Detection of quantitative trait loci for meat quality traits in cattle

Comparative characteristics of the genetic structure of the Syrian cattle breed compared to Holstein and Aberdeen-Angus breeds

OBJECTIVES

The objective of this study was to perform a comparative analysis of allelic diversity to reveal population-genetic characteristics of animal breeds, namely Shami (SH), Holstein (HLS), and Aberdeen-Angus (A-A).

MATERIALS AND METHODS

The genetic materials of SH breed animals represented by wool with hair follicles were collected from 39 SH heads in Syria. Also, genetic materials of HLS breed of American selection (n = 55, HLS) and bulls and cows of A-A breed bred at breeding enterprises in Russia (n = 30, A-A) were collected. Genetic differences between the cattle groups were studied using 11 microsatellite markers.

RESULTS

The cattle breed in Syria was characterized by high genetic diversity, 107 alleles, while the average number of alleles per microsatellite locus was 9.23, which is significantly higher than that in the animals of HLS (6.18) and A-A (5.00). When analyzing the genetic equilibrium for individual locus in SH breed, a deviation from equilibrium at four loci was revealed: TGLA227, SPS115, TGLA122, and ETH225; at one locus in HLS breed: SPS115, for A-A breed: at two loci, i.e., TGLA122 and ETH225. When assessing the level of genetic consolidation, a deficiency of heterozygotes was observed in two of the three studied breeds: 4.8% for SH and 8.0% for A-A. A slight excess of heterozygotes was found in the HLS breed at the level of 0.2%. The average comparative measurement of genetic variation in different populations value for 11 loci for all breeds was 0.069, which indicates that 93.1% of the total variability is due to the intra-breed diversity, and only 6.9% is due to the differences between breeds.

CONCLUSION

The analysis of the animals belonging to their breed has shown a 100% genetic consolidation and the compliance of individual animals with the respective breeds. The study of genetic distances, adjusted for small samples, revealed the smallest genetic distance between the SH breed and HLS breed, equaling 0.107. The A-A breed, which has its separate origin and has never been imported into the Syrian Arab Republic, adjoins this cluster as an independent branch. Microsatellites can be used as an essential criterion for assessing the population-genetic characteristics of groups of cattle of various breeds (degree of polymorphism, level of heterozygosity, fixation indices, genetic group membership).

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities

Previous research regarding Holstein cows has mainly focused on increasing milk yield. However, in order to maximize the economical profits of Holstein cattle farming, it is necessary to fully take advantage of Holstein bulls to produce high-grade beef. The present study aims to investigate different transcriptomic profiling of Holstein bulls and steers, via high-throughput RNA-sequencing (RNA-seq). The growth and beef quality traits of Holstein steers and bulls were characterized via assessment of weight, rib eye area, marbling score, shear force and intramuscular fat percentage of the longissimus lumborum (LL) muscle. The results indicated that castration improved the meat quality, yet reduced the meat yield. Subsequently, RNA-seq of the LL muscle from Holstein steers and bulls revealed a total of 56 differentially expressed genes (DEGs). We performed the functional enrichment analysis in Gene Ontology (GO) annotations of the DEGs using GOseq R package software and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using KOBAS tool. Through the integrated analysis of DEGs with reported QTLs and SNPs, seven promising candidate genes potentially affecting the beef quality of LL muscle following castration were discovered, including muscle structural protein coding genes (MYH1, MYH4, MYH10) and functional protein coding genes (GADL1, CYP2R1, EEPD1, SHISA3). Among them, MYH10, GADL1, CYP2R1, EEPD1 and SHISA3 were novel candidate genes associated with beef quality traits. Notably, EEPD1 was associated with both meat quality and reproduction traits, thus indicating its overlapping role in responding to hormone change, and subsequently inducing beef quality improvement. Our findings provide a complete dataset of gene expression profile of LL in Holstein bulls and steers, and will aid in understanding how castration influence meat yield and quality.

