E.E. Connor

Genomic imputation and evaluation using high-density Holstein genotypes

Genomic evaluations for 161,341 Holsteins were computed by using 311,725 of 777,962 markers on the Illumina BovineHD Genotyping BeadChip (HD). Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Holstein genotypes were from 1,510 animals with HD markers, 82,358 animals with 45,187 (50K) markers, 1,797 animals with 8,031 (8K) markers, 20,177 animals with 6,836 (6K) markers, 52,270 animals with 2,683 (3K) markers, and 3,229 nongenotyped dams (0K) with >90% of haplotypes imputable because they had 4 or more genotyped progeny. The Holstein HD genotypes were from 1,142 US, Canadian, British, and Italian sires, 196 other sires, 138 cows in a US Department of Agriculture research herd (Beltsville, MD), and 34 other females. Percentages of correctly imputed genotypes were tested by applying the programs findhap and FImpute to a simulated chromosome for an earlier population that had only 1,112 animals with HD genotypes and none with 8K genotypes. For each chip, 1% of the genotypes were missing and 0.02% were incorrect initially. After imputation of missing markers with findhap, percentages of genotypes correct were 99.9% from HD, 99.0% from 50K, 94.6% from 6K, 90.5% from 3K, and 93.5% from 0K. With FImpute, 99.96% were correct from HD, 99.3% from 50K, 94.7% from 6K, 91.1% from 3K, and 95.1% from 0K genotypes. Accuracy for the 3K and 6K genotypes further improved by approximately 2 percentage points if imputed first to 50K and then to HD instead of imputing all genotypes directly to HD. Evaluations were tested by using imputed actual genotypes and August 2008 phenotypes to predict deregressed evaluations of US bulls proven after August 2008. For 28 traits tested, the estimated genomic reliability averaged 61.1% when using 311,725 markers vs. 60.7% when using 45,187 markers vs. 29.6% from the traditional parent average. Squared correlations with future data were slightly greater for 16 traits and slightly less for 12 with HD than with 50K evaluations. The observed 0.4 percentage point average increase in reliability was less favorable than the 0.9 expected from simulation but was similar to actual gains from other HD studies. The largest HD and 50K marker effects were often located at very similar positions. The single-breed evaluation tested here and previous single-breed or multibreed evaluations have not produced large gains. Increasing the number of HD genotypes used for imputation above 1,074 did not improve the reliability of Holstein genomic evaluations.

Heat-stress abatement during the dry period: Does cooling improve transition into lactation?

Environmental factors, especially temperature and light exposure, influence the health and productivity of dairy cows during lactation, possibly via similar physiological mechanisms. For example, heat stress is a critical component of decreased milk yield during summer. However, less is known about the effect of heat stress during the dry period. The objective of this study was to evaluate the effects of heat stress prepartum under a controlled photoperiod on lactation performance and hepatic metabolic gene expression of periparturient multiparous Holstein cows (n = 16). Cows were dried off approximately 46 d before expected calving date and assigned to treatment randomly after blocking by mature equivalent milk production and parity. Treatments consisted of either heat stress (HT) or cooling (CL) with fans and sprinklers, both under a photoperiod of 14L:10D. Rectal temperature was measured twice daily during the dry period. After calving, cows were housed in a freestall barn with cooling devices, and milk yield was recorded daily up to 210 d in milk. Blood samples were taken from dry off until +42 d relative to calving for metabolites and from -2 until +2 d relative to calving for hormone analysis. Daily dry matter intake was measured from -35 to +42 d relative to calving. Liver biopsies were collected at dry off, -20, +2, and +20 d relative to calving for cows on HT (n = 5) and CL (n = 4) to measure mRNA expression of suppressors of cytokine signaling-2 (SOCS-2), insulin-like growth factor binding protein-5 (IGFBP-5), a key transcription factor in lipid biosynthesis (SREBP-1c), and enzymes of lipid metabolism (FASN, ACACA, and ACADVL) by real-time quantitative PCR. Heat stress increased rectal temperatures (39.2 vs. 38.8 degrees C), plasma prolactin concentrations at -1 (171 vs. 79 ng/mL) and 0 d (210 vs. 115 ng/mL) relative to calving, and decreased dry matter intake at 0 and +14 d relative to calving and 3.5% fat-corrected milk postpartum (26.1 vs. 35.4 kg/d) compared with CL cows. Relative to CL cows, hepatic mRNA expression of SOCS-2 and IGFBP-5 was downregulated in HT cows. Expression of ACADVL was upregulated in CL cows at d +2 but downregulated at d +20 relative to HT cows. Concentrations of C16:0 and cis C18:1 were greater in the milk and liver of CL cows compared with HT cows, which reflects greater lipid mobilization. These results suggest that heat-stress abatement in the dry period improves subsequent lactation, possibly via suppression of plasma prolactin surge around calving, SOCS-2 expression, and regulation of hepatic lipid metabolism.

