Effect of body condition change and health status during early lactation on performance and survival of Holstein cows

Body condition score (BCS) and disease records are commonly available in dairy operations. However, the effect of BCS changes (ΔBCS) considering specific health profiles has not been investigated extensively. The objective of this study was to assess the effects of different levels of ΔBCS on fertility, milk yield, and survival of Holstein cows diagnosed with reproductive disorders (REP; dystocia, twins, retained fetal membranes, metritis, and clinical endometritis), other health disorders (OTH; subclinical ketosis, left displaced abomasum, lameness, clinical mastitis, and respiratory disease), or with no disease events (HLT) within 40 days in milk (DIM). Data included lactation information from 11,733 cows calving between November 2012 and October 2014 in 16 herds across 4 geographical regions in the United States (Northeast, Midwest, Southwest, Southeast). Cows were evaluated for BCS at 5 ± 3 DIM (BCS5) and at 40 ± 3 DIM (BCS40) and the difference between BCS40 and BCS5 was classified as excessive loss of BCS (EL; ΔBCS ≤-0.75), moderate loss (ML; ΔBCS = -0.5 to -0.25), no change (NC; ΔBCS = 0), or gain of BCS (GN; ΔBCS ≥0.25). Multivariable logistic regression was used for assessing potential associations between the outcomes of interest and ΔBCS and health. The effect of the interaction term ΔBCS by health group was not statistically significant for any of the study outcomes. The odds of resumption of ovarian cyclicity (ROC), in GN, NC, and ML cows were 1.94 (95% CI: 1.57-2.40), 1.59 (1.28-1.97), and 1.27 (1.10-1.47) times greater than the odds of ROC in EL cows, respectively. The odds of pregnancy at 150 DIM (P150) in GN cows were 1.61 (1.20-2.17) times greater than the odds of P150 in EL cows. Cows with REP or OTH disorders had smaller odds of ROC compared with HLT cows [REP: OR = 0.65 (0.56-0.76) and OTH: OR = 0.79 (0.68-0.92)]. For pregnancy outcomes, REP cows had smaller odds of pregnancy at the first artificial insemination compared with HLT cows [0.70 (0.58-0.84)]. Similarly, REP cows had smaller odds of being diagnosed pregnant by 150 and 305 DIM compared with HLT cows [P150: 0.73 (0.59-0.87), P305: 0.58 (0.49-0.69)]. Overall, average daily milk within the first 90 DIM was greater in EL (39.5 ± 1.13 kg/d) and ML (38.9 ± 1.11 kg/d) cows than in NC (37.8 ± 1.12 kg/d) and GN (36.2 ± 1.12 kg/d) cows. On the other hand, average daily milk within the first 90 DIM was lower in REP (37.0 ± 1.11 kg/d) cows compared with OTH (38.7 ± 1.12 kg/d) and HLT cows (38.6 ± 1.11 kg/d). The magnitude of ΔBCS and the health status of early lactation cows should be considered when assessing subsequent cow performance and survival.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Prepartum supplement level and age at weaning: I. Effects on pre- and postpartum beef cow performance and calf performance through weaning

