How animal milk and plant-based alternatives diverge in terms of fatty acid, amino acid, and mineral composition

The decline in fresh milk in the Western world has in part been substituted by an increased consumption of plant-based beverages (PBB). These are often marketed as healthy and sustainable alternatives to milk and dairy foodstuff, although studies have suggested PBB to be of lower nutrient quality. The current study considered different brands of almond-, oat-, rice-, coconut- and soya-based beverages for a comparative analysis and found that they indeed presented lower contents of total protein, lipids, amino acids, and minerals than cow and goat milk. The only exception was given by soya-based beverages which approximated the protein content (3.47% vs. 3.42 and 3.25% in cow and goat milk, respectively) and amino acid composition of animal milk, and also demonstrated high mineral content. The natural presence of phyto-compounds in PBB characterised as antinutrients and their potential to exacerbate the issue of low nutrient quality by lowering bioavailability have been discussed.

Adipose tissue proteomic analyses to study puberty in Brahman heifers

The adipose tissue has been recognized as an active endocrine organ which can modulate numerous physiological processes such as metabolism, appetite, immunity, and reproduction. The aim of this study was to look for differentially abundant proteins and their biological functions in the abdominal adipose tissue between pre- and postpubertal Brahman heifers. Twelve Brahman heifers were divided into 2 groups and paired on slaughter day. Prepubertal heifers had never ovulated and postpubertal heifers were slaughtered on the luteal phase of their second estrous cycle. After ensuring the occurrence of puberty in postpubertal heifers, abdominal adipose tissue samples were collected. Mass spectrometry proteomic analysis identified 646 proteins and revealed that 171 proteins showed differential abundance in adipose tissue between the pre- and postpuberty groups (adjusted P-value < 0.05). Data are available via ProteomeXchange with identifier PXD009452. Using a list of 51 highly differentially abundant proteins as the target (adjusted P-value < 10-5), we found 14 enriched pathways. The results indicated that gluconeogenesis was enhanced when puberty approached. The metabolism of glucose, lipids, and AA in the adipose tissue mainly participated in oxidation and energy supply for heifers when puberty occurred. Our study also revealed the differentially abundant proteins were enriched for estrogen signaling and PI3K-Akt signaling pathways, which are known integrators of metabolism and reproduction. These results suggest new candidate proteins that may contribute to a better understanding of the signaling mechanisms that relate adipose tissue function to puberty. Protein-protein interaction network analysis identified 4 hub proteins that had the highest degrees of connection: PGK1, ALDH5A1, EEF2, and LDHB. Highly connected proteins are likely to influence the functions of all differentially abundant proteins identified, directly or indirectly.

Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty

Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 × 10^-6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 × 10^-5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.

Development and validation of a small SNP panel for feed efficiency in beef cattle

The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.

Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers

To understand genes, pathways, and networks related to puberty, we characterized the transcriptome of two tissues: the pituitary gland and ovaries. Samples were harvested from pre- and postpubertal Brahman heifers (same age group). Brahman heifers () are older at puberty compared with , a productivity issue. With RNA sequencing, we identified differentially expressed (DEx) genes and important transcription factors (TF) and predicted coexpression networks. The number of DEx genes detected in the pituitary gland was 284 ( < 0.05), and was the most DEx gene (fold change = 4.12, = 0.01). The gene promotes bone mineralization through transforming growth factor-β (TGFβ) signaling. Further studies of the link between bone mineralization and puberty could target . In ovaries, 3,871 genes were DEx ( < 0.05). Four highly DEx genes were noteworthy for their function: (a γ-aminobutyric acid [GABA] transporter), (), and () and its receptor . These genes had higher ovarian expression in postpubertal heifers. The GABA and its receptors and transporters were expressed in the ovaries of many mammals, suggesting a role for this pathway beyond the brain. The pathway has been known to influence the timing of puberty in rats, via modulation of GnRH. The effects of at the hypothalamus, pituitary gland, and ovaries have been documented. and its receptors are known factors in the release of GnRH, similar to and GABA, although their roles in ovarian tissue are less clear. Pathways previously related to puberty such as TGFβ signaling ( = 6.71 × 10), Wnt signaling ( = 4.1 × 10), and peroxisome proliferator-activated receptor (PPAR) signaling ( = 4.84 × 10) were enriched in our data set. Seven genes were identified as key TF in both tissues: , , , , , , and a novel gene. An ovarian subnetwork created with TF and significant ovarian DEx genes revealed five zinc fingers as regulators: , , , , and . Recent work of hypothalamic gene expression also pointed to zinc fingers as TF for bovine puberty. Although some zinc fingers may be ubiquitously expressed, the identification of DEx genes in common across tissues points to key regulators of puberty. The hypothalamus and pituitary gland had eight DEx genes in common. The hypothalamus and ovaries had 89 DEx genes in common. The pituitary gland and ovaries had 48 DEx genes in common. Our study confirmed the complexity of puberty and suggested further investigation on genes that code zinc fingers.

Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers

Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.

SNP detection using RNA-sequences of candidate genes associated with puberty in cattle

Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.

Prospecting major genes in dairy buffaloes

BACKGROUND

Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different.

RESULTS

The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits.

CONCLUSIONS

Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production.

Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle

Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

Estimation of genetic and phenotypic parameters for ultrasound and carcass merit traits in crossbred beef cattle

Miar, Y., Plastow, G. S., Bruce, H. L., Moore, S. S., Durunna, O. N., Nkrumah, J. D. and Wang, Z. 2014. Estimation of genetic and phenotypic parameters for ultrasound and carcass merit traits in crossbred beef cattle. Can. J. Anim. Sci. 94: 273–280. Ultrasound measurements of 852 crossbred steers along with carcass merit measurements on 756 of them were used to examine their genetic and phenotypic parameters. Traits including ultrasound backfat thickness (UBF), ultrasound ribeye area (UREA), ultrasound marbling (UMAR), carcass weight (CWT), carcass grade fat (CGF), carcass average backfat thickness (CABF), carcass ribeye area (CREA), carcass marbling score (CMAR), and carcass lean meat yield (CLMY) were measured on 6 yr of residual feed intake trials from 2003 to 2008. Pairwise bivariate animal models were performed for each combination of traits using ASReml software to estimate heritability, phenotypic and genetic correlations among the traits. Significant fixed effects (contemporary group, and sire breed), covariates (age of dam, slaughter weight, and start test age of animal), and random additive effect were fitted in the models. The heritability estimates for UBF, UREA, UMAR, CWT, CGF, CABF, CREA, CMAR, and CLMY were 0.31, 0.17, 0.37, 0.40, 0.22, 0.25, 0.24, 0.38, and 0.28, respectively. Most of the phenotypic correlations were significant (P<0.05). CWT had low to moderate phenotypic correlations with most of the traits. Results show that heavier CWT tends to have more UREA, CGF, CABF, and CREA. Genetic correlations among these traits varied from weak to strong, but most of them were not significantly different from zero. Greater CREA may lead to decreased UMAR, and UBF due to negative genetic correlations (−0.56±0.32, and −0.45±0.23, respectively). The results support the potential value of ultrasound technology in crossbreed beef cattle breeding programs to generate indicator traits for carcass quality. In addition, carcass lean meat yield correlated favourably with backfat thickness and rib eye area but correlated unfavourably with UMAR. The estimated genetic parameters for ultrasound and carcass merit traits can be incorporated into breeding programs that emphasize carcass quality in Canadian crossbred beef cattle populations.

A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle

High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARGC1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.

Sperm protamine deficiency correlates with sperm DNA damage in Bos indicus bulls

The primary purpose of spermatozoa is to deliver the paternal DNA to the oocyte at fertilization. During the complex events of fertilization, if the spermatozoon penetrating the oocyte contains compromised or damaged sperm chromatin, the subsequent progression of embryogenesis and foetal development may be affected. Variation in sperm DNA damage and protamine content in ejaculated spermatozoa was reported in the cattle, with potential consequences to bull fertility. Protamines are sperm-specific nuclear proteins that are essential to packaging of the condensed paternal genome in spermatozoa. Sperm DNA damage is thought to be repaired during the process of protamination. This study investigates the potential correlation between sperm protamine content, sperm DNA damage and the subsequent relationships between sperm chromatin and commonly measured reproductive phenotypes. Bos indicus sperm samples (n = 133) were assessed by two flow cytometric methods: the sperm chromatin structure assay (SCSA) and an optimized sperm protamine deficiency assay (SPDA). To verify the SPDA assay for bovine sperm protamine content, samples collected from testis, caput and cauda epididymidis were analyzed. As expected, mature spermatozoa in the cauda epididymidis had higher protamine content when compared with sperm samples from testis and caput epididymidis (p < 0.01). The DNA fragmentation index (DFI), determined by SCSA, was positively correlated (r = 0.33 ± 0.08, p < 0.05) with the percentage of spermatozoa that showed low protamine content using SPDA. Also, DFI was negatively correlated (r = -0.21 ± 0.09, p < 0.05) with the percentage of spermatozoa with high protamine content. Larger scrotal circumference contributes to higher sperm protamine content and lower content of sperm DNA damage (p < 0.05). In conclusion, sperm protamine content and sperm DNA damage are closely associated. Protamine deficiency is likely to be one of the contributing factors to DNA instability and damage, which can affect bull fertility.

Candidate genes and biological pathways associated with carcass quality traits in beef cattle

Karisa, B. K., Thomson, J., Wang, Z., Bruce, H. L., Plastow, G. S. and Moore, S. S. 2013. Candidate genes and biological pathways associated with carcass quality traits in beef cattle. Can. J. Anim. Sci. 93: 295–306. The objective of this study was to use the candidate gene approach to identify the genes associated with carcass quality traits in beef cattle steers at the University of Alberta Ranch at Kinsella, Canada. This approach involved identifying positional candidate genes and prioritizing them according to their functions into functional candidate genes before performing statistical association analysis. The positional candidate genes and single nucleotide polymorphisms (SNP) were identified from previously reported quantitative trait loci for component traits including body weight, average daily gain, metabolic weight, feed efficiency and energy balance. Positional candidate genes were then prioritized into functional candidate genes according to the associated gene ontology terms and their functions. A total of 116 genes were considered functional candidate genes and 117 functional SNPs were genotyped and used for multiple marker association analysis using ASReml®. Seven SNPs were significantly associated with various carcass quality traits (P≤0.005). The significant genes were associated with biological processes such as fat, glucose, protein and steroid metabolism, growth, energy utilization and DNA transcription and translation as inferred from the protein knowledgebase (UniprotKB). Gene network analysis indicated significant involvement of biological processes related to fat and steroid metabolism and regulation of transcription and translation of DNA.