Heat stress abatement during the dry period influences metabolic gene expression and improves immune status in the transition period of dairy cows

Heat stress (HT) and photoperiod affect milk production and immune status of dairy cows. The objective was to evaluate the effects of HT abatement prepartum under controlled photoperiod on hepatic metabolic gene expression and cellular immune function of periparturient Holstein cows (n=21). Cows were dried off 46 d before expected calving date and assigned to treatments by mature equivalent milk production. The treatments were 1) HT and 2) cooling (CL), both imposed during a photoperiod of 14L:10D. Rectal temperature was measured twice daily, whereas respiration rate was measured 3 times/wk at 1500 h during the entire dry period. After calving, cows were housed in a freestall barn with cooling, and milk yield was recorded daily up to 140 d in milk. Liver samples were taken at dry off, -20, 2, and 20 d relative to calving by biopsy. Under a similar schedule, neutrophil function was determined in blood of cows on HT (n=12) and CL (n=9). Blood samples were taken on -46, -32, -18, 0, 14, 28, and 42 d relative to calving for measurement of metabolites and were collected twice daily from -7 to 2 d relative to calving for prolactin (PRL) analysis. The HT cows had greater concentrations of PRL at 0 d relative to calving (150 vs. 93; SEM=11 ng/mL) and had higher afternoon rectal temperatures (39.4 vs. 39.0; SEM=0.04°C) and elevated respiration rates (78 vs. 56; SEM=2 breaths/min) during the prepartum period compared with CL cows. Relative to HT cows, CL cows had greater hepatic expression of PRL-R, SOCS-3, and CAV-1 mRNA. Neutrophil oxidative burst was greater in CL cows relative to HT cows at 2 d (61 vs. 42; SEM=6%) and at 20 d (62 vs. 49; SEM=5%) relative to calving, and phagocytosis was greater in CL cows at 20 d (47 vs. 33; SEM=4%) relative to calving compared with HT cows. Humoral response, as measured by IgG secretion against ovalbumin challenge, was greater for CL cows at -32 d (0.44 vs. 0.33; SEM=0.05 OD) and -21 d (0.60 vs. 0.50±0.04 OD) relative to calving compared with HT cows. These results suggest that HT abatement during the dry period improved innate and acquired immune status as measured by neutrophil function and immunoglobulin secretion against ovalbumin challenge, and altered hepatic gene expression related to PRL signaling in the periparturient period or subsequent lactation.

Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index

Functional genomic studies of the mammary gland require an appropriate collection of cDNA sequences to assess gene expression patterns from the different developmental and operational states of underlying cell types. To better capture the range of gene expression, a normalized cDNA library was constructed from pooled bovine mammary tissues, and 23,202 expressed sequence tags (EST) were produced and deposited into GenBank. Assembly of these EST with sequences in the Bos taurus Gene Index (BtGI) helped to form 5751 of the current 23,883 tentative consensus (TC) sequences. The majority (87%) of these 5751 assemblies contained only one to three mammary-derived EST. In contrast, 18% of the mammary EST assembled with TC sequences corresponding to 12 genes. These results suggest library normalization was only partially effective, because the reduction in EST for genes abundantly transcribed during lactation could be attributed to pooling. For better assessment of novel content in the mammary library and to add to existing annotation of all bovine sequence elements, gene ontology assignments, and comparative sequence analyses against human genome sequence, human and rodent gene indices, and an index of orthologous alignments of genes across eukaryotes (TOGA) were performed, and results were added to existing BtGI annotation. Over 35,000 of the bovine elements significantly matched human genome sequence, and the positions of some alignments (3%) were unique relative to those using human expressed sequences. Because 3445 TC sequences had no significant match with any data set, mammary-derived cDNA clones representing 23 of these elements were analyzed further for expression and novelty. Only one clone met criteria suggesting the corresponding gene was a divergent ortholog or expressed sequence unique to cattle. These results demonstrate that bovine sequence expression data serve as a resource for characterizing mammalian transcriptomes and identifying those genes potentially unique to ruminants.

