Traits In Livestock Research Articles

Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome

MicroRNAs (miRNAs) are recognized as gene expression regulators, indirectly orchestrating a plethora of biological processes. Single nucleotide polymorphism (SNP), one of the most common genetic variations in the genome, is established to affect miRNA functioning and influence complex traits and diseases. SNPs in miRNAs have also been associated with important production traits in livestock. Thus, the aim of our study was to reveal the SNP variability of miRNA genes in the genome of the pig, which is a significant farm animal and large-mammal human model. To this end, we applied the targeted sequencing approach, enabling deep sequencing of specified genomic regions. As a result, 73 SNPs localized in 50 distinct pre-miRNAs were identified. In silico analysis revealed that many of the identified SNPs influenced the structure and energy of the hairpin precursors. Moreover, SNPs localized in the seed regions were shown to alter targeted genes and, as a result, enrich different biological pathways. The obtained results corroborate a significant impact of SNPs on the miRNA processing and broaden the state of knowledge in the field of animal genomics. We also report the targeted sequencing approach to be a promising alternative for the whole genome sequencing in miRNA genes focused studies.

The influence of liver fluke infection on production in sheep and cattle: a meta-analysis

Liver flukes (Fasciola spp.) are important parasites of ruminant livestock worldwide, causing profound damage to animal health and productivity. Many reviews have discussed the results of decades of research on the impact of fluke on livestock traits such as weight gain and milk production, but there have been no known attempts to collate previous research in a quantitative manner or to determine the factors that vary between studies that find substantial effects of fluke and others concluding that effects of fluke are negligible. Here, we use meta-analysis to provide quantitative “global” estimates of the impact of liver fluke on animal performance, and to identify elements of study design (“moderators”) that influence variation between studies in their outcome. A literature search provided 233 comparisons of performance in fluke-infected and uninfected animals. We standardised these data as log response ratios and calculated effect size variances to weight studies by the accuracy of their estimates. We performed multi-level meta-analysis to estimate effects of fluke infection on daily weight gain, live weight, carcass weight, total weight gain and milk production. There were statistically-supported negative effects of fluke infection on daily weight gain, live weight and carcass weight (9%, 6% and 0.6% reductions, respectively), but not on total weight gain or milk production. A mixed-effects meta-analysis revealed that studies of younger animals found more severe effects of fluke on weight gain and that effects on live weight increased with time since infection. Limitations to the data that could be analysed, including a lack of statistical reporting in older papers and variation in the outcome variables measured, may have explained the relatively limited influence of modifiers that we detected. Our results provide, to our knowledge, the first quantitative estimate of the impact of liver fluke on performance across studies and highlight some elements of study design that can influence conclusions.

Parsing the microRNA genetics basis regulating skeletal muscle fiber types and meat quality traits in pigs.

Muscle fibers are closely related to human diseases and livestock meat quality. However, the genetics basis of microRNAs (miRNAs) in regulating muscle fibers is not completely understood. In this study, we constructed the whole genome-wide miRNA expression profiles of porcine fast-twitch muscle [biceps femoris (Bf)] and slow-twitch muscle [soleus (Sol)], and identified hundreds of miRNAs, including four skeletal muscle-highly expressed miRNAs, ssc-miR-378, ssc-let-7f, ssc-miR-26a, and ssc-miR-27b-3p. Moreover, we identified 63 differentially expressed (DE) miRNAs between biceps femoris vs. soleus, which are the key candidate miRNAs regulating the skeletal muscle fiber types. In addition, we found that the expression of DE ssc-miR-499-5p was significantly correlated to the expression of Myoglobin (r=0.6872, P<0.0001) and Myosin heavy chain 7 (MYH7; r=0.5408, P=0.0020), and pH45min (r=0.3806, P=0.0380) and glucose content (r=-0.4382, P=0.0154); while the expression of DE ssc-miR-499-3p was significantly correlated to the expression of Myoglobin (r=0.5340, P=0.0024) and pH45min (r=0.4857, P=0.0065). Taken together, our data established a sound foundation for further studies on the regulatory mechanisms of miRNAs in skeletal muscle fiber conversion and meat quality traits in livestock, and could provide a genetic explanation of the role of miRNAs in human muscular diseases.

Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits

Background: Transmembrane protein 95 ( TMEM95 ) plays a role in male fertility. Previous studies showed that genes with a significant impact on reproductive traits can also affect the growth traits of livestock. Thus, we speculated that the genetic variation of TMEM95 gene may have effects on growth traits of cattle. Results: Two SNPs were genotyped. The rs136174626 and rs41904693 were in the intron 4 and 3′-untranslated region, respectively. The linkage disequilibrium analysis illustrated that these two loci were not linked. The rs136174626 was associated with six growth traits of Nanyang cattle, four traits of Luxi cattle, and three traits of Ji’an cattle. For rs41904693 locus, the GG individuals had greater body height and abdominal girth in Ji’ an cattle than TT and TG individuals. In Jinnan cattle, GG and TT individuals had greater body height, height at hip cross, body length, and heart girth than TG individuals. The potential splice site prediction results suggest that the rs136174626 may influence the splicing efficiency of TMEM95, and the miRNA binding site prediction results showed that the rs41904693 may influence the expression of TMEM95 by affecting the binding efficiency of Bta-miR-1584 and TMEM95 3′-UTR. Conclusions: The findings of the study suggested that the two SNPs in TMEM95 could be a reliable basis for molecular breeding in cattle. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Tabla normal; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri,sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Times New Roman; mso-bidi-theme-font:minor-bidi;}

Polymorphisms in hormone-sensitive lipase and leptin receptor genes and their association with growth traits in Barki lambs.

Background and Aim:Marker-assisted selection has many advantages over conventional selection in animal breeding. The candidate gene approach has been applied to identify genetic markers associated with economically important traits in livestock. This study was established to investigate variation in the hormone-sensitive lipase (HSL) and leptin receptor (LEPR) genes, and their association with growth traits in Barki lambs.Materials and Methods:Records for birth weight (BW), pre-weaning average daily gain (ADG1), weaning weight (WW), post-weaning average daily gain (ADG2), and marketing weight (MW) were obtained from 247 Barki lambs. Polymerase chain reaction–single-stranded conformational polymorphism analyses were used to detect variation in exon 9 of HSL and exon 19 of LEPR. General linear models were used to test for associations between the variation in ovine HSL and LEPR, and growth traits.Results:The SSCP banding patterns for HSL showed three variants (H1, H2, and H3), which contained two nucleotide-sequence differences (c.1865C>T and c.2038T>C). Two SSCP banding patterns (L1 and L2) were observed for LEPR and these contained two nucleotide-sequence differences (c.2800G>A and c.2978C>G). The HSL genotype showed no effect on the studied traits. The LEPR genotype was proven to have significant effects (p<0.05) on ADG2 and MW. The presence of the L1 variant was associated (p<0.01) with decreased ADG2 and MW.Conclusion:The finding of an association between LEPR gene variation and growth rate after weaning in Barki lambs warrants efforts to improve this trait.

Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle.

Simple SummaryComplex traits that require observations over multiple time points for the same individual are called longitudinal traits. Understanding the genetic architecture of beef cattle growth cannot be limited simply to a genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the longitudinal weight–age using a growth curve approach. We compared three nonlinear models that described the body weight data of Chinese Simmental beef cattle. The parameters of the suitable model were treated as phenotypes of single-trait GWAS and multi-trait GWAS. We identified 87 significant single nucleotide polymorphisms (SNPs) associated with body weight. Many candidate genes associated with body weight were identified which may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci.

BackgroundThe development of high-throughput sequencing and genotyping methodologies has enabled the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits.FindingsGenomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as genome-wide association studies and transcriptomics using RNA sequencing. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies), and QTL enrichment in different livestock species such as cattle, pigs, sheep, and chickens.ConclusionsConsequently, GALLO is a useful package for annotation, identification of hidden patterns across datasets, and data mining previously reported associations, as well as the efficient examination of the genetic architecture of complex traits in livestock.

Analysis of X chromosome and autosomal genetic effects on growth and efficiency-related traits in sheep

