Production Traits In Cattle Research Articles

Polymorphisms of the SCD1 Gene and Its Association Analysis with Carcass, Meat Quality, Adipogenic Traits, Fatty Acid Composition, and Milk Production Traits in Cattle.

Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future.

A systematic review of effect of calving season and parity as non-genetic factors on milk production traits of cattle

A systematic review of effect of calving season and parity as non-genetic factors on milk production traits of cattle

129 The Relationship Between Pulmonary Arterial Pressure Expected Progeny Differences and Methane Emissions

Abstract The objective of this study was to determine the relationship between pulmonary arterial pressure (PAP) expected progeny differences (EPD) and methane emissions. Pulmonary arterial pressure is an indicator of pulmonary arterial hypertension in cattle and is especially relevant at high altitudes, with increasing importance in moderate elevation feedlot and finishing systems. Enteric methane emissions from cattle are increasingly emphasized due to their contribution of greenhouse gases in the agricultural sector. As pulmonary arterial hypertension continues to be an issue in high altitudes and feedlots, understanding relationships with methane emission rates will be useful for both concomitant selection with the goal of improving environmental sustainability. The PAP EPD data were collected on 123 total heifers (n = 37) and steers (n = 86) located on a ranch in southern Wyoming at an elevation of 2,194.56 meters. Gas emissions were collected using a GreenFeed system (C-Lock, Rapid City, South Dakota), which measures the gas fluxes of individual animals at the CSU ARDEC facility at an elevation of 1,557.53 meters. Individual animal methane emissions were measured as grams/day. A generalized linear regression model was used to regress average daily methane emissions (mean = 163.08, SD = 38.74, min = 87.72, max = 247.03) on PAP EPD (mean = -0.464, SD = 1.565, min = -6.382, max = 4.286), pen, and age in days (mean = 258.2, SD = 20.009, min = 200, max = 298). The PAP EPD (P = 0.484) did not account for a significant amount of variation in methane emissions. Additionally, the effect of pen (P < 0.05) and age (P < 0.05) were significant sources of variation for methane production. The effects of pen had a range of 60.916 units of methane emission/day (P < 0.05). Age of the individual was evaluated as a linear covariate and had a solution of 0.678 units of methane emission/day (P < 0.05), suggesting that older individuals had increased methane emissions. These results show no statistical relationship between PAP EPD and methane in these data. While preliminary results suggest that selection for low PAP EPD individuals will have no adverse effects on sustainability metrics, future research is needed to fully understand the relationship between beef cattle production traits and sustainability metrics.

Sequence-based GWAS meta-analyses for beef production traits

BackgroundCombining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations. We combined the summary statistics for four growth, nine morphology, and 15 carcass traits into 16 MA, using both fixed effects and z-score methods.ResultsThe fixed-effects method was generally more informative to provide indication on potentially causal variants, although we combined substantially different traits in each MA. In comparison with within-population GWAS, this approach highlighted (i) a larger number of quantitative trait loci (QTL), (ii) QTL more frequently located in genomic regions known for their effects on growth and meat/carcass traits, (iii) a smaller number of genomic variants within the QTL, and (iv) candidate variants that were more frequently located in genes. MA pinpointed variants in genes, including MSTN, LCORL, and PLAG1 that have been previously associated with morphology and carcass traits. We also identified dozens of other variants located in genes associated with growth and carcass traits, or with a function that may be related to meat production (e.g., HS6ST1, HERC2, WDR75, COL3A1, SLIT2, MED28, and ANKAR). Some of these variants overlapped with expression or splicing QTL reported in the cattle Genotype-Tissue Expression atlas (CattleGTEx) and could therefore regulate gene expression.ConclusionsBy identifying candidate genes and potential causal variants associated with beef production traits in cattle, MA demonstrates great potential for investigating the biological mechanisms underlying these traits. As a complement to within-population GWAS, this approach can provide deeper insights into the genetic architecture of complex traits in beef cattle.

