The inability of beef cattle to maintain full term pregnancies has become an economic concern for the beef industry. Herd management and nutritional improvements have alleviated environmental impacts ...on embryonic and fetal loss, yet additional gains can be made through genomic selection. The objectives of this study were to identify loci and gene-sets in crossbred beef heifers associated with the number of services required to become pregnant (TBRD) and heifer conception rate at first service (HCR1). Heifers (n = 709) from a commercial beef operation underwent one round of artificial insemination, before exposure to bulls for natural service for 50 days. Pregnancy and time of conception was determined by ultrasound 35 days after the breeding season. Heifers were genotyped using the GeneSeek (Lincoln, NE) Bovine GGP50K BeadChip prior to genome-wide association analyses (GWAA) conducted using an EIGENSTRAT-like model to identify loci associated (P < 1 × 10-5) with TBRD and HCR1. One locus was associated (P = 8.97 × 10-6) with TBRD on BTA19 and included the positional candidate gene ASIC2, which is differentially expressed in the endometrium of fertility classified heifers, and the positional candidate gene, SPACA3. Gene-set enrichment analyses using SNP (GSEA-SNP) data, was performed and identified one gene-set, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen as enriched (NES = 3.15) with TBRD and contained nine leading edge genes that contributed to the enrichment of the gene set. The enriched gene-set is involved in catalyzing oxidation-reduction reactions, which have been associated with oxidative stressors impacting pregnancy success. No loci were associated nor gene-sets enriched with HCR1. Identification of loci, positional candidate genes, gene-sets and leading edge genes enriched for fertility facilitate genomic selection that allows producers to select for reproductively superior cattle, reduce costs associated with infertility, and increase percent calf crop.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of ...this study was to use gene set enrichment analysis of SNP data (GSEA‐SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading‐edge genes) and upstream regulators associated with BRD in pre‐weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system. Holstein calves were sampled from commercial calf‐raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading‐edge genes identified in the dairy calf and beef cattle populations respectively. Six leading‐edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regulator. The genes, gene sets and upstream regulators associated with BRD have common functions associated with immunity, inflammation and pulmonary disease and provide insights into the mechanisms that are critical to BRD susceptibility in cattle.
Physiology deals with the functions of living organisms and their systems, and its scientific endeavors can be viewed as having temporally occurred in 3 phases. The first phase of physiology studies ...focused on determining the functions of particular organs and tissues and their functional differences according to physiological status. The second phase of studies focused on characterizing differences in these functions according to the environment, or productivity. The third phase of studies focuses on determining the physiological causes of differences in productivity. Distinguishing cause from effect in physiological systems of inter-related processes is problematic, such that science has struggled to identify the root physiological mechanisms and their role in the network of genes leading to differences in productivity. Genomics is the study of the entire genome and provides powerful new tools that will accelerate third-phase discoveries of causal physiological processes. That research exploits information on DNA polymorphisms known as markers, complete DNA sequence, RNA sequence, and RNA expression in particular tissues at specific life stages. Physiologists can determine the genetic cause of mutant animals, identify genetic differences between cases and controls, and identify genes responsible for differences in performance between average and above-average animals. In some species, physiologists can leverage genomic data being used to predict genetic merit in elite seedstock populations, as a starting point to identify genes that will then motivate detailed physiological studies in the organs or tissues and stages of life in which those genes are expressed. Such work will increase our knowledge of biology and may lead to novel approaches to manipulate animal performance.
Multiple genome-wide association analyses have investigated susceptibility to bovine paratuberculosis, but few loci have been identified across independent cattle populations. A SNP-based gene set ...enrichment analysis (GSEA–SNP) allows expanded identification of genes with moderate effects on a trait through the enrichment of gene sets instead of identifying only few loci with large effects. Therefore, the objective of this study was to identify genes that were moderately associated with
Mycobacterium avium
ssp.
paratuberculosis
(
Map
) tissue infection using GSEA–SNP in Holstein cattle from the Pacific Northwest (PNW;
n
= 205) and from the PNW and Northeast (PNW+NE;
n
= 245) which were previously genotyped with the Illumina BovineSNP50 BeadChip. The GSEA–SNP utilized 4389 gene sets from five databases. For each annotated gene in the UMD3.1 assembly (
n
= 19,723), the most significant SNP within each gene and its surrounding region (10 kb up- and downstream) was selected as a proxy for that gene. Any gene set with a normalized enrichment score > 2.5 was considered enriched. Thirteen gene sets (8 PNW GSEA–SNP; 5 PNW+NE) were enriched in these analyses and all have functions that relate to nuclear factor kappa beta. Nuclear factor kappa beta is critical to gut immune responses, implicated in host immune responses to other mycobacterial diseases, and has established roles in inflammation as well as cancer. Gene sets and genes moderately associated with
Map
infection could be used in genomic selection to allow producers to select for less susceptible cattle, lower the prevalence of the disease, and reduce economic losses.
