Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool.

We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.

Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data.

The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.

The first GHEP-ISFG collaborative exercise on forensic applications of massively parallel sequencing.

One of the main goals of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. The GHEP-ISFG supports several Working Commissions which develop different scientific activities. One of them, the Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications", organized its first collaborative exercise on forensic applications of MPS technology in 2019. The aim of this exercise was to assess the concordance between the MPS results and those obtained with conventional technologies (capillary electrophoresis and Sanger sequencing), as well as to compare the results obtained within the different MPS platforms and/or the different kits/panels and analysis software packages (commercial and open-access) available on the market. The seven participating laboratories analyzed some samples of the annual GHEP-ISFG proficiency test (EIADN No. 27 (2019)), using Ion Torrent™ or MiSeq FGx® platforms. Six of them sent autosomal STR sequence data, five laboratories performed MPS analysis of individual identification SNPs, four laboratories reported MPS data of Y-chromosomal STRs, and X-chromosomal STRs, three laboratories performed MPS analysis of ancestry informative SNPs and phenotype informative SNPs, two labs performed MPS analysis of the mitochondrial DNA control region, and only one lab produced MPS data of lineage informative SNPs. Autosomal STR sequencing results were highly concordant to the consensus obtained by capillary electrophoresis in the EIADN No. 27 (2019) exercise. Furthermore, in general, a high level of concordance was observed between the results of the participating laboratories, regardless of the platform used. The main discordances were due to errors during the analysis process or from sequence data obtained with low depth of coverage. In this paper we highlight some issues that still arise, such as standardization of the nomenclature for STRs analyzed by sequencing with MPS, the universal uptake of a nomenclature framework by the analysis software, and well established validation and accreditation of the new MPS platforms for use in routine forensic case-work.

Efecto de la condición sexual y pesos al sacrificio sobre las características de la canal y la calidad de la carne de cerdo / Effect of sexual condition and slaughter weight on pig carcass characteristics and meat quality

En las explotaciones porcinas de Venezuela, no es común comercializar canales provenientes de machos enteros a pesar de las ventajas que ofrece su producción, esto es debido a la preocupación de que un porcentaje indeterminado de canales presenten el defecto sensorial denominado olor sexual. Por ello se planificó un estudio con el objetivo de determinar el efecto de la condición sexual (machos enteros y castrados) y distintos pesos al sacrificio (83,8 ± 6,3; 95 ±5 ,0 y 106±6,0) sobre las características de la canal y calidad de la carne de cerdo. Para ello, se utilizaron 84 cerdos (42 machos castrados y 42 machos enteros), provenientes del cruzamiento de hembras F1 (Yorkshire × Landrace) y machos Dalland Tempo (B80) de la línea comercial Topigs. Los resultados muestran que los cerdos machos enteros presentaron menor espesor de grasa subcutánea que los cerdos castrados (P < 0,01). El área del ojo del lomo de los machos enteros superó en un 12,86 por ciento a los castrados (P < 0,01). Los cerdos machos enteros presentaron menor pérdida por goteo a las 24h y mayores pérdidas por cocción y resistencia al corte (P<0,01). El análisis sensorial reveló que los consumidores no fueron capaces de detectar el olor sexual (olor a orina) principal desventaja en el uso de éstas carnes en los rangos de pesos evaluados en el presente estudio. El uso de machos enteros es una alternativa viable para los productores por presentar mejores características de la canal que los machos castrados, esto sin detrimento de la calidad en sus carnes.