Abstract Context It is believed that the X chromosome plays an important role in influencing quantitative traits. Despite this, until recently, X-linked genetic effects have not been considered in models to estimate genetic parameters for economically important traits of livestock. Aims A large dataset was analysed to quantify autosomal additive genetic, X-linked additive genetic and maternal effects on growth and efficiency-related traits in Baluchi sheep. Methods Traits included bodyweight at birth, weaning (WW), 6 months (W6), 9 months and yearling age, pre- and post-weaning average daily gain, pre- and post-weaning Kleiber ratio, pre- and post-weaning efficiency of growth (EFb), and pre- and post-weaning relative growth rate. Each trait was analysed using the REML procedure fitting a series of eight univariate animal models. For each trait, the most appropriate model was selected by the Akaike information criterion and Bayesian information criterion. Key results The X-linked genetic effect was significant only in models fitted to EFb, where the estimate of X-linked heritability was 0.02 ± 0.01 from the best model. Other traits were not affected significantly by X-linked genetic effects. Estimates of autosomal heritability () for growth traits were between 0.06 ± 0.02 (post-weaning average daily gain, pre-weaning relative growth rate) and 0.22 ± 0.04 (bodyweight at yearling age), and ranged between 0.02 ± 0.01 (EFb) and 0.08 ± 0.02 (pre-weaning Kleiber ratio) for efficiency-related traits. Maternal effects significantly contributed to phenotypic variation of most traits, with larger effects on traits measured early in life. For EFb, the Spearman’s correlation between breeding values including and excluding X-linked effects was 0.95. It was 1.00 for traits that were not affected by X-linked genetic effects. Conclusions Although the proportion of phenotypic variance attributed to X-linked loci for most traits was zero, the importance of X-linked genetic effects should be at least tested in models when estimating variance components for growth and efficiency traits of Baluchi sheep. Implications As estimates of genetic parameters are breed-specific, we recommend for growth and efficiency traits of sheep that the importance of X-linked genetic effects should be evaluated to assess if these effects should be included in models used in genetic evaluation.

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data.

Simple SummaryIn this study, we estimated genetic diversity in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches, and detected regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome, which are still poorly characterized in the Maremmana breed. A sensitivity analysis on the parameters used to detect ROH and ROHet provided information which can be useful to guide studies on the detection of genomic runs in general, and in semi-feral cattle populations in particular. The average observed and expected heterozygosity were estimated at and , respectively. Pedigree-based average inbreeding (F) was estimated at . A total of ROH and ROHet were detected in the genomes of the 149 animals included in the study. Genes found to be within the identified ROH and ROHet islands (e.g., KCTD8, GNPDA2) point to phenotypic characteristics related to environmental adaptation and robustness of Maremmana cattle. These results are of important because they will help design and implement breeding and conservation strategies for Maremmana cattle, and provide guidelines for other local cattle breeds.Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches ( and ), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (, ). Pedigree-based average inbreeding (F) was estimated at . The correlation was low between F and genomic-based approaches ( with , with ), while it was higher between and (). The low correlation between F and coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.

INFLUENCE OF CROSSING OF UTERUSES OF UKRAINIAN BLACK-RIBBED AND HOLSTINA BREEDS WITH JERSEY BREED BULLS ON THE MAIN SELECTION SIGNS OF MEMORY

The presence of interbreeding genetic differences in certain dairy rocks provided the use of analytical crossing allows get an improvement in a number of economically important breeding traits in local livestock in terms of quality of dairy productivity, reproductive capacity and other economically useful features. It is established that the crossbreeds of the first generation are Ukrainian black-spotted dairy x Jersey breed (F1½UCHRM × ½D) in LLC "Khmilnytske" on production units have much higher rates than dairy productivity. Thus, hopes increased by (330–386 kg), milk fat – (26.0–29.7 kg) and protein – (17.3–20.2) kg under the same feeding conditions and maintenance. Much higher reproductive performance is observed in first-generation crossbreeds (F1½UCHRM × ½D): number of inseminations per one fertilization is significantly reduced; the number of heavy calves decreases and stillborn animals. High quality in terms of lightness of hotels in combined with a low incidence of newborn calves are a good basis for economic indicators of dairy farming cattle. The results of the study will be used for determining the most effective options for further crossbreeding on a certain part of the population (not more than 30%) in order to prevent a decrease reproductive capacity and viability of local cattle from cows domestic dairy breeds It is established that at interbreeding Holstein Jersey breeds in first generation crossbreeds (F1½Г × ½Д) there is a decrease in milk yield, but an increase in fat content milk. Live weight, number of heavy calves and decreased stillborn animals. The Holstein breed is the undisputed world breed leader among specialized dairy breeds. Holstein animals intensively and effectively used to improve the majority dairy breeds in Ukraine.

Identification of polymorphisms in the oocyte-derived growth differentiation growth factor 9 (GDF9) gene associated with litter size in New Zealand sheep (Ovis aries) breeds.

