Genome-Wide Association Study of Fiber Diameter in Alpacas.

The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (-log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.

Genetic diversity in creole pigs in south central Peru.

The creole pigs represent 67% of the national population in Peru. They are a source of economic income in rural communities, and due to their rusticity, they are not much labor demanding. However, knowledge about its genetic diversity remains scarce. The objective of this study was to determine the population structure and genetic diversity of creole pigs from rural communities in south central Peru. Thirteen microsatellites were used to characterize 120 creole pigs from the departments of Ayacucho (57) and Apurimac (63). The samples were taken from hair follicles and ear tissue. Nine microsatellites were highly polymorphic and informative (PIC > 0.5) for both departments. The Ayacucho population had a mean number of alleles (MNA) and expected heterozygosity (HE) of 8.8 and 0.68, respectively, while in the Apurimac population, these were 8.9 and 0.71, respectively. Both populations showed in less than 50% of their loci a deviation from Hardy-Weinberg equilibrium. There was a moderate genetic structure according to the analysis of molecular variance and the FST statistics (0.06), which was corroborated by Bayesian methods. In conclusion, the genetic diversity was mostly due to the intrapopulation variance (91%). Some individuals from Ayacucho shared similar alleles with those from Apurimac. This latter result may be due to their geographic proximity and the introduction of the same new exotic breeds. This is the first research on the genetic diversity of creole pigs in south central Peru. In fact, this study could serve as a basis for conservation strategies and actions in this region.

Transferibilidad de marcadores microsatélites de Anas platyrhynchos al pato criollo peruano Cairina moschata domestica / Cross species transferability of microsatellite markers from Anas platyrhynchos to Peruvian Muscovy Duck Cairina moschata domestica

Resumen El pato criollo peruano (Cairina moschata domestica) es una de las especies de mayor importancia económica en la alimentación humana. Las especies de patos forman grupos genéticos complejos y difíciles de reconocer, por lo que el uso marcadores microsatélites (SSR) identificados en una especie relacionada como Anas platyrhynchos, representa una opción atractiva, de menor costo y útil para resolver temas relacionados con la conservación de la diversidad genómica, flujo génico e hibridación entre poblaciones. El objetivo de la investigación fue evaluar la transferibilidad de 24 SSR identificados para A. platyrhynchos a las poblaciones peruanas de C. moschata doméstica y determinar el grado de polimorfismo (PIC) de los marcadores transferibles. Para ello, se obtuvo ADN a partir de plumas alares usando el método cloroformo-alcohol isoamílico. Los SSR se construyeron con una secuencia adicional de 19 pb (cola M13) y se utilizaron fluoróforos 6-FAM, VIC, NED y PET para su etiquetado. Los fragmentos amplificados fueron visualizados en geles de agarosa 2% y separados por electroforesis capilar en un secuenciador automático ABI 3130XL. Los resultados mostraron 7 SSRs con un valor PIC alto (PIC>0.5) y que el marcador CMO211 se expresaba con un tamaño molecular menor del de la referencia. En conclusión, el presente trabajo demostró que el 75% de los SSR diseñados para A. platyrhynchos son transferibles a C. moschata domestica; y que sólo 7 fueron altamente informativos. Demostrando así que los SSRs son útiles en la detección de polimorfismos en especies relacionadas y pueden ser usados para mejorar las poblaciones peruanas de patos criollos.

Abstract Peruvian Muskovy duck (Cairina moschata domestica) is one of the most economically important species in human nutrition. Duck species form complex genetic groups which are difficult to recognize, thus the use microsatellite markers (SSRs) identified already in Anas platyrhynchos (related species), represents a very attractive option for its cheapness and usefulness for solving issues related to conservation of genomic diversity, gene flow and hybridization between population. The main goal of this work was to evaluate the degree of polymorphism (PIC) and the transferability of 24 SSRs identified for A. platyrhynchos to C. moschata domestica. In this study, DNA collected from wing feathers was extracted using the chloroform-isoamyl alcohol method. SSRs were constructed with an additional 19 bp sequence (M13 tail) and 6-FAM, VIC, NED and PET fluorophores were used for their labeling. The amplified fragments were visualized on 2% agarose gels and separated by capillary electrophoresis in an automatic ABI 3130XL sequencer. Results showed 7 SSR with high PIC value (PIC> 0.5) and the CMO211 marker expressed in a smaller molecular size that the one used as reference. In conclusion, we showed that 75% of the SSR designed for A. platyrhynchos were transferable to C. moschata domestica as well as we found only 7 SSR highly informative, thus we proved that SSR are highly useful for detecting polymorphisms in related species and improved the Peruvian populations of Muskovy ducks.

Variabilidad genética y detección de error en filiación utilizando microsatélites en dos rebaños de alpacas Huacaya (Vicugna pacos) / Genetic variability of Peruvian Alpacas (Vicugna pacos) by using microsatellite markers

Determinar la variabilidad genética y evaluar la utilidad de microsatélites (STR) en la determinación de paternidad en alpacas blancas huacaya, pertenecientes al Centro Piloto de Mejoramiento Genético Munay Paqocha y el Fundo Itita, de la Sociedad Peruana de Criadores de Alpacas y Llamas (SPAR) Puno. Realizar la genotipificación y selección de marcadores STR útiles para la asignación de paternidad y parentesco. Metodología: Se evaluaron 10 marcadores STR a partir de ADN aislado de sangre y de folículos pilosos de 183 individuos colectados al azar procedentes de dos rebaños. Resultados y Conclusiones: Se observó un alto nivel de variabilidad alélica en el total de individuos analizados, y la presencia de alelos exclusivos entre poblaciones, con frecuencias menores al 1,5% en los loci LCA37, LCA90, LCA5, VOLP92, YWLL36, YWLL44 y YWLL08. Se propone la incorporación de tres marcadores adicionales, VOLP92, LCA94 y LCA90 para los análisis de variabilidad genética en alpacas. Los valores de FIS (0,016), y FST (0,003) reflejaron bajo niveles de endogamia. El rebaño del Fundo Itita presentó una mayor Ho (0,858) respecto a la He (0,848), mientras que por el contrario el rebaño del Centro Munay Paqocha presentó un menor valor de la Ho (0,815) respecto a la He (0,848), con una tendencia al déficit de heterocigotos. Los 10 marcadores presentaron una probabilidad de exclusión de parentesco adecuada, con un valor superior al 99,9%, cuando se conoce el genotipo de ambos padres, y un poder de discriminación mayor a 0,90...

To determine the genetic variability and the selection of STR markers useful for the evaluation of inbreeding, assignment of paternity and kinship, and the genotyping of two breeding herds of white huacayas alpacas Vicugna pacos, from the Pilot Center for Genetic Improvement Munay Paqocha and Fundo Itita, in Puno Perú. Methodology: 10 STR markers were assessed in 183 individuals, randomly selected. Results and Conclusions: We observed a high level of allelic variability in the total individuals, and unique alleles among populations with frequencies lower than 1.5% in loci LCA37, LCA90, LCA5, VOLP92, YWLL36, YWLL44 and YWLL08. We propose the addition of three markers, VOLP92, LCA94 and LCA90 for the genetic variability analysis in alpacas. FIS (0.016) and FST (0.003) values reflected low levels of inbreeding. Fundo Itita herd showed higher Ho (0.858) than He (0.848), while the herd of Munay Paqocha showed lower Ho (0.815) respect to He (0.848), with trending heterozygote deficit. The 10 markers showed an appropriate exclusion relationship probability, with a value greater than 99.9% when the genotype of both parents was known, and a power of discrimination greater than 0.9...