Objectives were to determine the interaction of prepartum supplement level and age at weaning on cow BW, BCS, milk production, reproduction, and calf performance up to weaning in a fall-calving system over 2 yr. Mature, multiparous, Angus × Simmental cows (yr 1: 326 cows, 9 pastures, BW = 632 ± 67 kg, and BCS = 5.7 ± 0.58; yr 2: 383 cows, 9 pastures, BW = 606 ± 70 kg, and BCS = 5.8 ± 0.74) were used in a split-plot design that included 3 supplement levels-no supplement (NS), low supplement (LS; 2.16 kg∙cow∙d), or high supplement (HS; 8.61 kg∙cow∙d)-and 2 ages at weaning-78 ± 11 d of age (early weaned; EW) or 186 ± 11 d of age (normal weaned; NW). Cows grazed endophyte-infected tall fescue/red clover pastures and were bunk fed supplement (70% dried distillers' grains with solubles and 30% soybean hulls) 103 ± 11 d prepartum to 2 ± 11 d postpartum. Cow BW was greater ( < 0.01) for cows fed HS at precalving (49 ± 11 d prepartum), postcalving (26 ± 11 d postpartum), and postbreeding (81 d after AI) compared with cows fed NS and LS. Prepartum supplementation did not affect ( ≥ 0.62) calf birth BW, percent of calves dead at birth, or percent of cows calving unassisted. Prepartum supplementation tended ( = 0.10) to improve AI conception. Early weaning increased ( ≤ 0.05) AI conception and postbreeding cow BW and BCS compared with cows with NW calves. Neither prepartum supplementation nor age at weaning affected ( ≥ 0.28) overall pregnancy rate. At time of early weaning, BW was increased ( = 0.05) for steers from cows fed LS compared with steers from cows fed NS. Steer BW at time of normal weaning and ADG between early and normal weaning was greater ( < 0.01) for EW steers compared with NW steers. A year × age at weaning interaction occurred ( < 0.01) for ultrasound marbling score at time of normal weaning. In yr 1, marbling was decreased ( = 0.04) for EW steers compared with NW steers; however, in yr 2, marbling was increased ( < 0.01) for EW steers compared with NW steers. In conclusion, there was no interaction between level of supplement during late gestation and age at weaning on cow BW, BCS, milk production, AI conception, and overall pregnancy rate in mature beef cows nor in their steer progeny's BW or ultrasound marbling. Both prepartum supplementation and early weaning improved cow BW, BCS, and reproduction. Minimal effects of dam prepartum supplement level on calf performance up to weaning were observed. Early weaning improved calf growth but had inconsistent effects on ultrasound marbling across years.

Beef cow prepartum supplement level and age at weaning: II. Effects of developmental programming on performance and carcass composition of steer progeny

Objectives were to determine the interaction of prepartum dam supplement level and age at weaning on growth performance, glucose and insulin concentrations, and carcass characteristics of steers (134 steers in yr 1; 147 steers in yr 2). Mature, multiparous Angus × Simmental cows were used in a split-plot design that included 3 supplement levels (no supplement [NS], 2.16 kg·cow·d [LS], and 8.61 kg·cow·d [HS]) and 2 ages at weaning (78 ± 11 d of age [early weaned; EW] or 186 ± 11 d of age [normal weaned; NW]). Cows grazed endophyte-infected tall fescue/red clover pastures and were bunk fed supplement (70% dried distiller's grains plus solubles and 30% soybean hulls) 103 ± 11 d prepartum to 2 ± 11 d postpartum. Dam prepartum supplement level did not affect ( ≥ 0.29) finishing phase growth performance or morbidity. The percentage of steers grading Average Choice or greater was increased ( = 0.04) for steers from cows fed HS compared to the percentage of steers from cows fed NS. Early weaning increased ( < 0.01) finishing phase initial BW and final BW and reduced ( < 0.01) G:F compared to normal weaning. A year × wean interaction ( = 0.04) occurred for ADG; EW resulted in reduced ( < 0.01) ADG compared to NW in yr 2. At slaughter, EW steers had greater ( < 0.01) HCW, yield grade, and back fat than NW steers. A year × wean interaction ( ≤ 0.05) occurred for quality grade distribution; in yr 2, EW steers had a greater ( < 0.01) proportion of carcasses that graded Low Choice or greater and Average Choice or greater than carcasses from NW steers. The EW steers had greater ( ≤ 0.05) occurrence of single antibiotic treatments in yr 2 and mortality due to respiratory disease than NW steers. A trend for a year × wean interaction ( ≤ 0.07) occurred for plasma insulin concentration and insulin:glucose; EW steers had numerically greater plasma insulin concentrations and insulin:glucose than NW steers in yr 1. In conclusion, these data suggest that there is no interaction between maternal level of supplement during late gestation and age at weaning on steer finishing phase performance, glucose and insulin concentrations, and carcass yield and quality characteristics. Overfeeding supplement to the dam did not affect finishing phase growth performance but did improve quality grades of steers. Early weaning increased HCW and improved carcass quality. Both dam supplement level and age at weaning are effective strategies in increasing beef quality and are independent of each other.

Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq

BACKGROUND

Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue.

RESULTS

As a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR.

CONCLUSIONS

Results of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues.

42 EFFECTS OF TRICHOSTATIN A TREATMENT ON GENE EXPRESSION OF CLONED MOUSE 2-CELL AND BLASTOCYST STAGE EMBRYOS

Trichostatin A (TSA) is a potent inhibitor of histone deacetylases and has been shown to improve cloned embryo pre-implantation and term development. We examined the effects of TSA treatment on cloned mouse embryonic gene expression using microarrays. Cloned mouse embryos were generated using long-term haematopoietic stem cells (LT-HSC) and terminally differentiated granulocytes (Gr-1) as nuclear donors, which have been shown to have significantly different cloning efficiencies (Sung et al. 2006 Nat. Gen. 38, 1323–1328). Late 2-cell and blastocyst stage cloned embryos and control, BDF1 in vivo and IVF embryos (n = 10 from each embryo type and stage, except LT-HSC blastocysts, where n = 5) were snap frozen in liquid nitrogen. Total RNA was isolated from individual embryos and amplified using the TargetAmp 2 round Aminoallyl aRNA amplification kit (Epicentre Biotechnologies, Madison, WI, USA). Amplified RNA from each embryo and a standard reference was labelled with Cy3 or Cy5 and hybridized to the mouse exonic evidence based oligonucleotide (MEEBO) microarray allowing for the interrogation of ~25 000 genes. After Loess normalization, ANOVA with false discovery rate (P < 0.001) was used to identify differentially expressed (DE) genes. A subset of the DE genes was verified by RT-qPCR. These two cell types drastically differed in their potential to give rise to morula/blastocyst stage embryos: LT-HSC: 4.1% v. Gr-1: 38.9%. When treated with 10 nM TSA (Sigma, St. Louis, MO, USA) for 10 h immediately after activation, the morula/blastocyst rate increased to 66.1% for the LT-HSC cloned embryos and to 69.3% for the Gr-1 cloned embryos. At the 2-cell stage, we identified 2172 DE genes between the TSA-treated and untreated LT-HSC embryos. There were 512 DE genes between the Gr-1 and Gr-1 TSA embryos. Interestingly, the cloned embryos were more similar to the in vivo and IVF embryos after TSA treatment at the 2-cell stage, as evidenced by hierarchical clustering and the reduced number of DE genes: LT-HSC v. in vivo = 2622 genes; LT-HSC TSA v. in vivo = 473; Gr-1 v. in vivo = 1448; Gr-1 TSA v. in vivo = 312. By the blastocyst stage, the effect of TSA was considerably less pronounced with 18 and 17 DE genes between the LT-HSC/TSA and Gr-1/TSA embryos, respectively. These data indicate that TSA treatment normalizes 2-cell cloned embryo gene expression, enabling significantly more embryos to develop to the blastocyst stage. Our findings demonstrate that TSA exerted the greatest effect on the LT-HSC embryos, which were the most difficult to reprogram by SCNT.

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Adipose-derived mesenchymal stem cells enhance healing of mandibular defects in the ramus of swine

PURPOSE

This study investigated the effect of adipose-derived mesenchymal stem cells (ASCs) injected locally or systemically on the bone regeneration of a 10-mm-diameter cylindrical noncritical-size defect in the ramus of the pig mandible.

MATERIALS AND METHODS

Fifteen Yorkshire pigs, weighing 60 to 80 kg, received bilateral 10-mm-diameter cylindrical surgical defects in each ramus of the mandible. Pigs received 1) a direct injection into the defect of 2.5 million carboxy-fluorescein diacetate succinimidyl ester-labeled ASCs from 1 of 2 pig donors (n = 6); 2) an ear vein injection of 5 million carboxy-fluorescein diacetate succinimidyl ester-labeled ASCs from 1 of 2 pig donors (n = 6); or 3) an ear vein injection of culture Dulbecco's Modified Eagle's Medium without stem cells (control; n = 3). Pigs from each treatment were sacrificed at 1 hour, 2 weeks, or 4 weeks after surgery. Healing of the defect was evaluated by dual-energy x-ray absorptiometry, micro-computed tomography, fluorescent microscopy, and histology.

