0.9550、0.0450,并且处于Hardy-Weinberg平衡状态;徐淮白山羊DGAT2基因不同基因型对徐淮白山羊体高有显著影响（P〈0.05）,而对其他体尺指标在统计学上无显著影响（P〉0.05）。结论：DGAT2基因内含子3的遗传多态性与徐淮白山羊生长性状存在相关。     

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.     

Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle

We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.     

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: μ-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.     

Effect of luteinizing hormone/choriogonadotropin receptor (LHCGR) gene on chicken reproductive traits

Luteinizing hormone/choriogonadotropin receptor (LHCGR) gene, potentially related to reproductive traits in chickens, was genotyped by using the Pooled DNA Sequencing, PCR–SSCP and Directing Sequencing techniques. 306 Erlang Mountain chickens form one line (SD03, a line that has been selected for egg quality from a local chicken breed in Sichuan province, China) were genotyped in this study. The associations between LHCGR polymorphisms and six reproductive traits [body weight at first egg (BWAFE), weight of first egg, age at first egg (AFE), number of eggs at 300 days of age (EN), body weight at 300 days of age and egg weight at 300 days of age (EWTA)] were estimated using the one-way analysis of variance method. Results showed that SNP +G4058A and SNP +T4099G of the LHCGR gene were significantly associated with BWFE and AFE. Birds with the AG genotype for the +G4058A SNP exhibited shorter AFE (P < 0.05) and greater EN than those of the GG and AA genotypes, suggesting a balancing selection (overdominance); the effect of allele C in SNP +C3021T and allele C in SNP +T4490C on EN and AFE is additive and may reflect the influence of positive selection. These alleles have promise as genetic markers for future marker-assisted selection.     

AluI polymorphism of the bovine growth hormone (GH) gene, resumption of ovarian cyclicity, milk production and loss of body condition at the onset of lactation in dairy cows

Relationships among GH genotype (AluI polymorphism), parity, metritis and interval from calving to first ovulation, milk production and body condition score (BCS) loss were determined in dairy cows (n = 307) on four large-scale farms in Hungary. Cows with systemic signs of puerperal metritis or mastitis were excluded. Time of the first postpartum (PP) ovulation was obtained from milk progesterone profiles. Based on GH genotype determination, groups of leucine homozygous cows (n = 246) and valine allele carriers (n = 61) were formed. All animals became cyclic during the study period. The average interval to first ovulation was 27.6 ± 0.69-d PP (mean ± S.D.). Genotype had no effect on the commencement of ovarian cyclicity. First ovulation occurred sooner after calving in pluriparous than in primiparous cows. The greater BCS loss cows had during the first 30-d PP, the longer they took to resume cyclic ovarian function. The interval from calving to first ovulation was substantially affected by farm, but not by mild cases of puerperal metritis. Genotype was not related to cumulative 30-d milk yield or BCS loss after calving. Primiparous cows had lower milk yield than pluriparous ones. Cows with metritis lost more body condition than healthy individuals in the first month postpartum. We concluded that, under field conditions, AluI polymorphism of the bovine GH gene had no effect on the interval from calving to first ovulation and could not be directly related to differences in milk yield and to the extent of BCS loss during the first month after calving in Holstein-Friesian cows.     

Effect of leptin gene polymorphism on the breeding value of milk production traits in Iranian Holstein

New molecular techniques focused on genome analysis, open new possibilities for more accurate evaluation of economiclly important traits in farm animals. Milk production traits are typical quantitative characteristics controlled by a number of genes. Mutations in their sequences may alter animal performance as well as their breeding values. In this study, we investigated the effect of Kpn2I restriction fragment length polymorphisms in the leptin gene, on bull breeding values for milk yield, fat, and protein yield, and their percentage. In order to test for an association between the leptin single-nucleotide polymorphism in exon 2 and milk productivity, we genotyped 134 Iranian Holstein bulls. Breeding values for milk-related traits (milk yield, fat, and protein yield and percentage) were estimated using the BLUP based on an animal model. The effect of the genotypes of Kpn2I polymorphism on the breeding values for milk-related traits was examined using least square methods. The T allele frequency was 0.425. Genotypes were distributed according to the Hardy-Weinberg equilibrium. Bulls with TT genotype had higher milk, fat and protein yield compared with TC and CC bulls (P < 0.05). Bulls with CC genotype had higher protein percentage compared with TT and TC bulls (P < 0.05). The association between leptin polymorphism with milk production traits suggests that this marker may be useful for selection based on molecular information.