Assessing selection signatures within and between selected lines of dual-purpose black and white and German Holstein cattle

The aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual-purpose black and white (DSN) population, as well as from generated sub-populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East-DSN and West-DSN sub-populations. In addition, two further sub-populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross-population extended haplotype homozygosity methodology (XP-EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright's fixation index (F_ST ). Chromosomal segments for the top 0.1 percentile of negative or positive XP-EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP-EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP-EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29-38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average F_ST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.

Genetic Polymorphisms in LTF/EcoRI and TLR4/AluI loci as candidates for milk and reproductive performance assessment in Holstein cattle

The aim of this study was to explore the genetic polymorphisms in LTF/EcoRI and TLR4/AluI loci and their association with milk and reproductive performance in Holstein cattle. A randomly selected 800 Holstein dairy cows from two dairy farms (400 animals each) in Egypt were used. Based on the two farm records, association between LTF/EcoRI genotypes and milk performance traits (order of lactation, daily milk yield, days in milk, corrected milk at 305 day and dry period) was carried out. Meanwhile, exploring of TLR4/AluI genotypes effect was done on data for reproductive performance (age at first freshening, calving interval, number of services per conception, ovarian rebound and days open). DNA was extracted from blood samples collected from Holstein dairy cows of the both farms and restriction analysis of 301-bp PCR products of LTF gene revealed two genotypes: AA genotype (301 bp) and AB genotype (301, 201 and 100 bp). Meanwhile, restriction analysis of 382-bp PCR products of TLR4 gene digested with AluI yielded two alleles (A and B) and three genotypes (AA, AB and BB). The A allele was indicated by two bands at 300 and 82 bp, and the B allele resulted in three fragments of 160, 140 and 82 bp. There was a significant association (p ≤ 0.05) between LTF genotypes and milk performance traits except for days in milk. The TLR4 genotypes had significant effects (p ≤ 0.05) on age at first freshening, calving interval, number of services per conception, ovarian rebound and days open. Ordinal logistic regression statistical model also revealed that it is possible to calculate high reproductive performance traits and to predict favourable dairy cows based on LTF and TLR4 genotypes. This research reveals the effectiveness of LTF/EcoRI and TLR4/AluI loci as candidates for reproductive performance assessment in Holstein cattle.

TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Factors influencing bovine intramuscular adipose tissue development and cellularity

Appearance, distribution, and amount of intramuscular fat (IMF), often referred to as marbling, are highly variable and depend on environmental and genetic factors. On the molecular level, the concerted action of several drivers, including hormones, receptors, transcription factors, etc., determines where clusters of adipocytes arise. Therefore, the aim of future studies remains to identify such factors as biological markers of IMF to increase the ability to identify animals that deposit IMF early in age to increase efficiency of high-quality meat production. In an attempt to unravel the cellular development of marbling, we investigated the abundance of markers for adipogenic differentiation during fattening of cattle and the transcriptome of muscle and dissected IMF. Markers of different stages of adipogenic differentiation are well known from cell culture experiments. They are usually transiently expressed, such as delta-like homolog 1 (DLK1) that is abundant in preadipocytes and absent during differentiation to mature adipocytes. It is even a greater challenge to detect those markers in live animals. Within skeletal muscles, hyperplasia and hypertrophy of adipocytes can be observed throughout life. Therefore, development of marbling requires, on the cellular level, recruitment, proliferation, and differentiation of adipogenic cells to store excess energy in the form of lipids in new cells. In a recent study, we investigated the localization and abundance of early markers of adipogenic differentiation, such as DLK1, in bovine muscle tissue. An inverse relationship between IMF content and number of DLK1-positive cells in bovine muscle was demonstrated. Considering the cellular environment of differentiating adipocytes in muscle and the secretory action of adipocytes and myocytes, it becomes obvious that cross talk between cells via adipokines and myokines may be important for IMF development. Secreted proteins can act on other cells, inhibiting or stimulating their function via autocrine and paracrine actions. Such factors with potential influence on IMF, among them, agouti signaling protein and thrombospondin 4, were identified in transcriptome analyses and further investigated. Furthermore, results from transcriptome analysis indicate involvement of genes that are not directly related to adipogenesis and lipid metabolism, providing new candidates for future research.

Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle

Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms and genes that lead to complex phenotypes, like meat quality, and the nutritional and healthfulness value of beef. Improvements in genome annotation and knowledge of gene function will contribute to more comprehensive analyses that will advance our ability to dissect the complex architecture of complex traits.

Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo

The Fas (APO-1, TNFRSF6) gene known as a member of the tumor necrosis factor receptor superfamily was selected for DNA marker development in Korean cattle. It is a cell membrane protein and mediates programmed cell death (apoptosis). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers related to economical traits at the genomic level. The sequences of whole exon and 1 kb range of both front and back of the gene were determined by direct-sequencing methods using 24 cattle. A total of 55 SNPs were discovered and we selected 31 common polymorphic sites considering their allele frequencies, haplotype-tagging status and linkage disequilibrium (LD) for genotyping in larger-scale subjects. The SNPs were confirmed genotype through the SNaPshot method (n = 274) and were examined for a possible genetic association between Fas polymorphisms and marbling score. So, the SNPs that were identified significant are g.30256G>C, g.31474C>A, g.31940A>G, and g.32982G>A. These results suggest that SNPs of Fas gene were associated with intramuscular fat content of meat quality traits in Korean cattle.

Novel SNP in the coding region of the FTO gene is associated with marbling score in Hanwoo (Korean cattle)

The fat mass and obesity associated (FTO) gene plays an important role in the regulation of energy homeostasis, fat deposition and obesity. For this reason, the FTO gene is a physiological and functional candidate gene for carcass and meat quality traits in beef cattle. The objectives of this study were to identify SNPs in the exonic regions of FTO gene and to evaluate the association of these SNPs with carcass traits in Hanwoo (Korean cattle). In this study, we newly identified two exonic SNPs in Hanwoo population. The g.125550A > T SNP was located in exon 3 and the g.175675C > T SNP was located in exon 6. Genotyping of the two SNP markers was carried out using PCR-RFLP analysis in Hanwoo steers to evaluate their association with carcass traits. As a result, g.125550A > T SNP genotype was significantly associated with effects on marbling score. Animals with the AA and TT homozygous genotypes had a significantly higher marbling score (p < 0.001) than those with AT heterozygous genotype, and this was significant after Bonferroni correction of the significance threshold (p = 0.003). Dominance effect was also observed for the marbling score (P < 0.05) with higher marbling score of homozygous animals. However, no significant associations with meat quality traits were observed for the g.175675C > T SNP. Our results suggest that the exonic SNP g.125550A > T in the FTO gene may be used as a DNA marker for the selection of Hanwoo with higher marbling.

A whole genome association study on meat palatability in hanwoo

A whole genome association (WGA) study was carried out to find quantitative trait loci (QTL) for sensory evaluation traits in Hanwoo. Carcass samples of 250 Hanwoo steers were collected from National Agricultural Cooperative Livestock Research Institute, Ansung, Gyeonggi province, Korea, between 2011 and 2012 and genotyped with the Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip. Among the SNPs in the chip, a total of 322,160 SNPs were chosen after quality control tests. After adjusting for the effects of age, slaughter-year-season, and polygenic effects using genome relationship matrix, the corrected phenotypes for the sensory evaluation measurements were regressed on each SNP using a simple linear regression additive based model. A total of 1,631 SNPs were detected for color, aroma, tenderness, juiciness and palatability at 0.1% comparison-wise level. Among the significant SNPs, the best set of 52 SNP markers were chosen using a forward regression procedure at 0.05 level, among which the sets of 8, 14, 11, 10, and 9 SNPs were determined for the respectively sensory evaluation traits. The sets of significant SNPs explained 18% to 31% of phenotypic variance. Three SNPs were pleiotropic, i.e. AX-26703353 and AX-26742891 that were located at 101 and 110 Mb of BTA6, respectively, influencing tenderness, juiciness and palatability, while AX-18624743 at 3 Mb of BTA10 affected tenderness and palatability. Our results suggest that some QTL for sensory measures are segregating in a Hanwoo steer population. Additional WGA studies on fatty acid and nutritional components as well as the sensory panels are in process to characterize genetic architecture of meat quality and palatability in Hanwoo.