RESULTS

Bone healing was accelerated in the ASC-injected treatment groups at 2 and 4 weeks after surgery compared with the control pigs.

CONCLUSIONS

Results from this animal model provide evidence that the injection of ASC locally into a bone defect or systemically can accelerate the healing of bone.

Transcriptomics comparison between porcine adipose and bone marrow mesenchymal stem cells during in vitro osteogenic and adipogenic differentiation

Bone-marrow mesenchymal stem cells (BMSC) are considered the gold standard for use in tissue regeneration among mesenchymal stem cells (MSC). The abundance and ease of harvest make the adipose-derived stem cells (ASC) an attractive alternative to BMSC. The aim of the present study was to compare the transcriptome of ASC and BMSC, respectively isolated from subcutaneous adipose tissue and femur of 3 adult pigs, during in vitro osteogenic and adipogenic differentiation for up to four weeks. At 0, 2, 7, and 21 days of differentiation RNA was extracted for microarray analysis. A False Discovery Rate ≤0.05 for overall interactions effect and P<0.001 between comparisons were used to determine differentially expressed genes (DEG). Ingenuity Pathway Analysis and DAVID performed the functional analysis of the DEG. Functional analysis of highest expressed genes in MSC and genes more expressed in MSC vs. fully differentiated tissues indicated low immunity and high angiogenic capacity. Only 64 genes were differentially expressed between ASC and BMSC before differentiation. The functional analysis uncovered a potential larger angiogenic, osteogenic, migration, and neurogenic capacity in BMSC and myogenic capacity in ASC. Less than 200 DEG were uncovered between ASC and BMSC during differentiation. Functional analysis also revealed an overall greater lipid metabolism in ASC, while BMSC had a greater cell growth and proliferation. The time course transcriptomic comparison between differentiation types uncovered <500 DEG necessary to determine cell fate. The functional analysis indicated that osteogenesis had a larger cell proliferation and cytoskeleton organization with a crucial role of G-proteins. Adipogenesis was driven by PPAR signaling and had greater angiogenesis, lipid metabolism, migration, and tumorigenesis capacity. Overall the data indicated that the transcriptome of the two MSC is relatively similar across the conditions studied. In addition, functional analysis data might indicate differences in therapeutic application.

Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes

Soybean rust, caused by Phakopsora pachyrhizi, is a destructive foliar disease in nearly all soybean-producing countries. To identify genes controlling resistance to soybean rust, transcriptome profiling was conducted in resistant and susceptible Glycine tomentella genotypes triggered by P. pachyrhizi infection. Among 38,400 genes monitored using a soybean microarray, at 5% false discovery rate, 1,342 genes were identified exhibiting significant differential expression between uninfected and P. pachyrhizi-infected leaves at 12, 24, 48, and 72 h post-inoculation (hpi) in both rust-susceptible and rust-resistant genotypes. Differentially expressed genes were grouped into 12 functional categories, and among those, large numbers relate to basic plant metabolism. Transcripts for genes involved in the phenylpropanoid pathway were up-regulated early during rust infection. Similarly, genes coding for proteins related to stress and defense responses such as glutathione-S-transferases, peroxidases, heat shock proteins, and lipoxygenases were consistently up-regulated following infection at all four time points. Whereas, subsets of genes involved in cellular transport, cellular communication, cell cycle, and DNA processing were down-regulated. Quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) on randomly selected genes from the different categories confirmed these findings. Of differentially expressed genes, those associated with the flavonoid biosynthesis pathway as well as those coding for peroxidases and lipoxygenases were likely to be involved in rust resistance in soybean, and would serve as good candidates for functional studies. These findings provided insights into mechanisms underlying resistance and general activation of plant defense pathways in response to rust infection.