In Venezuela, the pig production systems is not common to market carcasses coming from pigs in spite of its multiple advantages. This is due to the concerns arisen by the detection of sensory defect called boar taint in an undetermined percentage of carcasses. The objective of this study was to determine the effect of sexual condition (noncastrated or boars and castrated males) and different weights at slaughter (83.8 ± 6.3, 95 ± 5.0 and 106 ± 6) on carcass characteristics and meat quality. In order to persue this objective 84 crossbred pigs [DallandTempo (B80) X F1 Yorkshire × Landrace], including 42 boars and 42 castrated males were used. Non-castrated male pigs had lower backfat than castrated ones (P <0.01). The loin eye area of boars was 12.86 percent greater of that of castrated males (P <0.01). Boars had a lower drip loss at 24h and a higher cooking loss and shear force than castrated males (P<0.01). The sensorial analysis showed that consumers were not capable of detecting the boar taint defect, which is a main disadvantage of the use of boar meat in the weight range evaluated in the present study. The use of boars is a good alternative for pig producers due to better carcass characteristics compared to castrated males, without detriment of its meat quality.

Algunos parámetros de composición y calidad en leche cruda de vacas doble propósito en el municipio Machiques de Perijá estado Zulia Venezuela / Some composition parameters and quality on raw milk of dual purpose cows in the Machiques of Perijá country Zulia state Venezuela

El objetivo de este estudio fue evaluar los efectos de etapa de lactación, mestizaje, época del año y número de partos sobre la producción de leche (PL), crioscopía (CR), pH, acidez titulable (AT), proteínas totales (PT) y caseínas (CA) en leche cruda de un rebaño doble propósito. Se analizaron 926 muestras de leche del ordeño vespertino de un rebaño mestizo doble propósito (Holstein, Pardo suizo, Cebú, Criollo y Mosaico) mantenidos en un sistema de explotación semi-intensivo en Machiques, estado Zulia, Venezuela. Las vacas se agruparon de acuerdo al mestizaje (6 grupos), etapa de lactación (1 a 90 días, 91 a 180 días y > de 181 días) y número de partos (1, 2, y 3 o más partos). Fueron muestreadas durante el periodo de un año abarcando dos épocas del año (seca de noviembre a marzo y lluviosa de abril a octubre). Los datos fueron analizados a través del paquete estadístico SAS, utilizando un análisis de varianza y probando las medias por el método de los mínimos cuadrados, complementado con un análisis de correlación de Pearson para las variables dependientes. Se obtuvieron medias generales para PL de 3,109 Kg, CR -0,541, pH 6,72, AT 17,60 mL de NaOH 0,1 N/100 mL de leche, PT 3,66% y CA 2,40%. Se observaron diferencias significativas (P£0,05) entre mestizajes y etapas de lactación sobre todas las variables estudiadas, a diferencia de la época del año que solo afectó a la CA, y el número de partos que afectó a la PL, PT y CA. Se encontraron correlaciones significativas entre PL con CR, PT y CA, del pH con AT y la PT con CA. Se concluye que el mestizaje y la etapa de lactancia representan los factores que introducen mayor variabilidad en la calidad y composición proteica de la leche en animales mestizos doble propósito.

The aim of this research was to evaluate the effect of lactation stage, breed, year season and parity number on milk yield (MY), cryoscopy (CR), pH, acidity (TA), total protein (TP) and casein (CA) in raw milk of an herd of dual purpose. An evaluation was performed in 926 milk samples for the evening milking of a herd of dual purpose cattle (Holstein, Brown Swiss, Creole Zebu and Mosaic) maintained in a semi-intensive production system in Machiques, Zulia State, Venezuela. Cows were grouped according to the breed (6 groups), lactation stage (1 to 90 days, 91 to 180 days and > of 181 days) and parity number (1, 2, and 3 or more parturitions). Cows were sampled during a year period, including two seasons (dry of November to March and rainy of April to October). Data were analyzed through the statistical package SAS, using a variance analysis by testing mean differences through least square means procedure. In addition, Pearson product moment correlation analysis was performed. Overall means were for MY 3.109 Kg, CR -0.541, pH 6.72, TA 17.60 ml of NaOH 0.1 N/100 ml of milk, TP 3.66% and CA 2.40%. Statistical differences were observed (P<0.05) for breed and lactation stage in all the variables studied. However, year season only had effect on CA. On the other hand, parity number had effects on Y, TP, and CA. Significant correlation coefficients were found among MY with CR, TP and CA, of the pH with TA, and TP with CA. It is concluded that the breed and lactation stage represent the factors that introduce greater variation in the quality and protean composition of the raw milk of dual purpose cows.

