Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

Potential emigration of Siberian cattle germplasm on Chirikof Island, Alaska

Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.

Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

Background

As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle.

Results

Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development.

Conclusions

In summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3116-1) contains supplementary material, which is available to authorized users.

What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

BACKGROUND

Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.

RESULTS

We generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.

CONCLUSIONS

We demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms.

Pregnancy establishment and maintenance in cattle

A single ovulation, reciprocal embryo transfer study was used to investigate effects of oocyte competence and maternal environment on pregnancy establishment and maintenance in beef cows. Estrous cycles were synchronized in suckled beef cows and embryo donors were inseminated on d 0 (n = 810). Cows were classified on d 0 as having a small (<12.5 mm) or large (≥12.5 mm) ovulatory follicle and randomly chosen as donors or recipients to remove confounding effects of ovulatory follicle size on fertility. Embryos (n = 393) or oocytes (n = 44) were recovered on d 7, and all viable embryos were transferred into recipients (n = 354). All statistical analyses were conducted using the GLM procedure of SAS. Path analysis (with significance set at P < 0.10) was used to examine potential cause-effect relationships among the measured variables. Greater donor cow BW, circulating estradiol concentration at insemination, postpartum interval, and ovulatory follicle size directly increased (P < 0.10) fertilization success. Greater donor cow age was the only factor that directly decreased (P < 0.10) fertilization success. Viability of d-7 embryos was directly inhibited (P < 0.10) by rapid follicular growth rate from d -2 to 0 and heavier BW. Direct beneficial effects to embryo viability were increased serum progesterone concentration on d -2 and ovulatory follicle size. Pregnancy maintenance from d 7 to 27 was enhanced (P < 0.10) by increased serum estradiol concentration on d 0 and progesterone concentration on d 7 in the recipient cow. Increased follicular diameter in the recipient cow on d 0 was detrimental to pregnancy maintenance from d 7 to 27. This manuscript defines the complex interplay and relative contributions of endocrine and physical factors both prior and subsequent to fertilization that influence both oocyte competence and maternal environment and their roles in establishment and maintenance of pregnancy.

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen

A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1–V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4–99.9% of OTUs represented by more than one read, using Good’s coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.

Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

Background

WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1⁺ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms.

Results

Real-time quantitative PCR using DNA from the animal whose genome was sequenced (“Dominette”) and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR “a” pattern) of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms.

Conclusion

The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose sequences are highly conserved among individual cattle and breeds. The sequence diversity necessary for WC1 genes to function as a multi-genic pattern recognition receptor array is encoded in the genome, rather than generated by recombinatorial diversity or hypermutation.

Effects of reduced panel, reference origin, and genetic relationship on imputation of genotypes in Hereford cattle

The objective of this study was to investigate alternative methods of designing and using reduced SNP panels for imputing SNP genotypes. Two purebred Hereford populations, an experimental population known as Line 1 Hereford (L1, n = 240) and registered Hereford with American Hereford Association (AHA, n = 311), were used. Using different reference samples of 62 to 311 animals with 39,497 SNP on 29 autosomes and study samples of 57 or 62 animals for which genotypes were available for ~2,600 SNP (reduced panels), imputations were performed to predict the other ~36,900 loci that had been masked. An imputation package, including LinkPHASE and DAGPHASE, was used for imputation. Four reduced panels differing in minor allele frequency (MAF) and marker spacing were evaluated. Reduced panels included every 15th SNP across the genome (SNP_space), commercial Illumina Bovine3K Beadchip (SNP_3K), SNP with the highest MAF (SNP_MAF), and SNP with high MAF that were also evenly spaced across the genome (SNP_MS). Imputation accuracy was defined as the correlation of imputed genotypes and real genotypes. Reference samples were either from L1 or AHA. Among animals with genotypes, genetic relationships were estimated based on molecular marker genotypes or pedigree. Reduced panel design, number of animals in the reference sample, reference origin and genetic relationship between animals in the reference, and study samples all affected imputation accuracy (P < 0.001). Across genotyping schemes, imputed genotypes from SNP_MS had the greatest accuracy. A 0.1 increase in average pedigree relationship or average molecular relationship between reference and study samples increased imputation accuracy 10 to 20%. Using reference samples from the L1 population resulted in lower imputation accuracy than using reference samples from the admixed population AHA (P < 0.001). Increasing the number of animals in the reference panel by 100 individuals increased imputation accuracy by 8% when pedigree relationship was used as a covariate and 6% when molecular relationship was used as a covariate. We concluded that imputation accuracy would be increased through optimization of reduced panel design and genotyping strategy.