Influence of on-farm production practices on sensory and technological quality characteristics of pork loin

Quality of pork from pigs raised either traditionally (outdoor access or bedded settings with no sub-therapeutic antibiotics or growth promotants in feed) or conventionally (commercial indoor) was evaluated. Pork loins (m. longissimus thoracis et lumborum, LTL) from four hundred pigs from either traditional or conventional production systems (n=200) fed commercially formulated diets ad libitum were harvested at slaughter. Intramuscular crude fat content and lean color (L* and b*) values were significantly decreased in conventional pork loins. LTL from conventionally-raised pig carcasses showed increased (P<0.05) mean pH, moisture content and reduced cooking loss and shear force values and had increased tenderness and juiciness scores compared to those from traditionally-raised pig carcasses. Results indicated that pork from conventionally raised pigs was superior to that from traditionally raised pigs in terms of tenderness and juiciness, suggesting that consumers may value pork from traditionally raised pigs on the basis of factors other than eating quality and appearance.

Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle

The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers. The approach uses prior knowledge of gene functions to predict their biological role in the variation observed in a trait. It is suited to identify genes associated with complex traits where each gene has a relatively small effect. First, positional candidate genes were identified within the genomic positions of previously reported QTL associated with component traits related to RFI such as dry matter intake (DMI), growth, feed conversion ratio (FCR), average daily gain (ADG), and energy balance. Secondly, the positional candidate genes were prioritized into functional candidate genes according to their biological functions and their relationship with the biological processes associated with RFI including carbohydrate, fat and protein metabolism, thermoregulation, immunity and muscle activity. Single nucleotide polymorphisms (SNPs) located within the functional candidate genes were identified using mRNA sequences and prioritized into functional classes such as non-synonymous (nsSNP), synonymous (sSNP) or intronic SNP. A total of 117 nsSNP were considered as functional SNP and genotyped in steers at the University of Alberta ranch in Kinsella. Multiple marker association analysis in ASReml was performed using RFI data obtained from 531 beef steers. Twenty-five SNP were significantly associated with RFI (P < 0.05) accounting for 19.7% of the phenotypic variation. Using SIFT program to predict the effect of the SNP on the function of the corresponding protein, 3 of the 25 SNP were predicted to cause a significant effect on protein function (P < 0.05). One of the 3 SNP was located in the GHR gene and was also associated with a significant effect on the tertiary structure of the GHR protein (P < 0.05) as modeled using SWISSModel software. Least square means for each genotype were estimated and an over-dominance effect was observed for the SNP located in the GHR, CAST, ACAD11 and UGT3A1 genes. In addition, 2 other SNP showed a dominance effect and 3 genes had an additive effect. Gene network analysis performed in Ingenuity pathway analysis (IPA) software (Ingenuity Systems, www.ingenuity.com) indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling. The genes in this study, if validated in other beef cattle populations, may be useful for marker assisted selection for feed efficiency.

Microarray analysis in caudal medulla of cattle orally challenged with bovine spongiform encephalopathy

Bovine spongiform encephalopathy (BSE) is a fatal disorder in cattle characterized by progressive neurodegeneration of the central nervous system. We investigated the molecular mechanisms involved in neurodegeneration during prion infection through the identification of genes that are differentially expressed (DE) between experimentally infected and non-challenged cattle. Gene expression of caudal medulla from control and orally infected animals was compared by microarray analysis using 24,000 bovine oligonucleotides representing 16,846 different genes to identify DE genes associated with BSE disease. In total, 182 DE genes were identified between normal and BSE-infected tissues (>2.0-fold change, P < 0.01); 81 DE genes had gene ontology functions, which included synapse function, calcium ion regulation, immune and inflammatory response, apoptosis, and cytoskeleton organization; 13 of these genes were found to be involved in 26 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expression of five DE genes associated with synapse function (tachykinin, synuclein, neuropeptide Y, cocaine, amphetamine-responsive transcript, and synaptosomal-associated protein 25 kDa) and three DE genes associated with calcium ion regulation (parvalbumin, visinin-like, and cadherin) was further validated in the medulla tissue of cattle at different infection times (6, 12, 42, and 45 months post-infection) by qRT-PCR. These data will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species.

Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method

Fine mapping of quantitative trait loci (QTL) for 16 ultrasound measurements and carcass merit traits that were collected from 418 hybrid steers was conducted using 1207 SNP markers covering the entire genome. These SNP markers were evaluated using a Bayesian shrinkage estimation method and the empirical critical significant thresholds (α = 0.05 and α = 0.01) were determined by permutation based on 3500 permuted datasets for each trait to control the genome-wide type I error rates. The analyses identified a total of 105 QTLs (p < 0.05) for seven ultrasound measure traits including ultrasound backfat, ultrasound marbling and ultrasound ribeye area and 113 QTLs for seven carcass merit traits of carcass weight, grade fat, average backfat, ribeye area, lean meat yield, marbling and yield grade. Proportion of phenotypic variance accounted for by a single QTL ranged from 0.06% for mean ultrasound backfat to 4.83% for carcass marbling (CMAR) score, while proportion of the phenotypic variance accounted for by all significant (p < 0.05) QTL identified for a single trait ranged from 4.54% for carcass weight to 23.87% for CMAR.

Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle

The benefit of using genomic breeding values (GEBV) in predicting ADG, DMI, and residual feed intake for an admixed population was investigated. Phenotypic data consisting of individual daily feed intake measurements for 721 beef cattle steers tested over 5 yr was available for analysis. The animals used were an admixed population of spring-born steers, progeny of a cross between 3 sire breeds and a composite dam line. Training and validation data sets were defined by randomly splitting the data into training and testing data sets based on sire family so that there was no overlap of sires in the 2 sets. The random split was replicated to obtain 5 separate data sets. Two methods (BayesB and random regression BLUP) were used to estimate marker effects and to define marker panels and ultimately the GEBV. The accuracy of prediction (the correlation between the phenotypes and GEBV) was compared between SNP panels. Accuracy for all traits was low, ranging from 0.223 to 0.479 for marker panels with 200 SNP, and 0.114 to 0.246 for marker panels with 37,959 SNP, depending on the genomic selection method used. This was less than accuracies observed for polygenic EBV accuracies, which ranged from 0.504 to 0.602. The results obtained from this study demonstrate that the utility of genetic markers for genomic prediction of residual feed intake in beef cattle may be suboptimal. Differences in accuracy were observed between sire breeds when the random regression BLUP method was used, which may imply that the correlations obtained by this method were confounded by the ability of the selected SNP to trace breed differences. This may also suggest that prediction equations derived from such an admixed population may be useful only in populations of similar composition. Given the sample size used in this study, there is a need for increased feed intake testing if substantially greater accuracies are to be achieved.

Genetic parameters and genotype x environment interaction for feed efficiency traits in steers fed grower and finisher diets

The objective of this study was to examine the genetic parameters and genetic correlations of feed efficiency traits in steers (n = 490) fed grower or finisher diets in 2 feeding periods. A bivariate model was used to estimate phenotypic and genetic parameters using steers that received the grower and finisher diets in successive feeding periods, whereas a repeated animal model was used to estimate the permanent environmental effects. Genetic correlations between the grower-fed and finisher-fed regimens were 0.50 ± 0.48 and 0.78 ± 0.43 for residual feed intake (RFI) and G:F, respectively. The moderate genetic correlation between the 2 feeding regimens may indicate the presence of a genotype × environment interaction for RFI. Permanent environmental effects (expressed in percentage of phenotypic variance) were detected in the grower-fed steers for ADG (38%), DMI (30%), RFI (18%), and G:F (40%) and also in the finisher-fed steers for ADG (28%), DMI (35%), metabolic mid-weight (23%), and RFI (10%). Heritability estimates were 0.08 ± 0.10 and 0.14 ± 0.15 for the grower-fed steers and 0.42 ± 0.16 and 0.40 ± 17 for the finisher-fed steers for RFI and G:F, respectively. The dependency of the RFI on the feeding regimen may have serious implications when selecting animals in the beef industry. Because of the higher cost of grains, feed efficiency in the feedlot might be overemphasized, whereas efficiency in the cow herd and the backgrounding segments may have less emphasis. These results may also favor the retention (for subsequent breeding) of cows whose steers were efficient in the feedlot sector. Therefore, comprehensive feeding trials may be necessary to provide more insight into the mechanisms surrounding genotype × environment interaction in steers.

Season of testing and its effect on feed intake and efficiency in growing beef cattle

This study sought to assess whether residual feed intake (RFI) calculated by regressing feed intake (DMI) on growth rate (ADG) and metabolic mid-BW in 3 different ways led to similar estimates of genetic parameters and variance components for young growing cattle tested for feed intake in fall and winter seasons. A total of 378 beef steers in 5 cohorts were fed a typical high energy feedlot diet and had free-choice access to feed and water. Feed intake data were collected in fall or winter seasons. Climate data were obtained from the University of Alberta Kinsella meteorological station and Vikings AGCM station. Individual animal RFI was obtained by either fitting a regression model to each test group separately (RFI(C)), fitting a regression model to pooled data consisting of all cohorts but including test group as a fixed effect (RFI(O)), or fitting a regression to pooled data with test group as a fixed effect but within seasonal (fall-winter or winter-spring) groups (RFI(S)). Two animal models (M1 and M2) that differed by the inclusion of fixed effects of test group or season, respectively, were used to evaluate RFI measurements. Feed intake was correlated with air temperature, relative humidity, solar radiation, and wind speed (-0.26, 0.23, 0.30, -0.14 for fall-winter and 0.31, -0.04, 0.14, 0.16 for winter-spring, respectively), but the nature and magnitude of the correlations were different for the 2 seasons. Single trait direct heritability, model likelihood, direct genetic variance, and EBV accuracy estimates were greatest for RFI(C) and least for RFI(O) for both M1 and M2 models. A significant genetic correlation was also observed between RFI(O) and ADG, but not for RFI(C) and RFI(S). Including a season effect (M2) in the genetic evaluation of RFI(O) resulted in the smallest heritability, model LogL, EBV accuracy, and largest residual variance estimates. These results, though not conclusive, suggest a possible effect of seasonality on feed intake and thus feed efficiency.