Heat stress abatement during the dry period influences prolactin signaling in lymphocytes

Heat stress perturbs prolactin (PRL) release and affects dairy cow lactational performance and immune cell function. We hypothesized that greater PRL concentration in plasma of heat-stressed cows relative to cooled cows would decrease expression of prolactin receptor (PRL-R) mRNA and increase mRNA expression of suppressors of cytokine signaling (SOCS) in lymphocytes, altering their cytokine production. To test this hypothesis, multiparous Holstein cows were dried off 46 d before their expected calving date and assigned randomly to heat stress (HT; n=9) or cooling (CL; n=7) during the entire dry period. A second study was conducted the following year with an additional 21 cows (12 HT; 9 CL). Lymphocytes were isolated from cows at -46, -20, +2, and +20 d relative to expected calving date and mRNA expression of PRL-R, SOCS-1, SOCS-2, SOCS-3, cytokine-inducible SH2-containing protein (CIS), and heat shock protein 70 KDa A5 (HSPA5), and housekeeping genes hydroxymethylbilane synthase (HMBS), ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit (ATP5B), and ribosomal protein S9 (RPS9) was analyzed by quantitative real-time reverse transcriptase polymerase chain reaction (RT-PCR). Cows exposed to HT had greater PRL concentration in plasma compared with CL cows. Measurement of lymphocyte proliferation indicated that lymphocytes of CL cows proliferated more than those from HT cows and exressed more PRL-R mRNA and less SOCS-1 and SOCS-3 mRNA relative to HT cows. Further, lymphocytes from CL cows produced more tumor necrosis factor-alpha (TNF-alpha) than those from HT cows. These results suggest that changes in PRL-signaling pathway genes during heat stress are associated with differential cytokine secretion by lymphocytes and may regulate lymphocyte proliferation in dairy cows.

Effects of increased milking frequency on gene expression in the bovine mammary gland

BackgroundPrevious research has demonstrated that increased milking frequency of dairy cattle during the first few weeks of lactation enhances milk yield, and that the effect persists throughout the entire lactation period. The specific mechanisms controlling this increase in milk production are unknown, but suggested pathways include increased mammary epithelial cell number, secretory capacity, and sensitivity to lactogenic hormones. We used serial analysis of gene expression (SAGE) and microarray analysis to identify changes in gene expression in the bovine mammary gland in response to 4× daily milking beginning at d 4 of lactation (IMF4) relative to glands milked 2× daily (Control) to gain insight into physiological changes occurring within the gland during more frequent milking.ResultsResults indicated changes in gene expression related to cell proliferation and differentiation, extracellular matrix (ECM) remodeling, metabolism, nutrient transport, and immune function in IMF4 versus Control cows. In addition, pathways expected to promote neovascularization within the gland appeared to be up regulated in IMF4 cows. To validate this finding, immunolocalization of Von Willebrandts factor (VWF), an endothelial cell marker, and its co-localization with the nuclear proliferation antigen Ki67 were evaluated in mammary tissue sections at approximately d 7 and d 14 of lactation in cows milked 4× daily versus Controls to estimate endothelial cell abundance and proliferation within the gland. Consistent with expression of genes related to neovascularization, both abundance of VWF and its co-localization with Ki67 appeared to be elevated in cows milked 4× daily, suggesting persistent increased milk yield in response to increased milking frequency may be mediated or complemented by enhanced mammary ECM remodeling and neovascularization within the gland.ConclusionAdditional study is needed to determine whether changes in ECM remodeling and neovascularization of the mammary gland result in increased milk yield during increased milking frequency, or occur in response to an increased demand for milk production. Gene pathways identified by the current study will provide a basis for future investigations to identify factors mediating the effects of milking frequency on milk yield.

Use of residual feed intake in Holsteins during early lactation shows potential to improve feed efficiency through genetic selection

Improved feed efficiency is a primary goal in dairy production to reduce feed costs and negative impacts of production on the environment. Estimates for efficiency of feed conversion to milk production based on residual feed intake (RFI) in dairy cattle are limited, primarily due to a lack of individual feed intake measurements for lactating cows. Feed intake was measured in Holstein cows during the first 90 d of lactation to estimate the heritability and repeatability of RFI, minimum test duration for evaluating RFI in early lactation, and its association with other production traits. Data were obtained from 453 lactations (214 heifers and 239 multiparous cows) from 292 individual cows from September 2007 to December 2011. Cows were housed in a free-stall barn and monitored for individual daily feed consumption using the GrowSafe 4000 System (GrowSafe Systems, Ltd., Airdrie, AB, Canada). Animals were fed a total mixed ration 3 times daily, milked twice daily, and weighed every 10 to 14 d. Milk yield was measured at each milking. Feed DM percentage was measured daily, and nutrient composition was analyzed from a weekly composite. Milk composition was analyzed weekly, alternating between morning and evening milking periods. Estimates of RFI were determined as the difference between actual energy intake and predicted intake based on a linear model with fixed effects of parity (1, 2, ≥ 3) and regressions on metabolic BW, ADG, and energy-corrected milk yield. Heritability was estimated to be moderate (0.36 ± 0.06), and repeatability was estimated at 0.56 across lactations. A test period through 53 d in milk (DIM) explained 81% of the variation provided by a test through 90 DIM. Multiple regression analysis indicated that high efficiency was associated with less time feeding per day and slower feeding rate, which may contribute to differences in RFI among cows. The heritability and repeatability of RFI suggest an opportunity to improve feed efficiency through genetic selection, which could reduce feed costs, manure output, and greenhouse gas emissions associated with dairy production.

