Inheritance of the SLICK1 allele of PRLR in cattle.

The slick-hair phenotype in cattle is due to one of a series of mutations in the prolactin receptor (PRLR) that cause truncation of the C-terminal region of the protein involved in JAK2/STAT5 activation during prolactin signaling. Here we evaluated whether the inheritance of the SLICK1 allele, the first slick mutation discovered, is inherited in a fashion consistent with Hardy-Weinberg equilibrium. It was hypothesized that any deleterious effect of inheriting the allele on embryonic or fetal function would result in reduced frequency of the allele in offspring. A total of 525 Holstein and Senepol cattle produced from matings involving one or both parents with the SLICK1 allele were genotyped. The observed frequency of the SLICK1 allele (0.247) was not significantly different than the expected frequency of 0.269. These results support the idea that inheritance of the SLICK1 allele does not act in the embryo or fetus to modify its competence to complete development to term.

Correction to: Genes associated with survival of female bovine blastocysts produced in vivo.

The first error is on page 5. A sentence lists two genes as SCNA1A and SCNA2A but they should be SCN1A and SCN2A.

Genes associated with survival of female bovine blastocysts produced in vivo.

The objective was to characterize the transcriptome profile of in vivo-derived female embryos competent to establish and maintain gestation. Blastocysts from superovulated heifers were bisected to generate two demi-embryos. One demi-embryo was transferred into a synchronized recipient and the other part was used for RNA-seq analysis. Data on transcript abundance was analyzed for 4 demi-embryos that established and maintained pregnancy to day 60 (designated as PP) and 3 that did not result in a pregnancy at day 30 (designated as NP). Using a false discovery rate of P < 0.10 as cutoff, a total of 155 genes were differentially expressed between PP and NP embryos, of which 73 genes were upregulated and 82 genes were downregulated in the PP group. The functional cluster with the greatest enrichment score for embryos that survived, representing 28 genes (48% of the annotated genes), was related to membrane proteins, particularly those related to olfaction and neural development and function. The functional cluster with the greatest enrichment score for downregulated genes in embryos that survived included terms related to oxidative phosphorylation, mitochondrial function, and transmembrane proteins. In conclusion, competence of in vivo-derived female bovine embryos to survive after transfer is associated with increased expression of genes encoding transmembrane proteins, perhaps indicative of differentiation of the inner cell mass to epiblast, and decreased expression of genes involved in oxidative phosphorylation, perhaps indicative of reduced metabolic activity.

Molecular fingerprint of female bovine embryos produced in vitro with high competence to establish and maintain pregnancy†.

The objective was to identify the transcriptomic profile of in vitro-derived embryos with high competence to establish and maintain gestation. Embryos produced with X-sorted sperm were cultured from day 5 to day 7 in serum-free medium containing 10 ng/ml recombinant bovine colony-stimulating factor 2 (CSF2) or vehicle. The CSF2 was administered because this molecule can increase blastocyst competence for survival after embryo transfer. Blastocysts were harvested on day 7 of culture and manually bisected. One demi-embryo from a single blastocyst was transferred into a synchronized recipient and the other half was used for RNA-seq analysis. Using P < 0.01 and a fold change >2-fold or <0.5 fold as cutoffs, there were 617 differentially expressed genes (DEG) between embryos that survived to day 30 of gestation vs those that did not, 470 DEG between embryos that survived to day 60 and those that did not, 432 DEG between embryos that maintained pregnancy from day 30 to day 60 vs those where pregnancy failed after day 30, and 635 DEG regulated by CSF2. Pathways and ontologies in which DEG were overrepresented included many related to cellular responses to stress and cell survival. It was concluded that gene expression in the blastocyst is different between embryos that are competent to establish and maintain pregnancy vs those that are not. The relationship between expression of genes related to cell stress and subsequent embryonic survival probably reflects cellular perturbations caused by embryonic development taking place in the artificial environment associated with cell culture.