Summary
Milk production traits, such as 305‐day milk yield (305MY), have been under direct selection to improve production in dairy cows. Over the past 50 years, the average milk yield has nearly ...doubled, and over 56% of the increase is attributable to genetic improvement. As such, additional improvements in milk yield are still possible as new loci are identified. The objectives of this study were to detect SNPs and gene sets associated with 305MY in order to identify new candidate genes contributing to variation in milk production. A population of 781 primiparous Holstein cows from six central Washington dairies with records of 305MY and energy corrected milk were used to perform a genome‐wide association analysis (GWAA) using the Illumina BovineHD BeadChip (777 962 SNPs) to identify QTL associated with 305MY (P < 1.0 × 10−5). A gene set enrichment analysis with SNP data (GSEA‐SNP) was performed to identify gene sets (normalized enrichment score > 3.0) and leading edge genes (LEGs) influencing 305MY. The GWAA identified three QTL comprising 34 SNPs and 30 positional candidate genes. In the GSEA‐SNP, five gene sets with 58 unique and 24 shared LEGs contributed to 305MY. Identification of QTL and LEGs associated with 305MY can provide additional targets for genomic selection to continue to improve 305MY in dairy cattle.
Summary
The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of ...estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST) and the effective population size (Ne) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.
Johne's disease is a highly transmissible bacterial disease caused by Mycobacterium avium ssp. paratuberculosis (MAP). The objective of this study was to refine the locus associated with MAP tissue ...infection and the locus associated with tolerance to Johne's disease. Using a genome-wide association analysis, single nucleotide polymorphisms associated with MAP tissue infection and tolerance to Johne's disease on Bos taurus autosome (BTA)3 and BTA15, respectively, have previously been identified. A 235-kb region on BTA3 was evaluated with 42 single nucleotide polymorphisms, and a 193-kb region on BTA15 was evaluated with 54 single nucleotide polymorphisms in a group of 209 Holstein cows. Using a single marker association analysis and haplotype tests, we refined a region of 10.6kb on BTA3 as being associated with MAP tissue infection and a region of 6.5kb on BTA15 as being associated with tolerance to Johne's disease.
The U.S. inventory of beef cattle has declined since its peak in the 1980s to levels present in the early 1960s. Low cattle inventories have contributed to record high prices since 2009. The ...increased cattle values have also resulted in a subsequent increase in economic losses from disease. Reducing losses due to disease has become increasingly important in managing thin profit margins at feedlots. The objective of this study was to develop a bio-economic model to evaluate the economic cost of bovine respiratory disease complex (BRDC) in beef feedlots and estimate the potential net economic gain from using selection approaches to reduce BRDC prevalence. Treatment cost, mortality, and harvest data from approximately 1000 heifers and 1000 steers with similar numbers of cases and controls were taken from two commercial feedlots and two commercial processing facilities at harvest. These data were used to develop a Reed-Frost epidemiological model that simulated BRDC prevalence in a population of cattle on feed. Treatment cost was computed as a function of days on feed and the prevalence of cases. Losses due to mortality, and carcass quality discounts were also included to estimate total economic losses. Based on market prices, and carcass discounts, the average economic loss per BRDC case was estimated. To estimate the potential net economic gain from selection, the rate of genetic gain was estimated using a 16.2% national BRDC prevalence rate obtained over a 15-yr period and an estimated heritability for BRDC susceptibility of 21% from the 2000 cattle evaluated in this study. An @Risk model was used to estimate a 20-yr time frame of genetic selection with stochastic BRDC prevalence rates using historical USDA data. The model compared net economic gains for cattle feedlots that used selection to reduce BRDC and feedlots that approached reducing BRDC without selection. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2011-68004-30367 from the USDA National Institute of Food and Agriculture.
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