Dietary trans Fatty Acid Isomers Differ in Their Effects on Mammary Lipid Metabolism As Well As Lipogenic Gene Expression in Lactating Mice

The biological activities and mechanisms of action of individual transoctadecenoic acids (trans-18:1 FA) have not been completely elucidated. We examined the effects of several individual trans-18:1 FA isomers and trans-10, cis-12 conjugated linoleic acid (CLA) on fat synthesis, and expression of lipogenic genes in mammary and liver tissue in lactating mice. From d 6 to 10 postpartum, 30 lactating C57BL/6J mice were randomly assigned to either a control (CTR) diet containing 20 g/kg oleic acid or diets in which the oleic acid was either completely replaced by partially hydrogenated vegetable oil (PHVO), trans-7 18:1 (T7), trans-9 18:1 (T9), or trans-11 18:1 (T11) or partially replaced with 6.66 g/kg trans-10, cis-12 CLA. Milk fat percentage was decreased by CLA (44%), T7 (27%), and PHVO (23%), compared with CTR. In the mammary gland, CLA decreased the expression of genes related to de novo FA synthesis, desaturation, triacylglycerol formation, and transcriptional regulation. PHVO and T7 diets decreased the expression of 1-acylglycerol-3-phosphate O-acyltransferase and thyroid hormone responsive SPOT14 homolog (THRSP) mRNA. In contrast, dietary trans FA (tFA) did not affect hepatic lipogenic gene expression. However, mice fed CLA, T7, and PHVO diets had increased liver weights due to hepatic steatosis. Trans-7 18:1 was extensively desaturated to trans-7, cis-9 CLA in mammary and liver tissues. Dietary trans-7 18:1 could lead to milk fat depression in lactating mice, possibly through its desaturation product trans-7, cis-9 CLA. Also, the differences between the effects of trans-10, cis-12 CLA and other tFA could be attributed to its effects on carbohydrate response element binding protein and PPARgamma, in addition to sterol regulatory element binding transcription factor 1c and THRSP.

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BackgroundSeveral approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6× coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process.ResultsAn RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6× bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map.ConclusionAlignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6× sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

Heterogeneity in genetic and nongenetic variation and energy sink relationships for residual feed intake across research stations and countries

Our long-term objective is to develop breeding strategies for improving feed efficiency in dairy cattle. In this study, phenotypic data were pooled across multiple research stations to facilitate investigation of the genetic and nongenetic components of feed efficiency in Holstein cattle. Specifically, the heritability of residual feed intake (RFI) was estimated and heterogeneous relationships between RFI and traits relating to energy utilization were characterized across research stations. Milk, fat, protein, and lactose production converted to megacalories (milk energy; MilkE), dry matter intakes (DMI), and body weights (BW) were collected on 6,824 lactations from 4,893 Holstein cows from research stations in Scotland, the Netherlands, and the United States. Weekly DMI, recorded between 50 to 200 d in milk, was fitted as a linear function of MilkE, BW0.75, and change in BW (ΔBW), along with parity, a fifth-order polynomial on days in milk (DIM), and the interaction between this polynomial and parity in a first-stage model. The residuals from this analysis were considered to be a phenotypic measure of RFI. Estimated partial regression coefficients of DMI on MilkE and on BW0.75 ranged from 0.29 to 0.47 kg/Mcal for MilkE across research stations, whereas estimated partial regression coefficients on BW0.75 ranged from 0.06 to 0.16 kg/kg0.75. Estimated partial regression coefficients on ΔBW ranged from 0.06 to 0.39 across stations. Heritabilities for country-specific RFI were based on fitting second-stage random regression models and ranged from 0.06 to 0.24 depending on DIM. The overall heritability estimate across all research stations and all DIM was 0.15±0.02, whereas an alternative analysis based on combining the first- and second-stage model as 1 model led to an overall heritability estimate of 0.18±0.02. Hence future genomic selection programs on feed efficiency appear to be promising; nevertheless, care should be taken to allow for potentially heterogeneous variance components and partial relationships between DMI and other energy sink traits across environments when determining RFI.