Sobrediagnóstico de trastornos mentales y criterios diagnósticos del DSM: la perspectiva de Jerome Wakefieldx / Mental Disorders Over-Diagnosis and DSM diagnosis criteria: Jerome Wakefield's perspective

Resumen El sobrediagnóstico de trastornos mentales es una preocupación creciente, que se acentuó tras la publicación del DSM-V. Jerome Wakefield es un destacado crítico de la psicopatologización que, sin embargo, ha desarrollado un intenso trabajo para intentar delimitar mejor qué es un trastorno mental sin rechazar este concepto. Se realizó una revisión estructurada de la obra de este autor. Se resumen sus principales planteamientos y se realiza una valoración de su aporte al debate relativo a este tema.

Overdiagnosis of mental disorders is an increasing concern, which was accentuated after the publication of the DSM-V. Jerome Wakefield is a renowned critic of the psycopathologization that, however, has developed an intense work to try to better delimit what a mental disorder is without rejecting this concept. A structured review of the work of this author was carried out. His main approaches are summarized and an assessment of his contribution to the discussion in regards of this issue is performed.

Use of RNA-seq to determine variation in canine cytochrome P450 mRNA expression between blood, liver, lung, kidney and duodenum in healthy beagles.

RNA sequencing (RNA-seq) is a powerful tool for the evaluation and quantification of transcriptomes and expression patterns in animals, tissues, or pathological conditions. The purpose of this study was to determine the physiologic expression of cytochrome P450 (CYP) mRNA transcripts in whole blood, kidney, duodenum, liver, and lung in healthy, adult male (n = 4) and female (n = 4) beagles via RNA-seq. mRNA expression was above background (transcripts per million) for 45 canine CYPs, with liver, duodenum, and lung expressing a high number of xenobiotic metabolizing CYPs, while prominent endogenous metabolizing CYP expression was present in blood and kidney. The relative expression pattern of CYP2A13, 2B11, 2C21, 2D15, 2E1, 3A12, and 27A1 in liver, lung, and duodenum was verified through qPCR. This is the first global profiling of physiologic CYP mRNA expression in multiple canine tissues, providing a platform for further studies characterizing canine CYPs and changes in gene expression in disease states.

Evaluation of the efficacy of Grofactor, a beta-adrenergic agonist based on zilpaterol hydrochloride, using feedlot finishing bulls.

Beta-adrenergic agonists (ß-AA) have been shown to positively impact finishing performance and some carcass traits of feedlot cattle. Our objective was to evaluate the efficacy of a ß-AA on the basis of zilpaterol hydrochloride (Grofactor, Laboratorios Virbac México, Guadalajara, Mexico) on growth and DMI, carcass characteristics, and meat quality of finishing bulls. Forty-five bulls (75% 25% ) initially weighing 448.7 ± 2.58 kg were blocked by BW and randomly assigned to 1 of 3 diets, using pens of 3 animals, in a randomized complete block design: 1) daily feeding without ß-AA in the basal diet (Control), 2) daily feeding with 0.15 mg/kg BW of Grofactor added to the basal diet (ZHG), or 3) daily feeding with 0.15 mg/kg BW of Zilmax (MSD Salud Animal México, Mexico City, Mexico) added to the basal diet (ZHZ). The duration of the feeding period was 30 d with a subsequent 4-d withdrawal period. Compared with Control bulls, the group fed ZHG had a 12% better ( < 0.025) G:F ratio, and their final BW ( 0.094) and ADG ( 0.084) tended to be enhanced. Feedlot performance of ZHG and ZHZ bulls was similar, although the DMI was ∼4% lower ( 0.05) in ZHG bulls vs. the ZHZ and Control groups. The HCW ( 0.001) and dressing percentage ( 0.015) were higher by 20 kg and 3%, respectively, in ZHG bulls vs. Control bulls. The KPH fat was lower ( 0.007) in bulls fed ZHG than in nonsupplemented bulls, but other carcass characteristics were not different in the ZHG and ZHZ bulls, and noncarcass components were not affected by ZHG or ZHZ supplementation. At 48 h postmortem, ZHG bulls had lower ( 0.007) water holding capacity and trended toward ( 0.06) increased chroma and reduced pH ( 0.09) compared to Control bulls. However, compared to ZHZ bulls, ZHG bulls had higher ( 0.02) chroma and a trend ( 0.08) toward increased hue angle. At 14 d postmortem, meat quality variables did not differ between the 3 groups of bulls. Supplementation of ZH Grofactor improved feedlot performance and some carcass characteristics of finishing bulls without affecting meat quality. The effects of Grofactor on feedlot performance, carcass traits, and meat quality were similar to those of Zilmax.