Modeling tenderness for genetic and quantitative trait loci analyses

Tenderness is the one of the most important attributes of beef with regards to the intent of consumers to repurchase. Beef tenderness is frequently measured objectively as Warner-Bratzler shear force. However, to better understand the genetics underlying tenderness, better descriptors were derived herein. Two traits, adjusted shear force and aging rate, were calculated to incorporate measures of Warner-Bratzler shear force repeated over aging time of 2 muscles, longissimus dorsi (LD) and semitendinosus (ST). Analysis of these traits indicated that the shear forces of the 2 muscles are lowly correlated and aging rate, as calculated, was not correlated with adjusted shear force. Breed, SNP, and QTL effects were analyzed for the 4 traits (2 traits × 2 muscles). For adjusted shear force, the QTL were located on cattle chromosomes BTA 5, 18, 25, and 29. With the exception of the QTL on BTA 5, the adjusted shear force QTL were observed for either the LD or the ST but not both muscles. The QTL for aging rate were located on BTA 1, 4, 7, 11, 13, 19, and 20.

Genome-wide association analyses for carcass quality in crossbred beef cattle

Background

Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle.

This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR).

Results

At the genome wide level false discovery rate (FDR < 10%), eight SNP were found significantly associated with HCW. Seven of these SNP were located on Bos taurus autosome (BTA) 6. At a less stringent significance level (P < 0.001), 520 SNP were found significantly associated with mostly individual traits (473 SNP), and multiple traits (47 SNP). Of these significant SNP, 48 were located on BTA6, and 22 of them were in association with hot carcass weight. There were 53 SNP associated with percentage of rib bone, and 12 of them were on BTA20. The rest of the significant SNP were scattered over other chromosomes. They accounted for 1.90 - 5.89% of the phenotypic variance of the traits. A region of approximately 4 Mbp long on BTA6 was found to be a potential area to harbor candidate genes influencing growth. One marker on BTA25 accounting for 2.67% of the variation in LM7D may be worth further investigation for the improvement of beef tenderness.

Conclusion

This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting carcass quality traits in beef cattle. It also revealed many SNP that acted pleiotropically to affect carcass quality. This knowledge is important in selecting subsets of SNP to improve the performance of beef cattle.

Genome scan for meat quality traits in Nelore beef cattle

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

Genome-wide association analyses for growth and feed efficiency traits in beef cattle

A genome-wide association study using the Illumina 50K BeadChip included 38,745 SNP on 29 BTA analyzed on 751 animals, including 33 purebreds and 718 crossbred cattle. Genotypes and 6 production traits: birth weight (BWT), weaning weight (WWT), ADG, DMI, midtest metabolic BW (MMWT), and residual feed intake (RFI), were used to estimate effects of individual SNP on the traits. At the genome-wide level false discovery rate (FDR < 10%), 41 and 5 SNP were found significantly associated with BWT and WWT, respectively. Thirty-three of them were located on BTA6. At a less stringent significance level (P < 0.001), 277 and 27 SNP were in association with single traits and multiple traits, respectively. Seventy-three SNP on BTA6 and were mostly associated with BW-related traits, and heavily located around 30 to 50Mb. Markers that significantly affected multiple traits appeared to impact them in same direction. In terms of the size of SNP effect, the significant SNP (P < 0.001) explained between 0.26 and 8.06% of the phenotypic variation in the traits. Pairs of traits with low genetic correlation, such as ADG vs. RFI or DMI vs. BWT, appeared to be controlled by 2 groups of SNP; 1 of them affected the traits in same direction, the other worked in opposite direction. This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting growth and feed efficiency traits in beef cattle.

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Background

Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal’s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.

Results

The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.

Conclusions

These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.

Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle

Farm animals remain at risk of endemic, exotic and newly emerging viruses. Vaccination is often promoted as the best possible solution, and yet for many pathogens, either there are no appropriate vaccines or those that are available are far from ideal. A complementary approach to disease control may be to identify genes and chromosomal regions that underlie genetic variation in disease resistance and response to vaccination. However, identification of the causal polymorphisms is not straightforward as it generally requires large numbers of animals with linked phenotypes and genotypes. Investigation of genes underlying complex traits such as resistance or response to viral pathogens requires several genetic approaches including candidate genes deduced from knowledge about the cellular pathways leading to protection or pathology, or unbiased whole genome scans using markers spread across the genome. Evidence for host genetic variation exists for a number of viral diseases in cattle including bovine respiratory disease and anecdotally, foot and mouth disease virus (FMDV). We immunised and vaccinated a cattle cross herd with a 40-mer peptide derived from FMDV and a vaccine against bovine respiratory syncytial virus (BRSV). Genetic variation has been quantified. A candidate gene approach has grouped high and low antibody and T cell responders by common motifs in the peptide binding pockets of the bovine major histocompatibility complex (BoLA) DRB3 gene. This suggests that vaccines with a minimal number of epitopes that are recognised by most cattle could be designed. Whole genome scans using microsatellite and single nucleotide polymorphism (SNP) markers has revealed many novel quantitative trait loci (QTL) and SNP markers controlling both humoral and cell-mediated immunity, some of which are in genes of known immunological relevance including the toll-like receptors (TLRs). The sequencing, assembly and annotation of livestock genomes and is continuing apace. In addition, provision of high-density SNP chips should make it possible to link phenotypes with genotypes in field populations without the need for structured populations or pedigree information. This will hopefully enable fine mapping of QTL and ultimate identification of the causal gene(s). The research could lead to selection of animals that are more resistant to disease and new ways to improve vaccine efficacy.

Allelic polymorphism detected in the bovine FTO gene

Studies in humans have independently identified single nucleotide polymorphisms (SNPs) in the fat mass and obesity associated (FTO) gene associated with obesity in multiple populations. It was shown that FTO participated in the regulation of energy homeostasis and associated with increased lipolytic activity in adipocytes. To ascertain whether there were mutations in the bovine FTO gene, this study investigated the variation of the FTO gene through PCR-SSCP and sequencing. Five synonymous mutations, two missense mutations, and three intronic SNPs were identified in 614 cattle from five independent populations. Haplotype frequencies and linkage disequilibrium (LD) coefficients of these SNPs in three Chinese indigenous cattle breeds were analyzed. Two LD blocks were found in the Qinchuan and Nanyang cattle breeds and three LD blocks were found in the Jiaxian cattle breed, suggesting the possibility of a recombination hotspot between exon 5 and intron 5 of the bovine FTO gene. The variations detected here might have an impact on the FTO gene activity and function.

Quantitative trait loci associated with the immune response to a bovine respiratory syncytial virus vaccine

Infectious disease is an important problem for animal breeders, farmers and governments worldwide. One approach to reducing disease is to breed for resistance. This linkage study used a Charolais-Holstein F2 cattle cross population (n = 501) which was genotyped for 165 microsatellite markers (covering all autosomes) to search for associations with phenotypes for Bovine Respiratory Syncytial Virus (BRSV) specific total-IgG, IgG1 and IgG2 concentrations at several time-points pre- and post-BRSV vaccination. Regions of the bovine genome which influenced the immune response induced by BRSV vaccination were identified, as well as regions associated with the clearance of maternally derived BRSV specific antibodies. Significant positive correlations were detected within traits across time, with negative correlations between the pre- and post-vaccination time points. The whole genome scan identified 27 Quantitative Trait Loci (QTL) on 13 autosomes. Many QTL were associated with the Thymus Helper 1 linked IgG2 response, especially at week 2 following vaccination. However the most significant QTL, which reached 5% genome-wide significance, was on BTA 17 for IgG1, also 2 weeks following vaccination. All animals had declining maternally derived BRSV specific antibodies prior to vaccination and the levels of BRSV specific antibody prior to vaccination were found to be under polygenic control with several QTL detected.