Modulatory communication signal performance is associated with a distinct neurogenomic state in honey bees

Studies of animal communication systems have revealed that the perception of a salient signal can cause large-scale changes in brain gene expression, but little is known about how communication affects the neurogenomic state of the sender. We explored this issue by studying honey bees that produce a vibratory modulatory signal. We chose this system because it represents an extreme case of animal communication; some bees perform this behavior intensively, effectively acting as communication specialists. We show large differences in patterns of brain gene expression between individuals producing vibratory signal as compared with carefully matched non-senders. Some of the differentially regulated genes have previously been implicated in the performance of other motor activities, including courtship behavior in Drosophila melanogaster and Parkinson's Disease in humans. Our results demonstrate for the first time a neurogenomic brain state associated with sending a communication signal and provide suggestive glimpses of molecular roots for motor control.

The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution

Background

Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.

Results

We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500–15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.

Conclusion

Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.

Genomic dissection of behavioral maturation in the honey bee

Honey bees undergo an age-related, socially regulated transition from working in the hive to foraging that has been previously associated with changes in the expression of thousands of genes in the brain. To understand the meaning of these changes, we conducted microarray analyses to examine the following: (i) the ontogeny of gene expression preceding the onset of foraging, (ii) the effects of physiological and genetic factors that influence this behavioral transition, and (iii) the effects of foraging experience. Although >85% of approximately 5,500 genes showed brain differences, principal component analysis revealed discrete influences of age, behavior, genotype, environment, and experience. Young bees not yet competent to forage showed extensive, age-related expression changes, essentially complete by 8 days of age, coinciding with previously described structural brain changes. Subsequent changes were not age-related but were largely related to effects of juvenile hormone (JH), suggesting that the increase in JH that influences the hive bee-forager transition may cause many of these changes. Other treatments that also influence the onset age of foraging induced many changes but with little overlap, suggesting that multiple pathways affect behavioral maturation. Subspecies differences in onset age of foraging were correlated with differences in JH and JH-target gene expression, suggesting that this endocrine system mediates the genetic differences. We also used this multifactorial approach to identify candidate genes for behavioral maturation. This successful dissection of gene expression indicates that, for social behavior, gene expression in the brain can provide a robust indicator of the interaction between hereditary and environmental information.

6 EXPRESSION PROFILING OF SINGLE BOVINE EMBRYOS REVEALS SIGNIFICANT EFFECTS OF IN VITRO MATURATION, FERTILIZATION AND CULTURE

Cattle and sheep embryos transferred after in vitro production are often afflicted by large offspring syndrome (LOS), which has been correlated with the presence of serum and/or cell co-culture. Previous research indicates that post-fertilization culture affects blastocyst quality and gene expression, and in vitro oocyte maturation and fertilization impact developmental competence. To dissect the effects of in vitro maturation, fertilization, and culture, we compared the expression profiles of single bovine blastocysts generated by: (1) in vitro maturation, fertilization and culture (IVF, n = 15); (2) in vivo maturation, in vivo fertilization, and in vitro culture (IVD, n = 14); and (3) in vivo maturation, fertilization, and development (AI, n = 14). For in vitro culture, the embryos were cultured for 2 days in CR1aa medium with bovine serum albumin (BSA) and then transferred to CR1aa with 10% fetal bovine serum (FBS) with cumulus cells until Day 7, at which time the embryos were vitrified. IVD zygotes were surgically collected from two superovulated Holstein donor cows 24 h post-insemination and cultured in the same system. To conduct expression profiling, total RNA was isolated from individual thawed embryos. The RNA was subjected to three rounds of amplification utilizing a previously adapted and validated T7 linear amplification protocol. Amplified RNA from each embryo and from a standard reference was indirectly labeled with Cy3 or Cy5 by dye swap and hybridized to a custom bovine cDNA microarray containing ~6300 unique genes. After Loess normalization, an ANOVA model (GeneSpring 6.1 and SAS 9.0) was used to identify differentially expressed genes. The P-values were adjusted for multiple comparisons using the false discovery rate approach, and a e2-fold differential criterion was applied. A subset of the differentially expressed genes was verified by real-time RT-PCR. The blastocyst rates for IVF and IVD embryos were 37% and 75%, respectively. There were 305, 365, and 200 genes differentially expressed between the AI and IVD, the IVF and IVD, and the AI and IVF comparisons, respectively. Interestingly, 44 differentially expressed genes were identified between the AI embryos and both the IVF and the IVD embryos, making these potential candidates for LOS. There were 61 genes differentially expressed between the IVF embryos and the AI and IVD embryos. The Gene Ontology categories 'RNA processing' and 'RNA binding' were over-represented among the genes that were down-regulated in the IVF embryos, indicating an effect of in vitro oocyte maturation/fertilization on embryonic gene expression. This work was supported by USDA grants to X.Y., H.A.L., and X.C.T.

Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific downregulation of photosynthesis

Transcript profiling during susceptible (S) and hypersensitive response-associated resistance (R) interactions was determined in soybean (Glycine max). Pseudomonas syringae pv. glycinea carrying or lacking the avirulence gene avrB, was infiltrated into cultivar Williams 82. Leaf RNA was sampled at 2, 8, and 24 h postinoculation (hpi). Significant changes in transcript abundance were observed for 3,897 genes during the experiment at P < or = 0.000005. Many of the genes showed a similar direction of increase or decrease in abundance in both the S and R responses, but the R response generally showed a significantly greater degree of differential expression. More than 25% of these responsive genes had not been previously reported as being associated with pathogen interactions, as 704 had no functional annotation and 378 had no homolog in National Center for Biotechnology Information databases. The highest number of transcriptional changes was noted at 8 hpi, including the downregulation of 94 chloroplast-associated genes specific to the R response. Photosynthetic measurements were consistent with an R-specific reduction in photosystem II operating efficiency (phiPSII) that was apparent at 8 hpi for the R response with little effect in the S or control treatments. Imaging analyses suggest that the decreased phiPSII was a result of physical damage to PSII reaction centers.

Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci1

The purpose of this study was to develop and implement least squares interval-mapping models for joint analysis of breed cross QTL mapping populations and to evaluate the effect of joint analysis on QTL detected for economic traits in data from two breed crosses in pigs. Data on 26 growth, carcass composition, and meat quality traits from F2 crosses between commercially relevant pig breeds were used: a Berkshire x Yorkshire cross at Iowa State University (ISU) and a Berkshire x Duroc cross at the University of Illinois (UOI). All animals were genotyped for a total of 39 (ISU) and 32 (UOI) markers on chromosomes 2, 6, 13, and 18. Marker linkage maps derived from the individual and joint data were similar with regard to order and relative position, but some differences in absolute distances existed. Maps from the joint data were used in all analyses. The individual and joint data sets were analyzed using several least squares interval-mapping models: line-cross (LC) models with Mendelian and parent-of-origin effects; halfsib models (HS); and combined models (CB) that included LC and HS effects. Lack-of-fit tests between the models were used to characterize QTL for mode of expression and to identify segregation of QTL within parental breeds. A total of 26 (8), 47 (18), and 53 (16) QTL were detected at the 5% chromosome (genome)-wise level in the ISU, UOI, and joint data for the 26 analyzed traits. Of the 53 QTL detected in the joint data, only six were detected in both populations and for many, allele effects differed between the two crosses. Despite the lack of overlap between the two populations, joint analysis resulted in an increase in significance for many QTL, including detection of ten QTL that did not reach significance in either population. Confidence intervals for position also were smaller for several QTL. In contrast, 24 QTL, most of which were detected at chromosome-wise levels in the ISU or UOI population, were not detected in the joint data. Presence of paternally expressed QTL near the IGF2 region of SSC2 was confirmed, with major effects on backfat and loin muscle area, particularly in the UOI population, as well as one or more QTL for carcass composition in the distal arm of Chromosome 6. Results of this study suggest that joint analysis using a range of QTL models increases the power of QTL mapping and QTL characterization, which helps to identify genes for subsequent marker-assisted selection.