An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

BACKGROUND

A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines.

RESULTS

The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the draft bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the draft genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance.

CONCLUSIONS

The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function.

Analysis of copy number variations among diverse cattle breeds

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or approximately 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

Discovery of novel genetic networks associated with 19 economically important traits in beef cattle

Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F₂ animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (≤ 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.

The sequence of porcine alpha s1-casein cDNA: evidence for protein variants generated by altered RNA splicing

A cDNA library was constructed from mRNA isolated from lactating porcine mammary gland and screened with a bovine alpha s1-casein cDNA clone. Three classes of cDNA isolated varied in the number of bases within the coding region. The full length porcine alpha s1-casein cDNA is 1124bp and codes a preprotein of 206 amino acids. The other two classes of alpha s1-casein cDNA lacked 18bp and 60bp respectively when compared to the 1124-bp cDNA sequence. PCR amplification confirmed the presence of these sequences in total RNA. These differences appear to be due to altered RNA splicing.

Sequence of porcine beta-lactoglobulin cDNA

cDNAs encoding porcine beta-lactoglobulin were isolated and sequenced. The porcine beta-lactoglobulin cDNA is 768bp in length and encodes a pre-protein of 178 amino acids. One additional cDNA clone was found to encode an additional amino acid (lysine) in the mature protein.

Cloning and sequencing of the porcine kappa-casein cDNA

cDNA clones encoding porcine kappa-casein were isolated and sequenced. The porcine kappa-casein cDNA is 851 bp in length and encodes a preprotein of 188 amino acids.

The sequence of porcine beta-casein cDNA

Porcine cDNAs clones encoding beta-casein were isolated and sequenced. The porcine beta-casein cDNA is 1100bp in length, excluding the poly(A) tail, and encodes a preprotein of 232 amino acids.

Cloning and sequencing of the porcine lactoferrin cDNA

cDNA clones encoding the entire porcine lactoferrin protein were isolated and sequenced. The porcine lactoferrin cDNA sequence presented here is 2259bp in length and encodes a leader peptide of 19 amino acids and a mature protein of 684 amino acids. Comparisons with other lactoferrins indicate a single glycosylation site. The iron- and anion-binding sites, and the cysteine residues involved in disulphide bonds, are conserved between the lactoferrin proteins.

Detection of germline and somatic copy number variations in cattle

As a complement to the Bovine HapMap Consortium project, we initiated a systematic study of the copy numbervariation (CNV) within the same cattle population using array comparative genomic hybridization (array CGH). Oligonucleotide CGH arrays were designed and fabricated to cover all chromosomes with an average interval of 6 kb using the latest bovine genome assembly. In the initial screening, three Holstein bulls were selected to represent major paternal lineages of the Holstein breed with some maternal linkages between these lines. Dual-label hybridizations were performed using either Hereford L1 Dominette 01449 or L1 Domino 99375 as reference. The CNVs were represented by gains and losses of normalized fluorescence intensities relative to the reference. The data presented here, for the first time, demonstrated that significant amounts of germline and fewer somatic CNVs exist in cattle, that many CNVs are common both across diverse cattle breeds and among individuals within a breed, and that array CGH is an effective tool to systematically detect bovine CNV. Selected CNVs have been confirmed by independent methods using real-time (RT) PCR. The strategy used in this study, based on genome higher-orderarchitecture variation, is a powerful approach to generating resources for the identification of novel genomic variation and candidate genes for economically important traits.

Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population

A whole-genome scan was conducted on 328 F(2) progeny in a Wagyu x Limousin cross to identify quantitative trait loci (QTL) affecting palatability and fatty acid composition of beef at an age-constant endpoint. We have identified seven QTL on five chromosomes involved in lipid metabolism and tenderness. None of the genes encoding major enzymes involved in fatty acid metabolism, such as fatty acid synthase (FASN), acetyl-CoA carboxylase alpha (ACACA), solute carrier family 2 (facilitated glucose transporter) member 4 (SLC2A4), stearoyl-CoA desaturase (SCD) and genes encoding the subunits of fatty acid elongase, was located in these QTL regions. The present study may lead to a better-tasting and healthier product for consumers through improved selection for palatability and lipid content of beef.