Heifers from the same population (n = 195) were subsequently immunised with a 40-mer Foot-and-Mouth Disease Virus peptide (FMDV) in a previous publication. Several of these QTL associated with the FMDV traits had overlapping peak positions with QTL in the current study, including the QTL on BTA23 which included the bovine Major Histocompatibility Complex (BoLA), and QTL on BTA9 and BTA24, suggesting that the genes underlying these QTL may control responses to multiple antigens. These results lay the groundwork for future investigations to identify the genes underlying the variation in clearance of maternal antibody and response to vaccination.

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds

We performed a genome-wide association study for Warner–Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within μ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31–0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.

Genetic association of phosphodiesterase 1B (PDE1B) with carcass traits in Korean cattle

Quantitative trait loci for fat deposition and carcass traits have been identified in the vicinity of the gene encoding phosphodiesterase 1B (PDE1B) on bovine chromosome 5. Therefore, the PDE1B gene can be considered as a positional and functional candidate gene for carcass traits in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the PDE1B gene and to evaluate their associations with carcass traits in Korean cattle. Eight SNPs, g.440T>G, g.17122A>G, g.17507A>C, g.17575A>G, g.17607T>C, g.17609C>A, g.17692C>T, and g.17707C>G, were identified in the region ranged from exon 1 to intron 6. Five of them were used for association analysis because of their availability of restriction fragment length polymorphisms. As a result, g.17122A>G in intron 3 was significantly associated with backfat thickness (BFT), and g.17507A>C in exon 5 was associated with longissimus dorsi muscle area (LMA, P < 0.05). Animals with the AG genotype of g.17122 had thicker BFT than those with the AA genotype. Animals with the AA or AC genotype of g.17507A>C had larger LMA than those with the CC genotype. We suggested the PDE1B gene as a candidate gene for carcass traits of beef cattle. Fine mapping would be required for application to marker-assisted selection.

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole-genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4-5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome-wise basis, in combined-sire (seven QTL) or within-sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome-wise basis, in combined-sire (five QTL) or within-sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin-derived and Jersey-derived alleles on these two chromosomes, respectively.

Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations

BACKGROUND

Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diversifying selection. Such regions may contain genes of large phenotypic effect. However, few studies have attempted to address the power or efficacy of such an approach.

RESULTS

In this study, the patterns of allele frequency differences between two cattle breeds based on the Bovine HapMap study were compared with statistical evidence for QTL based on a linkage mapping study of an experimental population formed by a cross between the same breeds. Concordance between the two datasets was seen for chromosomes carrying QTL with strong statistical support, such as BTA5 and BTA18, which carry genes associated with coat color. For these chromosomes, there was a correspondence between the strength of the QTL signal along the chromosome and the degree of genetic differentiation between breeds. However, such an association was not seen in a broader comparison that also included chromosomes carrying QTL with lower significance levels. In addition, other chromosomal regions with substantial QTL effects did not include markers showing extreme between-breed genetic differentiation. Furthermore, the overall consistency between the two studies was weak, with low genome-wide correlation between the statistical values obtained in the linkage mapping study and between-breed genetic differentiation from the HapMap study.

CONCLUSIONS

These results suggest that genomic diversity scans are capable of detecting regions associated with qualitative traits but may be limited in their power to detect regions associated with quantitative phenotypic differences between populations, which may depend on the marker resolution of the study and the level of LD in the populations under investigation.

Quantitative trait loci for variation in immune response to a Foot-and-Mouth Disease virus peptide

Background

Infectious disease of livestock continues to be a cause of substantial economic loss and has adverse welfare consequences in both the developing and developed world. New solutions to control disease are needed and research focused on the genetic loci determining variation in immune-related traits has the potential to deliver solutions. However, identifying selectable markers and the causal genes involved in disease resistance and vaccine response is not straightforward. The aims of this study were to locate regions of the bovine genome that control the immune response post immunisation. 195 F2 and backcross Holstein Charolais cattle were immunised with a 40-mer peptide derived from foot-and-mouth disease virus (FMDV). T cell and antibody (IgG1 and IgG2) responses were measured at several time points post immunisation. All experimental animals (F0, F1 and F2, n = 982) were genotyped with 165 microsatellite markers for the genome scan.