Having the ability to control litter size is important for sheep farmers and breeders worldwide. However, making genetic gain in key livestock traits like reproductive performance needs typically a lot of time, and both the fecundity and fertility traits have a great economic importance. Attention has therefore turned to better understanding the genes that control reproductive performance. Of these genes, research has focussed on the growth differentiation growth factor 9 (GDF9) gene (GDF9). In this study, a PCR-single strand conformation polymorphism (PCR-SSCP) approach was used to investigate variation in this gene in separate groups of purebred Finnish Landrace sheep, Finnish Landrace×Texel-cross sheep and composite sheep of undefined breed background, but based on New Zealand Romney-type genetics. Three GDF9 variants (named A, B and C) were found, and upon DNA sequencing, the nucleotide substitutions c.978A>G, c.994G>A and c.1111G>A were revealed. The frequency of variant A (containing nucleotides c.978A, c.994G and c.1111G) in the Finnish Landrace, Finnish Landrace×Texel-cross and composite sheep was 0.86, 0.78 and 0.76, respectively. In these three sheep groups, the frequency of B (defined by the presence of nucleotides c.978G and c.994A) was 0.01, 0.03 and 0.23 and for C (containing c.1111A) was 0.13, 0.18 and 0.01, respectively. An animal model was used to estimate the additive effect of fertility data for Finnish Landrace×Texel-cross sheep and revealed an association between litter size and the c.1111G>A variation (p=.036), but this was not observed for the Finnish Landrace sheep (p=.27) or the composite sheep (p=.17). When all the sheep were analysed together, the presence of c.1111A was associated (p<.05) with increased litter size, when compared to ewes that had c.1111G. Litter size did not differ between sheep with and without c.994A in all three groups of sheep investigated. This study suggests that c.1111A could be a useful genetic marker for improving fecundity in New Zealand sheep breeds and that it could be introgressed into other breeds, but analysis of more sheep will be required to confirm the associations that have been observed here.

ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems

BackgroundMany favorable traits of crops and livestock and human genetic diseases arise from multiple single nucleotide polymorphisms or multiple point mutations with heterogeneous base substitutions at the same locus. Current cytosine or adenine base editors can only accomplish C-to-T (G-to-A) or A-to-G (T-to-C) substitutions in the windows of target genomic sites of organisms; therefore, there is a need to develop base editors that can simultaneously achieve C-to-T and A-to-G substitutions at the targeting site.ResultsIn this study, a novel fusion adenine and cytosine base editor (ACBE) was generated by fusing a heterodimer of TadA (ecTadAWT/*) and an activation-induced cytidine deaminase (AID) to the N- and C-terminals of Cas9 nickase (nCas9), respectively. ACBE could simultaneously induce C-to-T and A-to-G base editing at the same target site, which were verified in HEK293-EGFP reporter cell line and 45 endogenous gene loci of HEK293 cells. Moreover, the ACBE could accomplish simultaneous point mutations of C-to-T and A-to-G in primary somatic cells (mouse embryonic fibroblasts and porcine fetal fibroblasts) in an applicable efficiency. Furthermore, the spacer length of sgRNA and the length of linker could influence the dual base editing activity, which provided a direction to optimize the ACBE system.ConclusionThe newly developed ACBE would expand base editor toolkits and should promote the generation of animals and the gene therapy of genetic diseases with heterogeneous point mutations.

Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock.

Genome-Wide Association Studies (GWAS) in large human cohorts have identified thousands of loci associated with complex traits and diseases. For identifying the genes and gene-associated variants that underlie complex traits in livestock, especially where sample sizes are limiting, it may help to integrate the results of GWAS for equivalent traits in humans as prior information. In this study, we sought to investigate the usefulness of results from a GWAS on human height as prior information for identifying the genes and gene-associated variants that affect stature in cattle, using GWAS summary data on samples sizes of 700,000 and 58,265 for humans and cattle, respectively. Using Fisher's exact test, we observed a significant proportion of cattle stature-associated genes (30/77) that are also associated with human height (odds ratio = 5.1, p = 3.1e-10). Result of randomized sampling tests showed that cattle orthologs of human height-associated genes, hereafter referred to as candidate genes (C-genes), were more enriched for cattle stature GWAS signals than random samples of genes in the cattle genome (p = 0.01). Randomly sampled SNPs within the C-genes also tend to explain more genetic variance for cattle stature (up to 13.2%) than randomly sampled SNPs within random cattle genes (p = 0.09). The most significant SNPs from a cattle GWAS for stature within the C-genes did not explain more genetic variance for cattle stature than the most significant SNPs within random cattle genes (p = 0.87). Altogether, our findings support previous studies that suggest a similarity in the genetic regulation of height across mammalian species. However, with the availability of a powerful GWAS for stature that combined data from 8 cattle breeds, prior information from human-height GWAS does not seem to provide any additional benefit with respect to the identification of genes and gene-associated variants that affect stature in cattle.

Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review)

Copy number variations (CNVs) are repetitive genome segments, ranging from one thousand to several million base pairs and varying between individuals in a population. Due to a larger genome coverage compared to SNP markers, CNVs are important sources of genetic variation and are currently considered as an alternative type of DNA markers. The identification of CNV regions (CNVRs) which overlap with genes and quantitative trait loci (QTLs) in livestock genomes are of the greatest interest. In the review, the results of studies on CNV in various livestock species, are summarized and analyzed including the identification of candidate genes whose loci overlap with CNV regions. In addition, the methodological approaches for detection of copy number variations are briefly described. The number of identified CNVRs and a genome coverage ratio were 51-1265 and 0.5-20 % in cattle, 565 CNVRs and 5.84 % in pigs, 978 CNVR and 8.96 % in goats, 3488 CNVR and 2.7 % in sheep. Loci of functional candidate genes associated with economically significant traits overlap with CNVR in all livestock species. There were identified genes associated with growth and development indicators (MYH3 and GBP4 in cattle; ANP32B, GYS1 and CAV1 in pigs; MYLK4 in goats; SHE, BAG4, PIGY and ORMDL1 in sheep); affecting the reproductive traits and fertility (PRP1 and PRP6 in goats; PTGS1 in sheep); associated with meat productivity (KDM5B, ADAM8 and SHH in goats); responsible for various coat and skin colour phenotypes (KIT in pigs; ASIP, AHCY and ITCH in sheep and goats) and involved in the regulation of metabolic processes (PPARA, RXRA, ADD1, FASN and PPP1CA in sheep). The analysis of international experience showed that identified CNVs could be proposed as potential candidates for selection according to economically significant traits in livestock.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding.

Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.

Identification and validation of a novel candidate gene regulating net meat weight in Simmental beef cattle based on imputed next-generation sequencing.

ObjectivesGenome‐wide association studies (GWAS) represent a powerful approach to detecting candidate genes for economically important traits in livestock. Our aim was to identify promising candidate muscle development genes that affect net meat weight (NMW) and validate these candidate genes in cattle.Materials and methodsUsing a next‐generation sequencing (NGS) dataset, we applied ~ 12 million imputed single nucleotide polymorphisms (SNPs) from 1,252 Simmental cattle to detect genes influencing net meat yield by way of a linear mixed model method. Haplotype and linkage disequilibrium (LD) blocks were employed to augment support for identified genes. To investigate the role of MTPN in bovine muscle development, we isolated myoblasts from the longissimus dorsi of a bovine foetus and treated the cells during proliferation, differentiation and hypertrophy.ResultsWe identified one SNP (rs100670823) that exceeded our stringent significance threshold (P = 8.58 × 10−8) for a putative NMW‐related quantitative trait locus (QTL). We identified a promising candidate gene, myotrophin (MTPN), in the region around this SNP Myotrophin had a stimulatory effect on six muscle‐related markers that regulate differentiation and myoblast fusion. During hypertrophy, myotrophin promoted myotube hypertrophy and increased myotube diameters. Cell viability assay and flow cytometry showed that myotrophin inhibited myoblast proliferation.ConclusionsThe present experiments showed that myotrophin increases differentiation and hypertrophy of skeletal muscle cells, while inhibiting their proliferation. Our examination of GWAS results with in vitro biological studies provides new information regarding the potential application of myotrophin to increase meat yields in cattle and helpful information for further studies.

Correlations between single nucleotide polymorphisms in FABP4 and meat quality and lipid metabolism gene expression in Yanbian yellow cattle.