Influence of seasonal forage quality on glucose kinetics of young beef cows1

Extensive range livestock production systems in the western United States rely heavily on rangeland forages to meet the nutritional needs of grazing livestock throughout the year. Interannual variation in the quantity and quality of rangeland forage in the Northern Great Plains, as well as throughout much of the western United States, may play a pivotal role in how well grazing ruminants sequester nutrients in their tissues. This variation in forage quality may influence the ability of a beef cow to utilize dietary nutrients via changes in tissue responsiveness to insulin. Identifying specific periods and production states in which this phenomenon is manifested will provide insight into the development and implementation of strategic and targeted supplementation practices that improve nutrient utilization during times of nutritional imbalance and may improve the lifetime productivity of grazing range beef cows. A 2-yr study was conducted to monitor serum metabolites, glucose kinetics during glucose tolerance tests, and forage chemical composition every 90 d in young cows (2 to 4 yr of age; n = 28). In yr 1 and 2, cows were managed on 4 pastures varying in size from 36 to 76 ha in yr 1 and 49 to 78 ha in yr 2. Regardless of year, cow age, or cow physiological status, the main factor influencing glucose half-life was season of the year (P = 0.02). Effects of season on glucose half-life closely followed assessments describing forage quality, with glucose half-lives of 46, 39, 43, and 51 +/- 3.9 min for May, August, December, and March, respectively. Elevated glucose half-life during seasons in which forage quality is of lower nutritive value indicated that tissue responsiveness to the actions of insulin followed seasonal changes in forage quality. Glucose half-life tended (P = 0.09) to decrease between May and August, increased (P = 0.04) between December and March, and showed a tendency (P = 0.10) to decrease in seasons of greater nutrient density (May and August) compared with seasons of lower nutrient density (December and March). Seasonal changes in serum metabolites were also observed and corresponded with changes in forage quality. The results support our hypothesis that as the season progresses and forage quality declines, maternal tissues become less responsive to insulin, indicating that targeted supplementation with glucogenic precursors during these seasons of nutritional stress may improve cow performance.

Quantitative trait loci with additive effects on growth and carcass traits in a Wagyu-Limousin F2 population

A whole-genome scan for carcass traits [average daily gain during the pre-weaning, growth and finishing periods; birth weight; hot carcass weight and longissimus muscle area (LMA)] was performed on 328 F(2) progeny produced from Wagyu x Limousin-cross parents derived from eight founder Wagyu bulls. Nine significant (P </= 0.05) and four suggestive (P </= 0.1) QTL affecting seven growth and carcass traits were identified. Significant QTL were located on bovine chromosomes 2, 4, 7, 9, 12, 16, 17 and 29. A QTL previously reported on chromosome 2 for LMA was also detected in this study. These results provide insight into genetic differences between the Wagyu and Limousin breeds.

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.

Genetic partitioning of variation in ovulatory follicle size and probability of pregnancy in beef cattle1

The objectives of this research were to partition variation in ovulatory follicle size into genetic and nongenetic components and to assess the utility of ovulatory follicle size as an indicator trait associated with reproductive success in beef cattle. Data were collected during the years 2002 to 2005 from 780 beef females that ranged in age from 1 to 12 yr (mean of 2.4 observations per female). Data were analyzed with a multiple trait Gibbs sampler for animal models to make Bayesian inferences from flat priors. A chain of 500,000 Gibbs samples was thinned to every 200th sample to produce a posterior distribution composed of 2,500 samples. Heritability estimates (posterior mean +/- SD) were 0.16 +/- 0.03 for follicle size and 0.07 +/- 0.02 and 0.02 +/- 0.01 for pregnancy rate as a trait of the female and service sire, respectively. Posterior means of genetic correlations were all <0.10, with 0.00 contained within the respective 90% probability density posterior intervals. Results indicate that whereas follicle size is of greater heritability than pregnancy rate, its usefulness to improve reproductive rate is greatest as an ancillary phenotype in multiple trait selection.