Feed efficiency differences and reranking in beef steers fed grower and finisher diets

This 3-yr study used 490 steers to determine whether feedlot steers changed their feed efficiency (FE) ranking when fed a grower diet, then a finisher diet. The steers were crossbreds and were between 5 to 7 mo of age. There were 2 feeding periods each year. Within each year, approximately 90 steers had their diet switched from a grower to a finisher diet (feed-swap group), whereas another 90 steers were fed either the grower (grower-fed group) or the finisher (finisher-fed group) diet throughout the feeding trial. Each feeding test lasted for a minimum of 10 wk, and all steers were fed ad libitum. Individual animal feed intakes were collected using the GrowSafe feeding system, and BW were measured every 2 wk. Residual feed intake (RFI), G:F, and Kleiber ratio (KR) were computed at the end of each feeding period. For each measure of efficiency, animals were classified as low, medium, or high based on 0.5 SD from the mean. The majority of steers did not maintain the previous efficiency class in the second period. Approximately 58, 51, and 51% of steers in the feed-swap group, finisher-fed group, and the grower-fed group, respectively, changed their RFI measure by 0.5 SD. A low rank correlation occurred in all test groups but was less in the feed-swap group. Spearman rank correlations between the 2 feeding periods in the feed-swap group were 0.33, 0.20, and 0.31 for RFI, G:F, and KR, respectively. Classifications based on G:F and KR showed that a greater number of steers (P < 0.05) in the feed-swap group did not maintain their FE class from 1 feeding regimen to the other, whereas classification based on RFI did not show any difference (P > 0.05) between the proportions of individuals that changed or maintained their FE class. In the groups without a feed-swap, there was no difference (P > 0.05) in the proportion of steers that changed or maintained the same FE class for all FE measures. Our results suggest that diet type and feeding period affect the FE ranking in beef steers. A feedlot diet is ideal for evaluating the FE potential of steers for feedlot profitability; however, we suggest that tests involving less dense diets should be examined in an effort to understand the relationships between FE and feeder profitability.

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

The detection and mapping of genetic markers linked to quantitative trait loci (QTL) can be utilized to enhance genetic improvement of livestock populations. With the completion of the bovine genome sequence assembly, single nucleotide polymorphisms (SNP) assays spanning the whole bovine genome and research work on large scale identification, validation and analysis of genotypic variation in cattle has become possible. The objective of the present study was to perform a whole genome scan to identify and map QTL affecting milk production traits and somatic cell scores using linkage disequilibrium (LD) regression and 1536 SNP markers. Three and 18 SNP were found to be associated with only milk yield (MY) at a genome and chromosome wise significance (p < 0.05) level respectively. Among the 21 significant SNP, 16 were in a region reported to have QTL for MY in other dairy cattle populations and while the rest five were new QTL finding. Four SNP out of 21 are significant for the milk production traits (MY, fat yield, protein yield (PY), and milk contents) in the present study. Six and nine SNP were associated with PY at a genome and chromosome wise significant (p < 0.05) level respectively. Three and 17 SNP were found to be associated with FY at a genome and chromosome wise significant (p < 0.05) level. Five and seven SNP were mapped with somatic cell score at a genome and chromosome wise significant (p < 0.05) level respectively. The results of this study have revealed QTL for MY, PY, protein percentage, FY, fat percentage, somatic cell score and persistency of milk in the Canadian dairy cattle population. The chromosome regions identified in this study should be further investigated to potentially identify the causative mutations underlying the QTL.

Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattle

A SNP in the promoter region of insulin like growth factor-1 (IGF1) (c.-512C>T) was analysed for associations with 10 fat deposition and carcass merit traits in hybrid (n = 455), Angus (n = 204) and Charolais (n = 186) beef cattle populations. Significant associations of the SNP were found for ultrasound backfat thickness (P = 0.030), carcass average backfat (P = 0.015) and carcass lean meat yield (LMY) (P = 0.023) in the Angus beef population, with the 'CC' genotype showing higher fat depth and lower LMY than the 'TT' genotype. Analyses of transcription factor binding sites based on transcription element search system prediction revealed that the 'C' allele introduces a binding site for nuclear factor I, which has an adipose tissue-specific regulatory role and thus may contribute to the SNP effect on fat deposition in the population of pure Angus cattle, a breed with greater fat depth than the hybrid and Charolais breeds.

Bovine and ovine DNA microsatellites from the EMBL and GENBANK databases

Bovine and ovine microsatellite sequences were extracted from the EMBL and GENBANK databases. When analysed for number of alleles and degree of heterozygosity in the CSIRO cattle reference families, allele numbers range from 1 to 14 with heterozygosities, in the polymorphic systems ranging from 15.8% to 100%. Six (46%) of the 13 bovine systems tested gave specific and polymorphic products in sheep. Similarly 2 of the 4 ovine systems gave specific and polymorphic products in cattle. These data define 11 bovine and 8 ovine microsatellite systems which are associated with known genes and are thus useful for comparative mapping studies.