Analysis of the impact of DGAT1 p.M435L and p.K232A variants on pre-mRNA splicing in a full-length gene assay

DGAT1 is playing a major role in fat metabolism and triacylglyceride synthesis. Only two DGAT1 loss-of-function variants altering milk production traits in cattle have been reported to date, namely p.M435L and p.K232A. The p.M435L variant is a rare alteration and has been associated with skipping of exon 16 which results in a non-functional truncated protein, and the p.K232A-containing haplotype has been associated with modifications of the splicing rate of several DGAT1 introns. In particular, the direct causality of the p.K232A variant in decreasing the splicing rate of the intron 7 junction was validated using a minigene assay in MAC-T cells. As both these DGAT1 variants were shown to be spliceogenic, we developed a full-length gene assay (FLGA) to re-analyse p.M435L and p.K232A variants in HEK293T and MAC-T cells. Qualitative RT-PCR analysis of cells transfected with the full-length DGAT1 expression construct carrying the p.M435L variant highlighted complete skipping of exon 16. The same analysis performed using the construct carrying the p.K232A variant showed moderate differences compared to the wild-type construct, suggesting a possible effect of this variant on the splicing of intron 7. Finally, quantitative RT-PCR analyses of cells transfected with the p.K232A-carrying construct did not show any significant modification on the splicing rate of introns 1, 2 and 7. In conclusion, the DGAT1 FLGA confirmed the p.M435L impact previously observed in vivo, but invalidated the hypothesis whereby the p.K232A variant strongly decreased the splicing rate of intron 7.

Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China

In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.

Copy number variation of bovine DYNC1I2 gene is associated with body conformation traits in chinese beef cattle.

Previous, studies have shown that the dynein transporter compound has a role in diseases such as intellectual disability and cerebral malformations. However, the study of CNV in DYNC1I2 gene has not been reported. Q-PCR and data association analysis were used for DYNC1I2 gene copy in this study. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for DYNC1I2 gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. Association analysis indicate that CNV of DYNC1I2 gene showed a positive effect in cattle growth: in XN cattle, individuals with deletion types showed better performance on height at hip cross (P<0.05); individuals with duplication types have better performance on body length (P<0.05) in PN cattle; individuals with deletion types was significantly correlated with chest width and Hucklebone width (P<0.05) in QC cattle; individuals with duplication types in Yunling cattle were better than the normal types, and there was a significant correlation between copy number variant and chest depth (P<0.05). The results showed that CNV markers closely related to cattle production traits were detected at DNA level, which could be used as an important candidate molecular marker for marker-assisted selection of growth traits in Chinese cattle, and provided a new research basis for genetics and breeding of Chinese beef cattle.

Estimation of co-variance components and genetic parameters of fertility and production traits in crossbred cattle of Kerala

Estimation of co-variance components and genetic parameters of fertility and production traits will help to find out the relative importance of genetic and environmental components of each trait and to develop a genetic evaluation system for overall improvement in performances of crossbred cattle of Kerala. In the present study, major fertility trait considered was daughters pregnancy rate (DPR), measures the percentage of non-pregnant animals that become pregnant during each oestrous cycle. Data pertaining to 1180 crossbred cattle sired by 208 Frieswal bulls, spread over a period of 16 years from 2003 to 2019, maintained at different farms of Kerala Veterinary and Animal Sciences University and field centres of ICAR- Filed Progeny Testing Scheme were analysed in the study. Estimates of covariance components and genetic parameters were obtained using restricted maximum likelihood (REML) approach using average information (AI) algorithm. It was observed that DPR had low heritability (0.092 ± 0.03), compared to 305 days milk yield (MY) (0.170 ± 0.094) and fat percent (FP) (0.173 ± 0.072). Phenotypic (rp), genetic (rg) and residual (re) correlation indicated unfavourable association of fertility with production traits. The estimates of variance and (co)variance components were computed by multivariate animal model. The results indicated that DPR was having lower direct additive (σ2a) 0.046 and environmental variance (σ2c) 0.063 compared to other traits. Highest additive genetic variance (σ2a) 27035.8 was obtained for MY. The study estimates the magnitude of correlations and covariances of fertility and production traits. Since DPR had lower additive genetic variance and negative association with milk production traits in cattle, it would be included as an indirect measure in the evaluation and breeding programs of crossbred cattle of Kerala.