Results

Considerable variability in the immune responses across time was observed and sire, dam and age had significant effects on responses at specific time points. There were significant correlations within traits across time, and between IgG1 and IgG2 traits, also some weak correlations were detected between T cell and IgG2 responses. The whole genome scan detected 77 quantitative trait loci (QTL), on 22 chromosomes, including clusters of QTL on BTA 4, 5, 6, 20, 23 and 25. Two QTL reached 5% genome wide significance (on BTA 6 and 24) and one on BTA 20 reached 1% genome wide significance.

Conclusions

A proportion of the variance in the T cell and antibody response post immunisation with an FDMV peptide has a genetic component. Even though the antigen was relatively simple, the humoral and cell mediated responses were clearly under complex genetic control, with the majority of QTL located outside the MHC locus. The results suggest that there may be specific genes or loci that impact on variation in both the primary and secondary immune responses, whereas other loci may be specifically important for early or later phases of the immune response. Future fine mapping of the QTL clusters identified has the potential to reveal the causal variations underlying the variation in immune response observed.

Identification of QTL with effects on fatty acid composition of meat in a Charolais x Holstein cross population

A whole-genome scan was carried out to detect quantitative trait loci (QTL) influencing beef fatty acid composition using a CharolaisxHolstein population established using a balanced F2 and Backcross breeding design. The phenotypes considered in this study included a total of 24 fatty acid related traits determined in loin muscle samples of the 235 second-generation cross-bred bull calves of the herd. The QTL regression analysis performed, based on 165 microsatellite markers distributed across the 29 bovine autosomes, identified 34 QTL with F-ratios exceeding the 5% chromosome-wide significance threshold. Three of these QTL, one located on chromosome 1 (for the content on linoleic acid, C18:2n-6) and two on chromosome 10 (for the content of gamma-linoleic DPA-docosapentaenoic and DPA-docosapentaenoic, C20:3n-6 and C22:5n-3), also exceeded the 5% genome-wide significance level. A follow-up analysis correcting for intramuscular fat content showed that some of the QTL detected initially (e.g. those localised on chromosome 22) were influenced by fat deposition differences between the founder breeds. The coincident location of some of the linkage associations identified and QTL previously reported for beef fatty acid composition and other meat quality traits, in the same or other cattle populations, provides supporting evidence for the results reported here.

yellow0, a marker for low body weight in Drosophila melanogaster

Marker-assisted selection (MAS) is an important modern breeding technique, but it has been found that the effect of the markers for quantitative trait loci (QTL) is inconsistent, leading in some cases to MAS failure and raising doubts about its effectiveness. Here the model organism Drosophila melanogaster was employed to study whether an effective marker could be found and applied to MAS. We crossed the stock carrying the y (0) marker (a recessive mutation allele of the yellow gene on the X chromosome) with three other stocks carrying corresponding wild-type markers in an F2 design, and found that the y (0) marker was in significant association with low body weight (P<0.001). This association was consistent across different backgrounds and the marker effects in female and male were approximately 0.95 sigma (P) (phenotypic standard deviation) and 0.68 sigma (P), respectively. We next introgressed a fragment via the y (0) marker into a wild stock background over 20 generations of marker-assisted introgression (MAI), and constructed the introgression stock y (0)(OR)20 in which body weight decreased by 13% and 7%, in female and male, respectively, compared to the wild stock (P<0.0001). This indicated that there must be a single QTL for low body weight that is tightly linked to the y (0) marker. We then shortened the introgressed fragment to less than 1.5 cM by a deeper MAI using the y (0) marker and the white marker. This narrower fragment also resulted in a similar decrease in body weight to that induced by y (0)(OR)20, indicating that the QTL for low body weight is located within this less-than-1.5 cM interval. Molecular characteristics of the y (0) marker by PCR amplification and Southern blotting revealed that yellow gene was deficient in the y (0) stock, leading to disappearance of melanin from the cuticle and probably influencing the developmental process. The above results confirmed the existence of effective QTL markers applicable to MAS breeding schemes, and their potential application in breeding new stocks.