Near-term embryos in a Pristis pristis (Elasmobranchii: Pristidae) from Brazil.

This paper describes the record of a gravid Pristis pristis from the north coast of Maranhão State (Brazil) in May of 2009 by an artisanal vessel. Size, mass and rostrum length of the adult female were estimated at 5000 mm, 750000 g and 1536 mm, respectively. Total length (LT ) of miscarried embryos ranged from 755 to 800 mm and total mass from 890 to 1120 g. Although this is a single record, it indicates that P. pristis births may be taking place during May or coming months and there may be population differences between Central and South America.

Caracterización de la discapacidad en población con limitaciones permanentes en movilidad o autocuidado, Girón, Colombia / Characterization of disabled people with permanent limitations in mobility and self-care in Giron, Colombia

Objetivo: Determinar las características de la población con limitaciones permanentes en movilidad y autocuidado de 17 barrios del área urbana del municipio de Girón, Santander 2012-2013. Materiales y métodos: Se realizó un estudio descriptivo, observacional y transversal, que utilizó el Registro para la localización y caracterización de las personas con discapacidad (RLCPD), diseñado por el Departamento Administrativo Nacional de Estadística (DANE). Estudiantes de fisioterapia previamente entrenados entrevistaron a cuidadores o personas con discapacidad. Resultados: Se encuestó a 189 personas, el 50,3% mujeres, el 45,5% tenía entre 60 y 100 años de edad y el 79,9% presentó alteraciones en el movimiento del cuerpo, las manos, los brazos y las piernas. En relación con las actividades y la participación, al 91% se le dificultó caminar, correr, saltar; al 41,3% llevar, mover, utilizar objetos con las manos. En las funciones corporales comprometidas, el 60,3% correspondía a movilidad. La enfermedad general fue la mayor causa de discapacidad (33,9%). Conclusiones: Las personas con limitaciones permanentes en la movilidad y el autocuidado en el área urbana de Girón en un alto porcentaje son adultas mayores pertenecientes a un estrato socioeconómico. Las limitaciones en el movimiento predominantes son las de manos, brazos y piernas, teniendo afectación en al menos dos estructuras corporales

Objective: To determine the characteristics of people with permanent limitations in mobility and self-care in 17 districts of the urban area of Giron, Santander 2012-2013. Materials and methods: A descriptive, observational, cross-sectional study was conducted using the tool Register for the Location and characterization of the disabled people (RLCDP), designed by the National Administrative Department of Statistics (DANE). Previously trained physiotherapy students interviewed caregivers or disabled people. Results: A total of 189 people were studied of 50.3% women, and 45.5% between 60 and 100 years old. A large majority (79.9%) had alterations in body movement, hands, arms and legs. As regards activities and participation, 91% had difficult to walk, run, jump, and 41.3% found it difficult to lead, move, and use objects with hands. Of the bodily functions, 60.3% involved mobility. General illness diseases were the main cause of disability (33.9%). Conclusions: A high percentage of persons with permanent mobility limitations and caring for themselves in the urban area of Girona are older adults from socioeconomic level 2. The predominant mobility limitations are in the hands, arms, and legs, with involvement in at least two body structures

Evaluación de la susceptibilidad antimicrobiana de cepas de Salmonella spp. aisladas del beneficio porcino en Colombia / Evaluation of Antimicrobial susceptibility of Salmonella spp. strains isolated from Pork Carcasseson Colombia