A Meta-Analysis of the Associations Between Prolactin (PRL) Gene Polymorphism and Milk Production Traits in Cattle

A Meta-Analysis of the Associations Between Prolactin (PRL) Gene Polymorphism and Milk Production Traits in Cattle

Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits.

Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.

Single nucleotide polymorphisms in the bovine SLC2A12 and SLC5A1 glucose transporter genes – the effect on gene expression and milk traits of Holstein Friesian cows

In this study, novel single nucleotide polymorphisms (SNPs) were found in the 5′-regulatory regions (promoters) of the bovine glucose transporter (GT) genes SLC2A12 and SLC5A1. These polymorphisms were shown to associate with certain milk production traits in HF cows, including milk yield, milk composition, and somatic cell count. It was shown that the SNP g.-671C > G (NC_037336.1: g.72224078C > G) in the SLC2A12 gene could be an effective marker of cattle production traits and that genotypes CC and CG are associated with the best productivity. The polymorphisms found in the SLC5A1 gene promoter also influenced milk production traits in HF cows, albeit to a lesser extent, and we propose that these polymorphisms could be useful as genetic markers for milk production traits in marker-assisted selection (MAS); however, this must be confirmed on larger populations of cattle. In addition, the presence of polymorphisms within promoter regions appears to affect the expression of GT genes in the cow mammary gland and modify transcription factor (TF) binding capacity.

The effect of single-nucleotide polymorphism in the promoter region of bovinealpha-lactalbumin(LALBA) gene onLALBAexpression in milk cells and milk traits of cows

Polymorphisms of milk protein genes have been proposed as candidate markers for dairy production traits in cattle. In the present study, a polymorphism was detected in the 5'-flanking (promoter) region of the bovine alpha-lactalbumin (LALBA) gene, a T/C transition located at nucleotide -1,001 relative to the transcription start site g.-1001T > C (NC_037332.1:g.31183170T > C), which is recognizable with PstI restriction endonuclease. In silico analyses showed that this mutation created novel retinoid X receptor alpha and vitamin D receptor transcription factor binding sites. Real-time PCR found that cows with different genetic variants of the promoter demonstrated different levels of expression of LALBA mRNA in milk somatic cells (MSCs). The TT genotype cows demonstrated low expression, whereas those with CT demonstrated much higher expression (P < 0.05). ELISA analysis found milk LALBA protein levels also differed between the TT and CT cows (P < 0.05) and that these levels were not correlated with the mRNA abundance in MSC. Association analysis found that the g.-1001T > C polymorphism in the promoter region of the LALBA gene influenced milk production traits in Polish Holstein-Friesian cows. High daily milk yield and dry matter yield, and high lactose yield and concentration were associated with the TT genotype. The TT genotype cows also had a lower number of somatic cells in the milk, considered as an indicator of udder health status. Therefore, the TT genotype could be more desirable from the breeder's perspective.

Gene Editing for Improved Animal Welfare and Production Traits in Cattle: Will This Technology Be Embraced or Rejected by the Public?

Integrating technology into agricultural systems has gained considerable traction, particularly over the last half century. Agricultural systems that incorporate the public’s concerns regarding farm animal welfare are more likely to be socially accepted in the long term, a key but often forgotten component of sustainability. Gene editing is a tool that has received considerable attention in the last five years, given its potential capacity to improve farm animal health, welfare, and production efficiency. This study aimed to explore the attitudes of Brazilian citizens regarding the applications of gene editing in cattle that generate offspring without horns; are more resistant to heat; and have increased muscle tissue. Using a mixed-methods approach, we surveyed participants via face-to-face, using in-depth interviews (Study 1) and an online questionnaire containing closed-ended questions (Study 2). Overall, the acceptability of gene editing was low and in cases where support was given it was highly dependent on the type and purpose of the application proposed. Using gene editing to improve muscle tissue growth was viewed as less acceptable compared to using gene editing to reduce heat stress or to produce hornless cattle. Support declined when the application was perceived to harm animal welfare, to be profit motivated or to reinforce the status quo of intensive livestock systems. The acceptability of gene editing was reduced when perceptions of risks and benefits were viewed as unevenly or unfairly distributed among consumers, corporations, different types of farmers, and the animals. Interviewees did not consider gene editing a “natural” process, citing dissenting reasons such as the high degree of human interference and the acceleration of natural processes. Our findings raised several issues that may need to be addressed for gene editing to comply with the social pillar of sustainable agriculture.

Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed.

Milk production phenotypes are the main focus of genetic selection in dairy herds, and although there are many genes identified as related to the biology of these traits in pure breeds, little is known about crossbreed animals. This study aimed to identify potential genes associated with the 305-day milk yield in 337 crossbreed Gir × Holstein (Girolando) animals. Milk production records were genotyped for 45,613 single-nucleotide polymorphisms (SNPs). This dataset was used for a genome-wide association study (GWAS) using the 305-day milk yield adjusted for the fixed effects of herd and year and linear and quadratic effects of age at calving (in days) and calving factor averaged per animal. Genes within the significant SNPs were retrieved from the Bos taurus ARS-UCD1.2 assembly (bosTau9) for gene ontology analysis. In summary, the GWAS identified 52 SNPs associated [p ≤ 10–4, false discovery rate (FDR) = 8.77%] with milk production, including NUB1 and SLC24A2, which were previously described as related to milk production traits in cattle. The results suggest that SNPs associated mainly with NUB1 and SLC24A2 could be useful to understand milk production in Girolando and used as predictive markers for selecting genetic predisposition for milk yield in Girolando.

Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits.

Simple SummaryWith the rapid development of information technology and molecular biotechnology, animal molecular breeding technology is playing an increasingly important role in beef cattle breeding. Prosaposin (PSAP) is involved in regulating the growth and development of animals, and it is reported that PSAP is an important marker-assisted selection (MAS) in cattle herd. The purpose of this study was to explore the novel variants in 3’ UTR of cattle PSAP and evaluate their effects on the morphological traits of four Chinese cattle breeds. In this study, 13 variants were identified in the PSAP 3’ UTR from 501 individuals belonging to four cattle breeds. In Nanyang cattle, the distribution of haplotypes was different from the other three breeds. Two groups of haplotypes had association with morphological traits by changing the secondary structures of PSAP 3’ UTR rather than the miR-184 target sites. This study not only expands the genetic variation spectrum of cattle PSAP but also contributes to MAS genetics and breeding of Chinese cattle breeds.The purpose of this study was to explore functional variants in the prosaposin (PSAP) three prime untranslated region (3’ UTR) and clarify the relationship between the variants and morphological traits. Through Sanger sequencing, 13 variations were identified in bovine PSAP in four Chinese cattle breeds, with six of them being loci in 3’ UTR. In particular, Nanyang (NY) cattle had a special genotype and haplotype distribution compared to the other three breeds. NY cattle with ACATG and GCGTG haplotypes had higher morphological traits than GTACA and GTACG haplotypes. The results of dual-luciferase reporter assay showed that ACATG and GCGTG haplotypes affected the morphological traits of NY cattle by altering the secondary structure of PSAP 3’ UTR rather than the miR-184 target sites. The findings of this study could be an evidence of a complex and varying mechanism between variants and animal morphological traits and could be used to complement candidate genes for molecular breeding.

GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle.

Simple SummaryUnderstanding the genetic architecture underlying milk production traits in cattle is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we performed a genome-wide association study for milk production and quality traits in Holstein cattle. In the total of ten significant single-nucleotide polymorphisms (SNPs) associated with milk fat and protein, six are located in previously reported quantitative traits locus (QTL) regions. The study not only identified the effect of DGAT1 gene on milk fat and protein but also found several novel candidate genes. In addition, some pleiotropic SNPs and QTLs were identified that associated with more than two traits, these results could provide some basis for molecular breeding in dairy cattle.High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10−7), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.