A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls

Genetic improvement of livestock populations can be achieved through detection and mapping of genetic markers linked to quantitative trait loci (QTL). With the completion of the bovine genome sequence assembly, single nucleotide polymorphism (SNP) assays spanning the whole bovine genome and research work on large-scale identification, validation, and analysis of genotypic variation in cattle has become possible. A total of 462 Canadian Holstein Bulls were used to test the association between SNP and QTL. Single locus linkage disequilibrium regression model was implemented to perform a whole genome scan to identify and map QTL affecting conformation and functional traits. One thousand five hundred thirty-six SNP markers from introns and exons of potential QTL regions for economically important traits across the bovine genome were selected for association analysis. A total of 45 and 151 SNP were found to be associated with 17 conformation and functional traits at a genome- and chromosome-wise significance level, respectively. Among the 196 significant SNP, 169 of them are newly detected in this study, whereas 27 of them have been reported in previous literature and 161 of these were located in genes and are worth further investigating to potentially identify the causative mutations underlying the QTL. The single locus linkage disequilibrium regression method using SNP marker genotypes has proven to be a successful methodology for detecting and mapping QTL in dairy cattle populations.

Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle

The objective of this study was to quantify the extent of linkage disequilibrium (LD) on bovine chromosomes 19 and 29 and to study the pattern of selection signatures in beef and dairy breeds (Angus and Holstein) of Bos taurus. The extent of LD was estimated for 370 and 186 single nucleotide polymorphism markers on BTA19 and 29 respectively using the square of the correlation coefficient (r(2)) among alleles at pairs of loci. A comparison of the extent of LD found that the decline of LD followed a similar pattern in both breeds. We observed long-range LD and found that LD dissipates to background levels at a locus separation of about 20 Mb on both chromosomes. Along each chromosome, patterns of LD were variable in both breeds. We find that a minimum of 30 000 informative and evenly spaced markers would be required for whole-genome association studies in cattle. In addition, we have identified chromosomal regions that show some evidence of selection for economically important traits in Angus and Holstein cattle. The results of this study are of importance for the design and application of association studies.

Identification of polymorphisms influencing feed intake and efficiency in beef cattle

Feed efficiency is an economically important trait in beef cattle. Net feed efficiency, measured as residual feed intake (RFI), is the difference between actual feed intake and the predicted feed intake required for maintenance and gain of the animal. SNPs that show associations with RFI may be useful quantitative trait nucleotides for marker-assisted selection. This study identified associations between SNPs underlying five RFI QTL on five bovine chromosomes (BTA2, 5, 10, 20 and 29) with measures of dry matter intake (DMI), RFI and feed conversion ratio (FCR) in beef cattle. Six SNPs were found to have effects on RFI (P < 0.05). The largest single SNP allele substitution effect for RFI was -0.25 kg/day located on BTA2. The combined effects of the SNPs found significant in this experiment explained 6.9% of the phenotypic variation of RFI. Not all the RFI SNPs showed associations with DMI and FCR even though these traits are highly correlated with RFI (r = 0.77 and r = 0.62 respectively). This shows that these SNPs may be affecting the underlying biological mechanisms of feed efficiency beyond feed intake control and weight gain efficiency. These SNPs can be used in marker-assisted selection but first it will be important to verify these effects in independent populations of cattle.

Mature adipocytes may be a source of stem cells for tissue engineering

Adipose tissue contains a large portion of stem cells. These cells appear morphologically like fibroblasts and are primarily derived from the stromal cell fraction. Mature (lipid-filled) adipocytes possess the ability to become proliferative cells and have been shown to produce progeny cells that possess the same morphological (fibroblast-like) appearance as the stem cells from the stromal fraction. A closer examination of mature adipocyte-derived progeny cells may prove to be an emerging area of growth/metabolic physiology that may modify present thinking about adipose tissue renewal capabilities. Knowledge of these cells may also prove beneficial in cell-based therapies for tissue repair, regeneration, or engineering.

Polymorphisms and haplotypes in the bovine neuropeptide Y, growth hormone receptor, ghrelin, insulin-like growth factor 2, and uncoupling proteins 2 and 3 genes and their associations with measures of growth, performance, feed efficiency, and carcass merit in beef cattle1

Genes that regulate metabolism and energy partitioning have the potential to influence economically important traits in farm animals, as do polymorphisms within these genes. In the current study, SNP in the bovine neuropeptide Y (NPY), growth hormone receptor (GHR), ghrelin (GHRL), uncoupling proteins 2 and 3 (UCP2 and UCP3), IGF2, corticotrophin-releasing hormone (CRH), cocaine and amphetamine regulated transcript (CART), melanocortin-4 receptor (MC4R), proopiomelanocortin (POMC), and GH genes were evaluated for associations with growth, feed efficiency, and carcass merit in beef steers. In total, 24 SNP were evaluated for associations with these traits and haplotypes were constructed within each gene when 2 or more SNP showed significant associations. An A/G SNP located in intron 4 of the GHR gene had the largest effects on BW of the animals (dominance effect P < 0.01) and feed efficiency (allele substitution effect P < 0.05). Another A/G SNP located in the promoter region of GHR had similar effects but the haplotypes of these 2 SNP reduced the effects of the SNP located in intron 4. Three SNP in the NPY gene showed associations to marbling (P < 0.001) as well as with ADG, BW, and feed conversion ratio (FCR; P < 0.05). The combination of these 3 SNP into haplotypes generally improved the association or had a similar scale of association as each single SNP. Only 1 SNP in UCP3, an A/G SNP in intron 3, was associated with ADG (P = 0.025), partial efficiency of growth, and FCR (P < 0.01). Three SNP in UCP2 gene were in almost complete linkage disequilibrium and showed associations with lean meat yield, yield grade, DMI, and BW (P < 0.05). Haplo-types between the SNP in UCP3 and UCP2 generally reduced the associations seen individually in each SNP. An A/G SNP in the GHRL gene tended to show effects on residual feed intake, FCR, and partial efficiency of growth (P < 0.10). The IGF2 SNP most strongly affected LM area (P < 0.01), back fat, ADG, and FCR (P < 0.05). The SNP in the CART, MC4R, POMC, GH, and CRH genes did not show associations at P < 0.05 with any of the traits. Although most of the SNP that showed associations do not cause amino acid changes, these SNP could be linked to other yet to be detected causative mutations or nearby QTL. It will be very important to verify these results in other cattle populations.