Genome assembly anchored QTL map of bovine chromosome 14

Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 – 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb – 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb – 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle.

Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle

A genome scan to detect QTL influencing growth and carcass-related traits was conducted in a Charolais x Holstein crossbred cattle population. Phenotypic measurements related to growth and carcass traits were made on the 235 second-generation crossbred males of this herd (F2 and reciprocal backcrosses), which were born in 4 consecutive annual cohorts. Traits measured in vivo were related to birth dimensions, growth rates, and ultrasound measurements of fat and muscle depth. The animals were slaughtered near a target BW of 550 kg, and a wide range of postmortem traits were measured: visual assessment of carcass conformation and carcass fatness, estimated subcutaneous fat percentage, weights of kidney knob and channel fat, and weights of carcass components after commercial and full-tissue dissections. The whole population, including grandparents, parents, and the crossbred bulls, was genotyped initially for 139 genome-wide microsatellite markers. Twenty-six additional markers were subsequently analyzed to increase marker density on some of the chromosomes where QTL had been initially identified. The linear regression analyses based on the 165 markers revealed a total of 51 significant QTL at the suggestive level, 21 of which were highly significant (F-value >or=9; based on the genome-wide thresholds obtained in the initial scan). A large proportion of the highly significant associations were found on chromosomes 5 and 6. The most highly significant QTL was localized between markers DIK1054 and DIK082 on chromosome 6 and explained about 20% of the phenotypic variance for the total bone proportion estimated after the commercial dissection. In the adjacent marker interval on this chromosome, 2 other highly significant QTL were found that explain about 30% of the phenotypic variance for birth dimension traits (BW and body length at birth). On chromosome 5, the most significant association influenced the lean:bone ratio at the forerib joint and was flanked by markers DIK4782 and BR2936. Other highly significant associations were detected on chromosomes 10 (estimated subcutaneous fat percentage), 11 (total saleable meat proportion), 16 (prehousing growth rate), and 22 (bone proportion at the leg joint). These results provide a useful starting point for the identification of the genes associated with traits of direct interest to the beef industry, using fine mapping or positional candidate gene approaches.

Identification of quantitative trait loci affecting cattle temperament

In addition to its potential contribution to improving animal welfare, the study of the genetics of cattle behavior may provide more general insights into the genetic control of such complex traits. We carried out a genome scan in a Holstein x Charolais cross cattle population to identify quantitative trait loci (QTL) influencing temperament-related traits. Individuals belonging to the second-generation of this population (F(2) and backcross individuals) were subjected to 2 behavioral tests. The flight from feeder (FF) test measured the distance at which the animal moved away from an approaching human observer, whereas the social separation (SS) test categorized different activities which the animal engaged in when removed from its penmates. The entire population was genotyped with 165 microsatellite markers. A regression interval mapping analysis identified 29 regions exceeding the 5% chromosome-wide significance level, which individually explained a relatively small fraction of the phenotypic variance of the traits (from 3.8% to 8.4%). One of the significant associations influencing an FF test trait on chromosome 29 reached the 5% genome-wide significance level. Eight other QTL, all associated with an SS test trait, reached the 1% chromosome-wide significance level. The location of some QTL coincided with other previously reported temperament QTL in cattle, whereas those that are reported for the first time here may represent general loci controlling temperament differences between cattle breeds. No overlapping QTL were identified for the traits measured by the 2 different tests, supporting the hypothesis that different genetic factors influence behavioral responses to different situations.

Present and future applications of DNA technologies to improve beef production

Substantial improvements in production efficiency and quality of beef and dairy products have been made possible through manipulation of bovine genetics. The advent of modern breeds in the last two centuries, the institution of phenotypic selection practices and quantitative genetics, even the process of domestication in the distant past, have all represented means to make use of naturally occurring variation in the genome to tailor the animal for a desired outcome. We discuss the history of genome research in cattle and recent technological advances that promise a leap forward in the use of DNA sequence to facilitate selection, in which a detailed genome-level view for individual animals may provide comprehensive and relatively accurate assessment of the consequences, both desired and unintended, of genetic selection for livestock production.