FABP4 is a candidate gene for carcass and meat quality traits in livestock and poultry. However, the effects of FABP4 have not been examined in the Yanbian yellow cattle, an economically important local cattle breed in China. In this study, we characterized single nucleotide polymorphisms (SNPs) in FABP4 in this cattle breed and their associations with meat quality traits. Six SNPs (referred to as SNP1-6) were identified in FABP4 by direct sequencing and polymerase chain reaction-restriction fragment length polymorphism. The six SNPs were significantly correlated with meat quality traits. In particular, the GG and GA genotypes of SNP1 were significantly associated with water and fat contents and GG and AA genotypes of SNP1 were significantly associated with protein contents (P < 0.05). The fat content and marbling in heterozygous individuals at SNP2-6 were significantly higher than those in wild-type or mutant individuals (P < 0.05), while protein content was significantly higher in wild-type and mutant individuals than in heterozygous individuals (P < 0.05). A gene expression analysis indicated that the lipid metabolism-related genes FABP4, PPARγ, ANGPTL4, and LPL show similar expression patterns with respect to FABP4 genotypes, with the highest levels in wild-type individuals and the lowest levels in mutants. In conclusion, FABP4 SNPs can be used for marker-assisted selection in Yanbian yellow cattle breeding.

A missense mutation in the coding region of the toll-like receptor 4 gene affects milk traits in Barki sheep.

ObjectiveMilk production is one of the most desirable traits in livestock. Recently, the toll-like receptor (TLR) has been identified as a candidate gene for milk traits in cows. So far, there is no information concerning the contribution of this gene in milk traits in sheep. This study was designed to investigate the TLR 4 gene polymorphisms in Barki ewes in Egypt and then correlate that with milk traits in order to identify potential single nucleotide polymorphisms (SNPs) for these traits in sheep.MethodsA part of the ovine TLR 4 gene was amplified in Barki ewes, to identify the SNPs. Consequently; Barki ewes were genotyped using polymerase chain reaction-single strand conformation polymorphism protocol. These genotypes were correlated with milk traits, which were the daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP).ResultsAge and parity of the ewe had a significant effect (p<0.05 or p<0.01) on DMY, FP, and TSP. The direct sequencing identified a missense mutation located in the coding sequence of the gene (rs592076818; c.1710C>A) and was predicted to change the amino acid sequence of the resulted protein (p.Asn570Lys). The association analyses suggested a significant effect (p<0.05) of the TLR genotype on the FP and PP, while the DMY tended to be influenced as well (p = 0.07). Interestingly, the presence of the G allele tended to increase the DMY (+40.5 g/d) and significantly (p<0.05 or p<0.01) decreased the FP (−1.11%), PP (−1.21%), and TSP (−7.98%).ConclusionThe results of this study suggested the toll-like receptor 4 (TLR4) as a candidate gene to improve milk traits in sheep worldwide, which will enhance the ability to understand the genetic architecture of genes underlying SNPs that affect such traits.

Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3′UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.

The use of poly additive Nabicat in the feeding of laying hens

In modern poultry farming the most urgent tasks are to search for and test new environmentally safe feed and economically justifi ed additives that stimulate productivity, positively aff ect the health of poultry, and consequently increase the livability of livestock and other important zootechnical traits. In order to maintain physiologically normal processes of life, metabolism and increase the level of productivity of poultry it needs mineral components and their chelated compounds. The purpose of this work was to increase the egg productivity of poultry by using the silicon-containing poly additive Nabicat in feeding young hens and laying hens. The researches have been carried out on the poultry cross Highsex Brown under the environments in CJSC “Poultry Farm “Volzhskaya” in the Sredneakhtubinsky area in the Volgograd region. In this paper, The optimal dose of the introduction of the silicon-containing poly additive Nabicat in the diets of young and laying hens of the cross Highsex Brown has been scientifi cally justifi ed and the biological value of using an organic form of silicon has been determined. The positive infl uence of the optimal dose of poly additive on growth, consumption, and digestibility, nutrient metabolism in the poultry body, as well as egg productivity and quality of the resulting egg has been revealed. Thus, the average egg productivity per 1 hen in the control group during the experiment period was 321,3 pcs., and in the 1st, 2nd and 3rd experimental groups it was 322,6 pcs., 325,8 and 325,7 pcs., which was higher than in the control group by 0,40 %, 1,40 and 1,37 %, respectively. The average egg weight in the 1st experimental group exceeded the control by 0,43 g or 0,68 %, in the 2nd experimental group by 1,16 g or 1,84 %, in the 3rd experimental group by 0,81 g or 1,28 %. The economic eff ectiveness of using the organic silicon additive in the composition of Nabicat poly additive in the feeding of laying hens has been proved. The economic eff ect due to the use of diff erent doses of the introduction of silicon-containing poly additive Nabicat in compound feed for laying hens of the 1st experimental group was 141,66 rubles, the 2nd experimental group 962,76 rubles, and the 3rd experimental group 821,89 rubles.