Quantitative evolutionary genomics: differential gene expression and male reproductive success in Drosophila melanogaster

We combined traditional quantitative genetics and oligonucleotide microarrays to examine within-population genetic variation in a trait closely related to fitness. The trait, male reproductive success under competitive conditions (MCRS), is of central importance to both life-history and sexual-selection theory. We identified 27 candidate genes whose expression levels were associated with within-population variation in MCRS. "High" MCRS was associated with low expression of a cytochrome P450 that causes pesticide resistance, suggesting a fitness cost to resistance. Two groups of metabolic proteins (glutathione transferases and phosphatases) were significantly over-represented, and a large portion of the candidates are genes involved in oxidative stress resistance, energy acquisition or energy storage. Genes expressed in accessory glands and testes were not over-represented among differentially expressed genes, but testis-expressed genes were significantly more likely to be upregulated in high MCRS genotypes. Finally, nine candidate genes that we identified had no previous functional annotation, and this experiment suggests that they play a role in male reproductive success.

Identification of quantitative trait loci for chemical/inflammatory nociception in mice

Sensitivity to pain is widely variable, and much of this variability is genetic in origin. The specific genes responsible have begun to be identified, but only for thermal nociception. In order to facilitate the identification of polymorphic, pain-related genes with more clinical relevance, we performed quantitative trait locus (QTL) mapping studies of the most common assay of inflammatory nociception, the formalin test. QTL mapping is a technique that exploits naturally occurring variability among inbred strains for the identification of genomic locations containing genes contributing to that variability. An F2 intercross was constructed using inbred A/J and C57BL/6J mice as progenitors, strains previously shown to display resistance and sensitivity, respectively, to formalin-induced nociception. Following phenotypic testing (5% formalin, 25 microl intraplantar injection), mice were genotyped at 90 microsatellite markers spanning the genome. We provide evidence for two statistically significant formalin test QTLs - chromosomal regions whose inheritance is associated with trait variability - on distal mouse chromosomes 9 and 10. Identification of the genes underlying these QTLs may illuminate the basis of individual differences in inflammatory pain, and lead to novel analgesic treatment strategies.

Lactational performance of first-parity transgenic gilts expressing bovine alpha-lactalbumin in their milk

The goal of this study was to determine whether the presence of the bovine alpha-lactalbumin transgene in first-lactation gilts enhances lactational performance and litter growth. Transgenic and sibling nontransgenic gilts were bred to nontransgenic boars. Litters were standardized to 10 piglets within 24 h of farrowing. Milk production was measured by the weigh-suckle-weigh method on d 3, 6, 9, and 12 of lactation. Bovine alpha-lactalbumin was present in the colostrum and milk of transgenic gilts throughout lactation. The expression of the transgene was associated with alterations in composition of mammary secretions, especially in early lactation. Lactose concentrations were greater (P < 0.05) in mammary secretions of transgenic gilts during the first 12 h postpartum compared with controls. In contrast, total solids concentration in mammary secretions from transgenic gilts were lower (P < 0.05) relative to controls during the first 6 h postpartum. Transgenic gilts produced more milk than controls on d 3, 6, and 9 of lactation (P < 0.01). By d 12, differences in milk production between transgenic and control sows were no longer different. Lactose intake by transgenic-reared litters was greater than lactose intake by control-reared litters on d 6 of lactation (P < 0.05). Total solids intake was significantly greater (P < 0.05) by transgenic-reared litters on d 3 and 6 compared to control-reared litters. The day x genotype interaction on litter weight gain after birth was highly significant (P = 0.011), with transgenic-reared litters gaining weight at a greater rate than control-reared piglets. Expression of the transgene was associated with increased milk production in lactating gilts and increased growth of transgenic-reared piglets. Increased lactose synthesis in response to the presence of the transgene may result in increased milk production in early lactation, leading to increased milk component intake by transgenic litters, and ultimately to increased growth of litters reared by first-parity transgenic gilts.