OBJETIVOS: el estudio buscó establecer patrones de resistencia antimicrobiana de 155 cepas de Salmonella spp., aisladas de la superficie de canales de cerdo, procedentes de plantas de beneficio en Colombia. METODOLOGIA:mediante el método de difusión en disco (Bauer et. Kirby, 1966) se evaluaron nueve antimicrobianos: Amoxicilina y ácido clavulánico (30 ug), Ampicilina (10 ug), Ceftiofur (30 ug), Ciprofloxacina (5 ug), Cloranfenicol (30 ug), Florfenicol (30 ug), Gentamicina (10 ug), Sulfadiazina y Trimetoprim (25 ug) y Tetraciclina (30 ug). RESULTADOS:los resultados confirmaron la presencia de cepas multiresistentes de Salmonella spp. de origen porcino, mostrando 30 patrones diferentes de multiresistencia; el más común fue Ampicilina, Amoxicilina, Cloranfenicol, Florfenicol y Tetraciclina en el 16,77% (n=26) de las cepas. Tetraciclina y Florfenicol fueron los antimicrobianos menos efectivos en el 94,84% (n=147) y 47,74% (n=74) de cepas resistentes, respectivamente. DISCUSION:se deben consolidar los sistemas de monitoreo, y de vigilancia y control de las resistencias antimicrobianas para prevenir, con un enfoque de cadena productiva, la diseminación de cepas multiresistentes en alimentos de origen animal, como parte integral del sistema de gestión de inocuidad de los alimentos en Colombia.

OBJECTIVE: this study was aimed to establish the patterns of antimicrobial resistance in 155 strains of Salmonella spp. isolated from pig carcasses in slaughter house in Colombia. METHODOLOGY: using the disc diffusion method (Bauer & Kirby, 1966) we evaluated nine antibiotics: amoxicillin-clavulanic acid (30 ug), ampicillin (10 ug), ceftiofur (30 ug), ciprofloxacin (5 ug), chloramphenicol (30 ug), florfenicol (30 ug), gentamicin (10 ug), sulfadiazine / trimethoprim (25 ug) and tetracycline (30 ug). RESULTS: the results confirm the presence of multiresistant strains of Salmonella spp. in pig slaughter house, showing 30 different patterns of multidrug resistance, the most common was ampicillin, amoxicillin, chloramphenicol, florfenicol and tetracycline in 16.77% (n = 26) strains. Tetracycline and florfenicol were less effective with 94.84% (n = 147) and 47.74% (n = 74) of the resistant strains, respectively. DISCUSSION: it must consolidate monitoring programs and surveillance and control systems to prevent the spread of multiresistant strains in foods of animal origin, with an approach of supply chain of pork, as an essential element of food safety system in Colombia.

Bovine and murine tissue expression of insulin like growth factor-I.

The genomic architecture and expression of the Igf-1 gene are complex yielding multiple IGF-I transcript isoforms with putative functional contributions to growth and metabolism. Using RNA-seq on different tissues, physiological states, and species, the breadth of transcripts expressed was determined. Tissues from pre- and post-pubertal heifers and mature mice were collected and the transcript isoforms characterized. Three different IGF-I isoforms were detected in heifers with Class 1 transcripts most abundantly expressed. The pituitary reduced IGF-I expression post-pubertally whereas the uterus increased expression. Murine IGF-I transcript expression was more diverse utilizing multiple exons, start sites, and 3'UTRs. The RNA-seq methodology to characterize expression profiles permits assessment of the transcript isoforms yielding insight into functional roles of each transcript.

RNA sequencing to study gene expression and single nucleotide polymorphism variation associated with citrate content in cow milk.

The technological properties of milk have significant importance for the dairy industry. Citrate, a normal constituent of milk, forms one of the main buffer systems that regulate the equilibrium between Ca(2+) and H(+) ions. Higher-than-normal citrate content is associated with poor coagulation properties of milk. To identify the genes responsible for the variation of citrate content in milk in dairy cattle, the metabolic steps involved in citrate and fatty acid synthesis pathways in ruminant mammary tissue using RNA sequencing were studied. Genetic markers that could influence milk citrate content in Holstein cows were used in a marker-trait association study to establish the relationship between 74 single nucleotide polymorphisms (SNP) in 20 candidate genes and citrate content in 250 Holstein cows. This analysis revealed 6 SNP in key metabolic pathway genes [isocitrate dehydrogenase 1 (NADP+), soluble (IDH1); pyruvate dehydrogenase (lipoamide) ß (PDHB); pyruvate kinase (PKM2); and solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1)] significantly associated with increased milk citrate content. The amount of the phenotypic variation explained by the 6 SNP ranged from 10.1 to 13.7%. Also, genotype-combination analysis revealed the highest phenotypic variation was explained combining IDH1_23211, PDHB_5562, and SLC25A1_4446 genotypes. This specific genotype combination explained 21.3% of the phenotypic variation. The largest citrate associated effect was in the 3' untranslated region of the SLC25A1 gene, which is responsible for the transport of citrate across the mitochondrial inner membrane. This study provides an approach using RNA sequencing, metabolic pathway analysis, and association studies to identify genetic variation in functional target genes determining complex trait phenotypes.