Utilización de carnes empacadas al vacío en la elaboración de productos fermentados / Utilization of vacuum packed meat in the making of fermented products

Se evaluó el tiempo óptimo del empacado al vacío para la carne molida de res (CMEV) basándose en el número de Lactobacillus presentes en ella, se comparó ésta con carne molida previamente congelada (CMPC) y posteriormente se determinó la eficiencia de las CMEV en la elaboración de productos cárnicos fermentados y se compararon estos productos con aquellos elaborados con o sin agregado de cultivo iniciador. Tres experimentos fueron realizados. El método matemático correspondió al diseño completamente al azar. Las comparaciones entre las medias se efectuaron contrastes ortogonales. El tiempo de empacado afectó el crecimiento de los Lactobacillus (P<0,01), se seleccionó como tiempo óptimo un período de 14 días, ya que el número de lactobacillus en este período no se diferenció significativamente del obtenido a los 21 días. La CMEV por un período de 14 días mostró medias de pH menor y logaritmo del número de Lactobacillus mayor que las CMPC almacenadas durante el mismo período de tiempo (P<0,01). La CMEV no presentó ni E. coli, ni coliformes, mientras que la CMPC no presentó E. Coli pero sí coliformes. Los productos cárnicos fermentados presentaron pH diferente significativamente según el tratamiento y tiempo de fermentación (P<0,01). Fue evidente la interacción (P<0,05) entre ambos factores para esta variable. La Pérdida de peso solamente fue afectada por el tiempo de fermentación. Para pérdida de cocción ambas fuentes de variación fueron significativa (P<0,05) y la interacción resultó no significativa (P>0,05). El empacado al vacío de la carne molida de res demostró ser una excelente técnica en la elaboración de productos cárnicos fermentados, procedimiento alternativo que pudiera sustituir el empleo de cultivos iniciadores en la elaboración de estos productos

Contenido de colesterol en el músculo longissimus de bovinos venezolanos / Cholesterol content of beet longissimus from slaughter cattle of venezuelan

Se seleccionó una muestra de 149 bovinos sacrificados en un matadero venezolano. Después de la evaluación y clasificación de las canales, se tomaron bistéks del solomo, con el objeto de estudiar el efecto de la clase de animal, por su condición sexual (62 toros, 67 novillos, 20 novillas), la edad dentaria (2.5, 3.5, 4.0 años), el tipo racial (17 mestizos lecheros y 132 mestizos Cebú), madurez fisiológica (A o B), categoría oficial en canal (optima, Excelente, Selecta o Superior), marmoleo (cuatro niveles desde "Nada" hasta "Pequeña cantidad"), grado de acabado ("Uniforme"; "Desuniforme", "En parches" y "Desprovisto") y el espesor de grasa de cobertura del solomo (1=0,1-0,2 cm; 2=0,3-0,4 cm; 3=0,5-0,9 cm and 4=>1,0 cm) sobre la concentración (mg/100 g de tejido fresco) de colesterol, determinar, la condición sexual, la clasificación de la canal, el nivel de marmoleo, el grado de acabado o el espesor de la grasa de cobertura sobre el solomo no tuvieron efecto significativo sobre el contenido de colesterol del longissimus. Sin embargo, los mestizos lecheros superaron a los mestizos Cebú en 12,2 mg/100 g de colesterol muscular (P=0,08). La media general de la muestra y su dispersión (66,6 ñ 16 mg/100 g) no muestra valores distintos a los obtenidos con ganado igual o mejor cebado en otras latitudes