Homogeneity of recombination rate within a conserved region on BTA3 that contains QTL

The D3S20-D3S34-D3S3 region on BTA3 contains quantitative trait loci (QTL) controlling milk production traits. This region also displays extensive conservation of synteny among several species including cattle, humans, mice and sheep. In this study, we evaluated the adjacent intervals D3S20-D3S34 and D3S34-D3S3 for differences in recombination rate (theta) among bulls in order to assess the suitability of population-based estimates of theta for marker assisted selection and to explore the relationship between variation in theta and chromosome breakpoints associated with mammalian evolution. Using sperm typing, thetaD3S20-D3S34 and theta D3S34-D3S3 were estimated for six triply heterozygous bulls. Recombination frequency ranged from 6.2 to 12.5% and from 9.7 to 19.2% for the D3S20-D3S34 and D3S34-D3S3 intervals, respectively. However, significant variation in theta was not detected between bulls for either interval (D3S20-D3S34 chi(2)5 d.f.=2.59, P < 0.90; D3S34-D3S3 chi(2)5 d.f.=3.72, P < 0.75). The observed differences in theta were most readily attributed to differences in allele-specific amplification efficiencies among bulls. Our results suggest that the positions of QTL in this region can be reliably determined from population data and therefore accurate marker-assisted selection can be performed for desirable alleles without concern for variation in theta. Furthermore, when considered with results of earlier studies, these findings support a correlation between the existence of evolutionary breakpoints or chromosome rearrangements and variation in theta.

Early weaning and postweaning nutritional management affect feedlot performance of angus x simmental heifers and the relationship of 12th rib fat and marbling score to feed efficiency

Early-weaned Angus x Simmental heifers were used to evaluate the effects of postweaning nutritional management on feedlot performance, carcass merit, and the relationship of intramuscular and subcutaneous fat deposition to the feed efficiency among heifers fed for a high-quality market. Sixteen heifers were weaned at 73+/-5.5 d of age and grazed on endophyte-infected tall fescue for 18 mo before entering the feedlot (early-weaned-P). Eighty heifers from the following year's calf crop were weaned at 71+/-5.5 d of age and allowed either ad libitum access to a 25% concentrate diet (early-weaned-25C) or limit-fed a 90% concentrate diet (early-weaned-90C) to achieve a similar ADG. Following a 119-d growing period, 16 early-weaned-90C and 16 early-weaned-25C calves were paired based on BW and growth rate and individually fed during the finishing period along with the early-weaned-P heifers. Ultrasound measurements of s.c. and i.m. fat were recorded at approximately 60-d intervals throughout the finishing period. Feed efficiency was regressed against s.c. and i.m. fat, and i.m. fat was regressed on s.c. fat. Despite a similar ADG, early-weaned-90C calves gained more efficiently (P < or = 0.05) in the feedlot than early-weaned-25C calves. Heifers finished as yearlings tended (P < or = 0.10) to gain faster but gained less efficiently (P < or = 0.01) than early-weaned-90C heifers finished as calves. The rate of s.c. and i.m. fat deposition was similar between early-weaned-90C and early-weaned-25C heifer calves. The calves were grouped together for comparison to yearlings. Feed efficiency decreased quadratically (P < or = 0.01) as s.c. fat cover increased. The rate at which feed efficiency decreased relative to increasing s.c. fat cover was similar regardless of age at feedlot entry. However, heifers finished as calves gained more efficiently (P < or = 0.01) than yearlings at any given fat thickness. Feed efficiency decreased linearly (P < or = 0.01) as i.m. fat increased among heifers finished as calves. Additionally, heifers finished as calves deposited i.m. fat at a faster rate relative to s.c. fat (P < or = 0.01) than yearlings. These data suggest that heifers finished as calves produce high-quality carcasses with less s.c. fat cover while gaining more efficiently than heifers finished as yearlings.