A radiation hybrid map for the bovine Y Chromosome

Screening a bovine Y Chromosome-specific DNA library resulted in 34 new microsatellites, six of which mapped to the pseudoautosomal region (PAR), and 28 localized to the Y-specific region. These microsatellites, together with 23 markers previously mapped to the bovine Y Chr, were scored on a 7000-rad cattle-hamster radiation hybrid (RH) panel. Retention frequency of individual markers ranged from 18.5% to 76.5% with an average of 48.4%. Markers with high retention frequency (>55%) were found to exist in multiple copies on the Y Chr. Thirteen markers were placed on the PAR RH map with the AmelY gene proximal to the pseudoautosomal boundary and 46 markers, including Sry and Tspy gene, on the Y-specific region of the RH map. The microsatellites developed and mapped in this work will be useful for comparative mapping of cattle, sheep, and goat, studying the origin, evolution, and migration of bovidae species and provide an initial platform to develop a high-resolution map of the Y Chr and positional cloning of Y-specific genes.

An integrated comparative map of the porcine X chromosome

The objectives of this study were to assign both microsatellite and gene-based markers on porcine chromosome X to two radiation hybrid (RH) panels and to develop a more extensive integrated map of SSC-X. Thirty-five microsatellite and 20 gene-based markers were assigned to T43RH, and 16 previously unreported microsatellite and 15 gene-based markers were added to IMpRH map. Of these, 30 microsatellite and 12 gene-based markers were common to both RH maps. Twenty-two gene-based markers were submitted to BLASTN analysis for identification of orthologues of genes on HSA-X. Single nucleotide polymorphisms (SNPs) were detected for 12 gene-based markers, and nine of these were placed on the genetic map. A total of 92 known loci are present on at least one porcine chromosome X map. Thirty-seven loci are present on all three maps; 31 loci are found on only one map. Location of 33 gene-based markers on the comprehensive map translates into an integrated comparative map that supports conservation of gene order between SSC-X and HSA-X. This integrated map will be valuable for selection of candidate genes for porcine quantitative trait loci (QTLs) that map to SSC-X.

Interval mapping of carcass and meat quality traits in a divergent swine cross

An autosomal scan of the swine genome with 119 polymorphic microsatellite (ms) markers and data from 116 F2 barrows of the University of Illinois Meishan x Yorkshire Swine Resource Families identified genomic regions with effects on variance in carcass composition and meat quality at nominal significance (p-value <0.05). Marker intervals on chromosomes 1, 6, 7, 8 and 12 (SSC1, SSC6, SSC7, SSC8, SSC12) with phenotypic effects on carcass length, 10th rib backfat thickness, average backfat thickness, leaf fat, loin eye area and intramuscular fat content confirm QTL effects identified previously based on genome wide significance (p-value <0.05). Several marker intervals included nominally significant (p-value <0.05) dominance effects on leaf fat, 10th rib backfat thickness, loin eye area, muscle pH and intramuscular fat content.

Generation and exploration of a dense genetic map in a region of a QTL affecting corpora lutea in a Meishan x Yorkshire cross

Previously genomic scans revealed quantitative trait loci (QTL) on porcine Chromosome 8 (SSC8) as significantly affecting the number of corpora lutea (CL) in swine. In one study, statistical evidence for the putative QTL was found in the chromosomal region defined by the microsatellites (MS) SW205, SW444, SW206, and SW29. A Yeast Artificial Chromosome library was screened by using the corresponding primers for clones containing these MS by PCR. From five positive YAC clones, 10 additional MS were isolated and mapped to SSC8 with the INRA-University of Minnesota porcine Radiation Hybrid (IMpRH) panel. The genetic map position of the QTL has been refined by addition of these 10 markers. The QTL evaluation included pedigrees of F2-intercross Meishan x Yorkshire design, with phenotypic data of 108 F2 female offspring and genotypic data for 29 MS markers on SSC8. The analysis was performed by using the least squares regression method. The calculated QTL effect for CL obtained by the multilocus least squares method showed a maximum test statistic (F value = 13.98) at position 99 cM between three MS derived from YACs containing SW205 and SW1843 spanning an interval of 7.1 cM. The point-wise (nominal) P-value was 5.21 x 10-6 corresponding to a genome-wide P-value of 0.009. The additive QTL effect explained 17.4% of the phenotypic variance.

Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping

Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and Göttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

Porcine factor V: cDNA cloning, gene mapping, three-dimensional protein modeling of membrane binding sites and comparative anatomy of domains

Factor V is a plasma protein essential for blood coagulation. This protein is involved in activated protein C resistance, the most common inherited thrombotic disorder known. We utilized the polymerase chain reaction to clone the porcine factor V gene by generating overlapping clones amplified with primers chosen by comparison with known nucleotide sequences. The porcine factor V cDNA contig encodes a predicted 2258-amino acid protein, making it the largest in comparison to the bovine, human, and murine proteins. Porcine factor V has the highest level of homology with bovine factor V, but also has high levels of conservation of important residues with all the species. Radiation hybrid mapping assigned the porcine factor V gene to chromosome 4. Three-dimensional models of factor V were generated and used to analyze membrane-binding sites in terms of conserved, and therefore likely important residues.

Identification and radiation hybrid mapping of members of the porcine proteasome/ubiquitin system

We report the identification and radiation hybrid mapping of members of the proteasome/ubiquitin system in pigs that, so far, have only been identified in humans and cattle. Expressed sequence tags (ESTs) were constructed from ten oligo(dT)-primed individually tagged, directionally cloned and normalized cDNA libraries from peripheral blood cells (PBC), spleen (Sp), thymus (Th), lymph node (LN) and bone marrow (BM) from immunologically naive and challenged pigs as part of an implant-associated orthopedic infection model. The ESTs mapped using the 7000 rad IMpRH panel (Hawken et al., 1999) were ubiquitin fusion-degradation 1 like protein (UFD1L), ubiquitin activating enzyme E1 and ubiquitin-S27a fusion protein which mapped to porcine chromosomes 14, 7 and X, respectively.

Epinephrine fails to enhance performance of food-deprived rats on a delayed spontaneous alternation task

Increases in blood glucose levels after epinephrine injection appear to contribute to the hormone's effects on learning and memory. The present experiment evaluated whether epinephrine-induced enhancement of spontaneous alternation performance would be attenuated in fasted rats that had blunted increases in circulating glucose levels after injections of epinephrine. Rats deprived of food for 24 h prior to injection of epinephrine exhibited significant attenuation of the increase in blood glucose levels seen in fed rats. When the rats were tested on a delayed spontaneous alternation task, epinephrine enhanced performance in fed rats but not in rats deprived of food for 24 h. These findings are consistent with the view that hyperglycemia subsequent to epinephrine injections contributes to the memory-enhancing effects of epinephrine.

A first-generation porcine whole-genome radiation hybrid map

A whole-genome radiation hybrid (WG-RH) panel was used to generate a first-generation radiation map of the porcine (Sus scrofa) genome. Over 900 Type I and II markers were used to amplify the INRA-University of Minnesota porcine Radiation Hybrid panel (IMpRH) comprised of 118 hybrid clones. Average marker retention frequency of 29.3% was calculated with 757 scorable markers. The RHMAP program established 128 linkage groups covering each chromosome (n = 19) at a lod >/= 4.8. Fewer than 10% of the markers (59) could not be placed within any linkage group at a lod score >/=4.8. Linkage group order for each chromosome was determined by incorporating linkage data from the swine genetic map as well as physical assignments. The current map has an estimated ratio of approximately 70 kb/cR and a maximum theoretical resolution of 145 kb. This initial map forms a template for establishing accurate YAC and BAC contigs and eventual positional cloning of genes associated with complex traits.

A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea

Reproductive traits have low heritabilities, are expressed in only one sex, and are not measurable until sexual maturity (Avalos and Smith, Anim Prod 44:153, 1987). Using traditional methods, selection for reproductive traits is relatively less effective than selecting for growth or carcass traits. Traits most affected by a small number of genes with major effects rather than many genes with small effects are most amenable to MAS. As part of our porcine genome scan to identify quantitative trait loci (QTLs) of economic importance in marker-assisted selective (MAS) breeding programs, we examined 8 reproductive and farrowing traits in the University of Illinois (UI) Meishan x Yorkshire Resource Family. Gilts were genotyped with 119 microsatellite markers (MS) with intervals averaging 24 cM over all 18 porcine autosomes. F-ratios supporting QTL location were calculated by the least squares regression method. Results suggestive of linkage at the 5% genome-wide level were observed for the number of stillborn piglets on Chromosome (Chr) 4 (SSC4) (p-value = 0.0001), corpora lutea on SSC8 (p-value = 0.00027), and gestation length on SSC9 (p-value = 0.00019). Results for additional loci relevant to litter size, number of corpora lutea on SSC15 and 7 (p-value = 0.0029 and 0.0028 at 107 and 150 cM, respectively), gestation length on SSC15 and 1 (p-value = 0.0017 and 0.0069 at 96 and 166 cM, respectively), uterine length on SSC7 and 5 (p-value = 0.0044 and 0.0075 at 148 and 1 cM, respectively) and piglets born per litter on SSC6 (p-value = 0.0075 at 102 cM), were not statistically significant at the 5% genome-wide level. Thus, the use of a linked marker to facilitate selection for reproductive traits has considerable potential. By using linked markers, selection can be applied to both sexes before sexual maturity, making genetic selection considerably more efficient and less costly.