Polymorphisms in the bovine leptin promoter associated with serum leptin concentration, growth, feed intake, feeding behavior, and measures of carcass merit

Leptin is the hormone product of the obese gene synthesized and secreted predominantly by white adipocytes. It functions as a lipostatic signal regulating BW, food intake, energy expenditure, reproduction, and certain immune system functions. Although previous studies have identified polymorphisms in the coding regions of the leptin gene in cattle that show considerable associations with feed intake, milk quality and quantity, and carcass fatness, no such associations have been reported for the leptin promoter. The current study reports associations between SNP in the 5' untranslated promoter region of the bovine leptin gene with serum leptin concentration, growth, BW, feed intake, feeding behavior, and carcass merit in hybrid cattle (n = 150). The study showed that animals with the TT genotype of a less frequent cytosine/thymine (C/ T) substitution (UASMS2; frequency of thymine allele equals 0.21) detected at position 528 in the bovine leptin promoter (GenBank Accession No. AB070368) show 48 and 39% increases in serum leptin concentration (P < 0.001), 39 and 31% increases in backfat thickness (P < 0.001), and 13 and 9% increase in marbling score (P = 0.01), compared with CC or CT genotypes, respectively. Animals with the TT genotype also show significantly higher feed intake (P < 0.001), growth rate, metabolic BW (P < 0.05), and live weight at slaughter (P < 0.10). Animals with the GG genotype of a more frequent cytosine/guanine (C/G) substitution (UASMS3; frequency of G allele equals 0.59) at position 1759 in the bovine leptin promoter (GenBank Accession No. AB070368) also show higher feed intake (P = 0.001), growth rate (P < 0.10), and BW (P < 0.01). The thymine allele of UASMS2 and the guanine allele of UASMS3 were separately associated with higher feeding duration (P < 0.05). The two SNP show significant linkage disequilibrium and could also be relevant in predicting other characteristics, such as milk yield and quality in cattle. These results, however, represent the initial associations of the polymorphisms with these traits, and further efforts are required to validate these findings in other populations.

Genetic and phenotypic relationships of feed intake and measures of efficiency with growth and carcass merit of beef cattle1

Feed intake and efficiency of growth are economically important traits of beef cattle. This study determined the relationships of daily DMI, feed:gain ratio [F:G, which is the reciprocal of the efficiency of gain (G:F) and therefore increases as the efficiency of gain decreases and vice versa, residual feed intake (RFI), and partial efficiency of growth (efficiency of ADG, PEG) with growth and carcass merit of beef cattle. Residual feed intake was calculated from phenotypic regression (RFIp) or genetic regression (RFIg) of ADG and metabolic BW on DMI. An F1 half-sib pedigree file containing 28 sires, 321 dams, and 464 progeny produced from crosses between Alberta Hybrid cows and Angus, Charolais, or Alberta Hybrid bulls was used. Families averaged 20 progeny per sire (range = 3 to 56). Performance, ultrasound, and DMI data was available on all progeny, of which 381 had carcass data. Phenotypic and genetic parameters were obtained using SAS and ASREML software, respectively. Differences in RFIp and RFIg, respectively, between the most and least efficient steers (i.e., steers with the lowest PEG) were 5.59 and 6.84 kg of DM/d. Heritabilities for DMI, F:G, PEG, RFIp, and RFIg were 0.54 +/- 0.15, 0.41 +/- 0.15, 0.56 +/- 0.16, 0.21 +/- 0.12, and 0.42 +/- 0.15, respectively. The genetic (r = 0.92) and phenotypic (r = 0.97) correlations between RFIp and RFIg indicated that the 2 indices are very similar. Both indices of RFI were favorably correlated phenotypically (P < 0.001) and genetically with DMI, F:G, and PEG. Residual feed intake was tendentiously genetically correlated with ADG (r = 0.46 +/- 0.45) and metabolic BW (r = 0.27 +/- 0.33), albeit with high SE. Genetically, RFIg was independent of ADG and BW but showed a phenotypic correlation with ADG (r = -0.21; P < 0.05). Daily DMI was correlated genetically (r = 0.28) and phenotypically (r = 0.30) with F:G. Both DMI and F:G were strongly correlated with ADG (r > 0.50), but only DMI had strong genetic (r = 0.87 +/- 0.10) and phenotypic (r = 0.65) correlations with metabolic BW. Generally, the phenotypic and genetic correlations of RFI with carcass merit were not different from zero, except genetic correlations of RFI with ultrasound and carcass LM area and carcass lean yield and phenotypic correlations of RFI with backfat thickness (P < 0.01). Daily DMI had moderate to high phenotypic (P < 0.01) and genetic correlations with all the ultrasound and carcass traits. Depending on how RFI technology is applied, adjustment for body composition in addition to growth may be required to minimize the potential for correlated responses to selection in cattle.

Genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit of feedlot cattle1

Leptin is the hormone product of the obese gene that is synthesized and predominantly expressed by adipocytes. This study estimated the genetic variation in serum leptin concentration and evaluated the genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit. There were 464 steers with records for serum leptin concentration, performance, and efficiency of gain and 381 steers with records for carcass traits. The analyses included a total of 813 steers, including those without phenotypic records. Phenotypic and genetic parameter estimates were obtained using SAS and ASREML, respectively. Serum leptin concentration was moderately heritable (h2 = 0.34 +/- 0.13) and averaged 13.91 (SD = 5.74) ng/mL. Sire breed differences in serum leptin concentration correlated well with breed differences in body composition. Specifically, the serum leptin concentration was 20% greater in Angus-sired steers compared with Charolais-sired steers (P < 0.001). Consequently, ultrasound backfat (27%), carcass 12th-rib fat (31%), ultrasound marbling (14%), and carcass marbling (15%) were less in Charolais- than Angus-sired steers (P < 0.001). Conversely, carcass LM area (P = 0.05) and carcass lean meat yield (P < 0.001) were greater in Charolais- compared with Angus-sired steers. Steers with greater serum leptin concentration also had greater DMI (P < 0.001), greater residual feed intake (P = 0.04), and partial efficiency of growth (P = 0.01), but did not differ in feed conversion ratio (P > 0.10). Serum leptin concentration was correlated phenotypically with ultrasound backfat (r = 0.41; P < 0.001), carcass 12th-rib fat (r = 0.42; P < 0.001), ultrasound marbling (r = 0.25; P < 0.01), carcass marbling (r = 0.28; P < 0.01), ultrasound LM area (r = -0.19; P < 0.01), carcass LM area (r = -0.17; P < 0.05), lean meat yield (r = -0.38; P < 0.001), and yield grade (r = 0.32; P < 0.001). The corresponding genetic correlations were generally greater than the phenotypic correlations and included ultrasound backfat (r = 0.76 +/- 0.19), carcass 12th-rib fat (r = 0.54 +/- 0.23), ultrasound marbling (r = 0.27 +/- 0.22), carcass marbling (r = 0.76 +/- 0.21), ultrasound LM area (r = -0.71 +/- 0.19), carcass LM area (r = -0.75 +/- 0.20), lean meat yield (r = -0.59 +/- 0.22), and yield grade (r = 0.39 +/- 0.26). Serum leptin concentration can be a valuable tool that can be incorporated into appropriate selection programs to favorably improve the carcass merit of cattle.

Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle

Feed intake and feed efficiency of beef cattle are economically relevant traits. The study was conducted to identify QTL for feed intake and feed efficiency of beef cattle by using genotype information from 100 microsatellite markers and 355 SNP genotyped across 400 progeny of 20 Angus, Charolais, or Alberta Hybrid bulls. Traits analyzed include feedlot ADG, daily DMI, feed-to-gain ratio [F:G, which is the reciprocal of the efficiency of gain (G:F)], and residual feed intake (RFI). A mixed model with sire as random and QTL effects as fixed was used to generate an F-statistic profile across and within families for each trait along each chromosome, followed by empirical permutation tests to determine significance thresholds for QTL detection. Putative QTL for ADG (chromosome-wise P < 0.05) were detected across families on chromosomes 5 (130 cM), 6 (42 cM), 7 (84 cM), 11 (20 cM), 14 (74 cM), 16 (22 cM), 17 (9 cM), 18 (46 cM), 19 (53 cM), and 28 (23 cM). For DMI, putative QTL that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (93 cM), 3 (123 cM), 15 (31 cM), 17 (81 cM), 18 (49 cM), 20 (56 cM), and 26 (69 cM) in the across-family analyses. Putative across-family QTL influencing F:G that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 3 (62 cM), 5 (129 cM), 7 (27 cM), 11 (16 cM), 16 (30 cM), 17 (81 cM), 22 (72 cM), 24 (55 cM), and 28 (24 cM). Putative QTL influencing RFI that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (90 cM), 5 (129 cM), 7 (22 cM), 8 (80 cM), 12 (89 cM), 16 (41 cM), 17 (19 cM), and 26 (48 cM) in the across-family analyses. In addition, a total of 4, 6, 1, and 8 chromosomes showed suggestive evidence (chromosome-wise, P < 0.10) for putative ADG, DMI, F:G, and RFI QTL, respectively. Most of the QTL detected across families were also detected within families, although the locations across families were not necessarily the locations within families, which is likely because of differences among families in marker informativeness for the different linkage groups. The locations and direction of some of the QTL effects reported in this study suggest potentially favorable pleiotropic effects for the underlying genes. Further studies will be required to confirm these QTL in other populations so that they can be fine-mapped for potential applications in marker-assisted selection and management of beef cattle.