Estrés postraumático en población infantojuvenil post 27F / Post-traumatic stress disorder in young population after the natural disaster on February 27, 2010

Introduction: the post-traumatic stress disorder (PTSD) is one of the most frequent consequences of exposure to natural disasters, disabling both children and adults. Objectives: to describe prevalence of probable PTSD in children who experienced the disaster that occurred in southern Chile in february 2010. Methodology: the sample consisted of 1,300 participants aged 9-16 from the Bío Bío region. The study took place six months after the event occurred. The Child PTSD Symptom Scale (CPSS) and a questionnaire to assess socio-demographic aspects and potential PTSD predictors were used. Results: The overall rate of probable PTSD was 30.4 percent in the young population of females and 15.0 percent in males. The most strongly linked factors to the presence of PTSD were deteriorating family relationships after the event and intense fear and life threatening experiences during the event. Conclusions: results show the need for implementing preventive programs on young population affected by disasters that also include the response of the families involved.

Introducción: el trastorno de estrés postraumático (TEPT) es una de las consecuencias de la exposición a desastres naturales más frecuente y discapacitante tanto en niños y niñas como en adultos. Objetivos: se describe la prevalencia de probable TEPT en niños, niñas y adolescentes que vivieron el desastre natural de febrero de 2010 en el sur de Chile. Metodología: se estudió una muestra de 1.300 participantes de 9 a 16 años de la región del Bío Bío. La aplicación se realizó a seis meses de ocurrido el evento. Se empleó la Escala Infantil de Síntomas de Trastorno de Estrés Postraumático CPSS y un cuestionario de aspectos sociodemográficos y de potenciales factores predictores de estrés postraumático. Resultados: la tasa total probable de TEPT fue de 30,4 por ciento en la población infantojuvenil de sexo femenino y de 15,0 por ciento en la de sexo masculino. Los factores que aparecieron más fuertemente vinculados a la presencia de TEPT fueron el empeoramiento de las relaciones familiares posterior al evento y la experiencia de miedo intenso y de riesgo vital durante el evento. Conclusiones: los resultados indican la importancia de implementar programas preventivos en población infantojuvenil afectada por desastres que consideren también la respuesta de las familias.

Genetic variants in a lipid regulatory pathway as potential tools for improving the nutritional quality of grass-fed beef.

The aim of this study was to evaluate the effect of genetic variants on candidate genes corresponding to the sterol recognition element-binding protein-1 (SREBP-1) signaling pathway and stearoyl-CoA desaturases (SCD1 and SCD5) on muscle fatty acid (FA) composition of Brangus steers fattened on grass. FA profiles were measured on Longissimus lumborum muscle samples using a gas chromatography-flame ionization detection technique. A total of 43 tag single-nucleotide polymorphisms on the SCD1, SCD5, SREBP-1, SCAP, INSIG1, INSIG2, MBTPS1, MBTPS2, and SRPR genes were genotyped on 246 steers to perform a marker-trait association study. To evaluate the influence of the Indicine breed in the composite breed, additional groups of 48 Angus, 18 Hereford, 75 Hereford x Angus, and 36 Limousin x Hereford-Angus steers were also genotyped. To perform the association analysis, FA data were grouped according to the number of carbon atoms and/or number of double bonds (i.e. SFA, MUFA, PUFA, etc.). In addition, different indexes that reflect the activity of FA desaturase and elongase enzymes were calculated. SCD1 markers significantly affected C14:1/(C14:0 + C14:1) and C18:1/(C18:0 + C18:1) indexes, whereas one SNP in SCD5 was correlated with the C16:1/(C16:0 + C16:1) index. Polymorphisms in the signal recognition particle receptor (SRPR) gene were associated with all the estimated desaturase indexes. Because the evaluated markers showed no effect on total lipid content of beef, this work supports the potential utilization of these markers for the improvement of grass-fed beef without undesirable side effects.

Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors.

Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.

Genetic markers of body composition and carcass quality in grazing Brangus steers.

The somatotropic axis is a major regulatory pathway of energy metabolism during postnatal growth in mammals. Genes involved in this pathway influence many economically important traits. The association of selected SNPs in these genes with carcass traits was examined in grazing Brangus steers. These traits included final live weight, ultrasound backfat thickness (UBFT), rib-eye area, kidney fat weight, hot carcass weight, and intramuscular fat percentage (%IMF). Genomic DNA (N = 246) was genotyped for a panel of 15 tag SNPs located in the growth hormone receptor (GHR), insulin-like growth factor I, insulin-like growth factor-binding protein 6, pro-melanin-concentrating hormone, suppressor of cytokine signaling 2, and signal transducer and activator of transcription 6 (STAT6) genes. Allelic and haplotype frequencies were compared with those of a sample of European breeds (N = 177 steers). Two tag SNPs in the GHR affected %IMF; one of them (ss86273136) was also strongly associated with UBFT (P < 0.003). The frequency of the most favorable GHR haplotype for %IMF was lower in Brangus steers. Moreover, the haplotype carrying two unfavorable alleles was present at a frequency of 31% in this group. Four tag SNPs on STAT6 had a significant effect on UBFT. One of these, SNP ss115492467, was also associated with %IMF. The STAT6 haplotype, including all the alleles favoring UBFT, was the most abundant variant (34%) in the European cattle, while it had a frequency of 14% in the Brangus steers. The four less favorable variants (absent in the European cattle) were found at a frequency of 38% in the Brangus steers. These results support the association of GHR and STAT6 SNP with carcass traits in composite breeds, such as Brangus, under grazing conditions.

Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys.

Two high-density single nucleotide polymorphism (SNP) genotyping arrays have recently become available for bovine genomic analyses, the Illumina High-Density Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom Genome-Wide BOS 1 Array (648,874 SNP). These products each have unique design and chemistry attributes, and the extent of marker overlap and their potential utility for quantitative trait loci fine mapping, detection of copy number variation, and multibreed genomic selection are of significant interest to the cattle community. This is the first study to compare the performance of these 2 arrays. Deoxyribonucleic acid samples from 16 dairy cattle (10 Holstein, 6 Jersey) were used for the comparison. An independent set of DNA samples taken from 46 Jersey cattle and 18 Holstein cattle were used to ascertain the amount of SNP variation accounted by the 16 experimental samples. Data were analyzed with SVS7 software (Golden Helix Inc., Bozeman, MT) to remove SNP having a call rate less than 90%, and linkage disequilibrium pruning was used to remove linked SNP (r² ≥ 0.9). Maximum, average, and median gaps were calculated for each analysis based on genomic position of SNP on the bovine UMD3.1 genome assembly. All samples were successfully genotyped (≥ 98% SNP genotyped) with both platforms. The average number of genotyped SNP in the Illumina platform was 775,681 and 637,249 for the Affymetrix platform. Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci. Both Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are well designed and provide high-quality genotypes and similar coverage of informative SNP. Despite fewer total SNP on BOS 1, 19% more SNP remained after linkage disequilibrium pruning, resulting in a smaller gap size (5.2 vs. 6.9 kb) in Holstein and Jersey samples relative to BovineHD. However, only 224,115 Illumina and 241,038 Affymetrix SNP remained following removal of SNP with a minor allele frequency of zero in Holstein and Jersey samples, resulting in an average gap size of 11,887 bp and 11,018 bp, respectively. Combining the 354,348 informative (r² ≥ 0.9), polymorphic (minor allele frequency ≥ 0), unique SNP data from both platforms decreased the average gap size to 7,560 bp. Genome-wide copy number variant analyses were performed using intensity files from both platforms. The BovineHD platform provided an advantage to the copy number variant data compared with the BOS 1 because of the larger number of SNP, higher intensity signals, and lower background effects. The combined use of both platforms significantly improved coverage over either platform alone and decreased the gap size between SNP, providing a valuable tool for fine mapping quantitative trait loci and multibreed animal evaluation.

Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (P<0.05) birth weight, yet cattle with the large/large genotype had approximately 5.1% greater (P<0.05) percentage of fat within LM and more LM per BW than cattle with small/large or small/small genotypes. Genotype-to-phenotype relationships were not detected in multibreed analyses. The ETH10 locus appears to be associated with growth and carcass traits in Angus and Brangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5.

Variants in the pregnancy-associated plasma protein-A2 gene on Bos taurus autosome 16 are associated with daughter calving ease and productive life in Holstein cattle.

Reproductive disorders in dairy herds have a negative effect on farm profitability and sustainability of milk production. Given the substantial evidence of the role of the pregnancy-associated plasma protein (PAPP) gene family in the regulation of reproduction in humans and mice, its role in insulin-like growth factor metabolism, quantitative trait loci effects in the mouse, and location of a calving ease QTL on bovine chromosome 16, the PAPP-A2 gene was chosen as a candidate gene to perform an association study for reproductive health in cattle. Single nucleotide polymorphisms (SNP) were identified in coding and conserved noncoding regions of the PAPP-A2 gene in 3 dairy breeds. A total of 7 tag SNP were genotyped in 662 Holstein bulls (UCD-bulls) to perform marker trait association analysis. Three SNP (SNP 13, 15, and 16) were in strong linkage disequilibrium in Holsteins, showing significant positive associations with daughter calving ease, productive life, milk yield, and protein yield. These results were validated by genotyping SNP15 in a larger population of 992 bulls from the cooperative dairy DNA repository (CDDR-bulls). Our results demonstrate that the PAPP-A2 gene is associated with reproductive health in Holstein cattle and that the identified SNP can be used as genetic markers in dairy breeding due to their positive association with reproductive and productive traits. Functional studies need to be conducted to identify the mechanisms for the association of SNP with these traits.

Single nucleotide polymorphisms in the growth hormone-insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: population genetic analyses and association of genotypes with reproductive phenotypes.

The growth endocrine axis influences reproduction. The objectives of this study were to evaluate population genetic characteristics of SNP genotypes within genes of the GH-IGF axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers (n = 650) and to test the association of these genotypes with measures of reproduction. These objectives were achieved using 73 SNP within 7 genes on chromosome 5 and the pregnancy-associated plasma protein A2 (PAPP-A2) and GH-receptor genes, which map to chromosomes 16 and 20, respectively. The SNP were elucidated by resequencing conserved regions of each gene by using DNA from familial-unrelated cattle of a multibreed discovery population. A multiplex SNP assay yielded 59 biallelic SNP useful for evaluating genetic identity and distance. Specifically, the divergence of straightbred Brahman cattle was approximately 15.5% from 5 Bos taurus-influenced breed groups. In the straightbred groups used as a validation population, only 3 SNP had minor allele frequencies >10%. These SNP were in the genes PAPP-A2 (ss115492449-A/C and ss115492450-G/T within intron 10) and signal transducers and activators of transcription 2 (STAT2; ss252841035-A/G within the 5' untranslated region), and they met the conditions of Hardy-Weinberg equilibrium (P > 0.31). The other 56 SNP were useful for assigning each animal into ancestral clusters (n = 3 proportions) to account for population stratification in genotype to phenotype association analyses. The 2 SNP in the PAPP-A2 gene influenced (P < 0.05) traits indicative of first-calf heifer rebreeding (i.e., calving interval, days to calving, and pregnancy rate). A STAT2 SNP genotype (i.e., GG) × primary ancestral cluster interaction (P < 0.05) suggested heifers primarily of B. taurus ancestry had a reduction of approximately 16.4 ± 0.1% in calving interval and days to calving relative to heifers clustering primarily as Bos indicus ancestry. Even though additional research is needed to delineate the allelic variation attributed to genes of the GH-IGF axis, results of this study provide support for STAT2 and PAPP-A2 as potential candidate genes associated with first-calf heifer rebreeding traits.