Interval mapping of growth in divergent swine cross

A genomic scan of 18 swine autosomal chromosomes was constructed with 119 polymorphic microsatellite (ms) markers to identify quantitative trait loci (QTL) for 11 growth traits in the University of Illinois Meishan x Yorkshire Swine Resource Family. A significant QTL effect was found for post-weaning average daily gain (ADG) between 5.5 and 56 kg of body weight that mapped between markers SW373 and SW1301 near the telomere of Chromosome (Chr) 1 q (SSC1). This QTL effect had a nominal (pointwise) p-value of 0.000007, a genome wide p-value of 0.012, and accounted for 26% of the F2 phenotypic variance. The same chromosome region also had significant effects on ADG between birth and 56 kg body weight (p-value =. 000227), and on ADG between 35 and 56 kg (p-value =.00077). These observations suggest that a significant QTL for post-weaning growth resides on SSC1.

Evolution of the trappin multigene family in the Suidae

Trappins are a group of secretory proteins containing a WAP motif with an anchoring domain. Previous studies showed that their genes, especially those of pig, have undergone rapid evolution, which produced trappins with a broad spectrum of actions. To understand the evolution of such a rapidly evolving multigene family, we isolated trappin genes of the Artiodactyla, including pig, wart hog, collared peccary, hippopotamus, and cow, by means of polymerase chain reaction (PCR). Two genes newly isolated from wart hog are orthologs of trappin-1 (SPAI) and trappin-2 (elafin), the others are novel members of the trappin family and named trappins-6 to 11. The divergence of the sequences is greatest in the region that encodes the reactive site, and intron sequences appear to be more highly conserved than the protein-coding sequences, especially among the pig paralogs. Phylogenetic analysis showed that the trappin multigene family members of pig were generated through gene duplication after the divergence of the Suidae (pig and wart hog) and Tayassuidae (collared peccary). Similarities in the gene structure with seminal vesicle clotting proteins (REST) and WAP motif-containing proteins suggest that trappins are naturally occurring fusion proteins created through exon shuffling between ancestral REST and WAP motif-coding genes.

Physical ordering of six YACs from the RN region in pigs

Six YAC clones representing five microsatellite markers from the RN region were mapped by fluorescent in situ hybridization (FISH) on pig metaphase chromosomes and their relative order was determined by pairwise multicolour FISH. Two of the microsatellites viz., Sw120 and Sw936 flank RN as well as the remaining three microsatellites Sw1683, Sw2083 and Sw1309. The results assigned the RN locus to the distal part of the 15q25 band. The linear order of the microsatellites was compared with the available linkage mapping data.

Mapping genes located on human chromosomes 2 and 12 to porcine chromosomes 15 and 5

Informative microsatellites associated with two genes on HSA12 (lysozyme, LYZ; tumour necrosis factor receptor, TNFR) and one gene on HSA2 (glutamic acid decarboxylase 1, GAD1) were mapped in the US Meat Animal Research Center (MARC) swine reference population and the physical assignment of a-lactalbumin (LALBA) was determined. A comparative map for HSA2 and HSA12 with SSC15 and SSC5, respectively, was developed by combining the results from this study with published type I loci mapped in both species. One rearrangement between HSA2 and SSC15 was detected while the number of rearrangements between HSA12 and SSC5 were numerous. These results indicated that conservation of synteny does not imply a conservation of gene order and that additional type I markers need to be mapped in the pig to fully understand the chromosomal rearrangements that occurred during the evolution of mammals.