Exploration of Neuropeptide Y Gene Variants and its Association with Growth, First Lactation Reproduction and Production Traits in Sahiwal Cattle

Background: Neuropeptide Y (NPY), a 36-AA neurotransmitter involved in the control of appetite, feeding and energy homeostasis. The bovine NPY gene is located on chromosome 4 and consists of four exons. Earlier studies have reported that genes involved in feed intake regulation, energy production and energy regulation may affect different growth and production traits in cattle. Information associating NPY SNP to reproduction and production traits in dairy cattle is, however, limited. Hence, the present study was planned to explore SNPs in NPY gene and its possible association with reproduction and first lactation production traits in Sahiwal cattle. Methodology: DNA samples were isolated from blood that has collected from hundred and three Sahiwal cows. Three regions of NPY were amplified using designed primer pairs. The sequencing of the targeted regions was done in 103 Sahiwal cows. Least squares analysis of variance was carried out for unequal and non-orthogonal data using the technique described by Harvey (1990) to study effect of non-genetic factors. Significance of differences based on genotypes effect of growth, reproduction and production traits were tested by general linear models.Result: Sequence data analysis revealed two transversions in NPY gene. For these identified nucleotide variations, positions were A72073973C (intron 3) and C72068620A (intron 3). This is the first report of the presence of NPY gene polymorphism in purebred Bos indicus of Indian origin. For SNP A72073973C, performances of animals with homozygote AA genotype exhibited significantly higher milk production (P≤0.01) and growth performance (P≤0.05) than heterozygote genotype. Heterozygous genotype exhibited superior performance for the SNP C72068620A which was found to be significantly associated (P≤0.05) with 18M wt, WFS, WFC, FCI and FL305DMY.

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

BackgroundThe cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.ResultsA total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations’ historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds.ConclusionThe current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.

Across-breed genomic prediction for body weight in Siberian cattle populations

Body weight (BW) is an important heritable phenotype and related to other functional and production traits in cattle. The past decade has seen an increase in emphasis on genome wide association studies (GWAS) for detecting single nucleotide polymorphisms (SNPs) that are associated with quantitative phenotypes. Prediction of phenotypes using across-breed GWAS information [genomic prediction (GP)] is an also important research area but received less attention from the community. Understanding the link between major genes and common ancestors within and between breeds will contribute to a deeper understanding of GP across breeds. The aims of the present study were two-fold: 1) to examine genetic structure and to detect associated SNPs for BW using various single and multiple locus genomic models and 2) genomic prediction of BW using Siberian cattle populations based on across-breed genomic information. The most obvious finding to emerge from this study was the increase in the across-GP accuracy when gene segregation in both related populations was found. These findings have significant implications for the understanding of the way in which common ancestors and/or the presence of quantitative trait loci might affect the accuracy of the GP results.

MALDI–TOF-MS-based high throughput genotyping of mutations associated with body measurement traits in cattle

Exploration of genes in relation to body measurement traits through large-scaled mutation identification is highly conductive for the genomics-assisted breeding of superior productivity cattle. In this investigation, 31 objective mutations were genotyped synchronously in 384 yellow cattle of 8 breeds through the application of optimized MALDI-TOF-MS and multiplex PCR techniques. High genotyping rate was obtained as well as greatly decreased cost which was below one thirtieth of the routine analysis. Results from genotyping revealed 23 mutations as valid mutations in the studied cattle population with gene heterozygosity and effective allele number varying from 0.0052 to 0.4998 and 1.0052 to 1.9991, respectively. Among the 23 effective mutations, 12 was classified as moderate polymorphism (0.25 < PIC < 0.5) while the other 11 belonged to low polymorphism (PIC < 0.25), 7 mutations did not obey the HW equilibrium (p < 0.05) and linkage mainly appeared between mutations of UCP2 and PTHR1 genes. Furthermore, 8 body measurement traits in the 384 cattle were recorded to validate their association with tag mutations, and significant correlations were found in 12 mutations of 9 genes including PTHR1, CDK6, IHH, HHIP, GHRL, COL1A1, INS, GDF5 and UCP2, of which, PTHR1 was proved to be the most potential contributor to bone modeling in cattle. Results highlight the potential application value of 12 novel mutations in enhancing cattle production traits as well as the high genotyping rate achieved by MALDI-TOF-MS coupled with multiplex PCR technique.