Rapid DNA extraction of pig ear tissues

Kunhareang, Sajee; Zhou, Huitong; Hickford, Jonathan G. H.

doi:10.1016/j.meatsci.2010.02.028

Cited by 8 publications

(7 citation statements)

References 5 publications

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“…Las modificaciones realizadas tomando como base los mé-todos de extracción de ADN de Aljanabi & Martínez (1997) y Kunhareang et al (2010) permitieron mejorar la calidad del extracto de ADN de muestras de aleta caudal de tilapia. La adición de tritón al 0.5% en la mezcla del amortiguador de extracción fue lo más relevante de las modificaciones realizadas.…”

Section: Discussionunclassified

“…Las muestras fueron guardadas a -20 °C por 24 horas. La extracción del ADN total se realizó mediante la combinación y modificaciones de los métodos descritos por Cawthom et al(2011), Aljanabi & Martínez(1997) y Kunhareang et al (2010) modificado, que consistió en colocar las muestras de la aleta caudal en un tubo de microcentrífuga de 1.5 mL, al cual se le agregó 800 µL de buffer de digestión (10 mM TRIS-HCL pH 8.0; 25 mM EDTA pH 8.0; 20 mM NaCl; 2% SDS; tritón 0.5%, PVP 2%, mercaptoetanol 1%, 7 µL de proteinasa K 20 mg/mL), se agitó en vortex por 30 segundos, se dejó reposar los tubos en forma horizontal por 15 minutos y se incubaron a 55 °C por 1 hora. Se centrifugó a 14000 r.p.m.…”

Section: Materials Y Métodosunclassified

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Diferenciación genética de tilapia roja y gris (Oreochromis niloticus) mediante microsatélites y marcadores SCAR como indicadores del sexo genético

2017

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TRABAJOS ORIGINALES© Los autores. Este artículo es publicado por la Revista Peruana de Biología de la Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos. Este es un artículo de acceso abierto, distribuido bajo los términos de la Licencia Creative Commons Atribución-NoComercial-CompartirIgual 4.0 Internacional.(http://creativecommons.org/licenses/by-nc-sa/4.0/), que permite el uso no comercial, distribución y reproducción en cualquier medio, siempre que la obra original sea debidamente citadas. Para uso comercial, por favor póngase en contacto con editor.revperubiol@gmail.com. Fuentes de financiamiento: El presente trabajo se realizó gracias al financiamiento del canon minero otorgado a la Universidad Nacional de Trujillo. Información sobre los autores:MA que realizó la parte experimental. LS-T realizó la parte experimental. ZP realizo el diseño experimental y planificación; MA, LS-T, ZP revisaron y aprobaron el manuscrito.Los autores no incurren en conflictos de intereses. Presentado:04/01/2017 Aceptado:22/09/2017 Publicado online: 28/10/2017 ResumenEl objetivo del trabajo fue realizar la estandarización de los protocolos moleculares, diferenciar los linajes de la tilapia roja y gris mediante microsatélites de ADN y evaluar los marcadores SCAR-5F-X/5R y SCAR-5F/5R-Y como indicadores del sexo genético de O. niloticus. El microsatélite UNH106 permitió diferenciar genéticamente los linajes de la tilapia roja de la gris. Los microsaté-lites UNH136, UNH115 y UNH995 presentaron loci monomórficos tanto en la tilapia roja como en la gris en el lote poblacional del Centro Experimental de Genética de la Universidad Nacional de Trujillo. Se describen los tamaños de fragmentos para los microsatélites y del gen de referencia β actin. También se confirmó la efectividad de los marcadores SCAR como informativos en la determinación del sexo genético evaluados en hembras XX y YY y machos XY y YY de O. niloticus roja y hembras XX y machos XY de O. niloticus gris.Palabras clave: Tilapia; Oreochromis; microsatélites; marcadores SCAR; determinación del sexo. AbstractThe aims of this work was to develop a standardized molecular protocols, to differentiate red and gray tilapia lineages using DNA microsatellites and to evaluate SCAR-5F-X/5R and SCAR-5F/5R-Y markers associated with the phenotypic sex of O. niloticus. The UNH106 microsatellite allowed differentiating genetically the lineages of red tilapia from gray. The markers UNH136, UNH115 and UNH995 presented monomorphic loci in both the red and gray tilapia in the population stock of the Centro Experimental de Genética of the Universidad Nacional de Trujillo. Fragment sizes for microsatellites and the reference gene β actin are described. The effectiveness of SCAR markers as informative in the determination of the genetic sex in XX and YY females and XY y YY males of red tilapia and XX females and XY males of gray tilapia was also confirmed.

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Section: Discussionunclassified

Section: Materials Y Métodosunclassified

Diferenciación genética de tilapia roja y gris (Oreochromis niloticus) mediante microsatélites y marcadores SCAR como indicadores del sexo genético

2017

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“…The pig ear samples (ear pluck) were obtained under a general breeding monitoring procedure. The collection of ear samples is a standard practice in pig breeding [ 15 ].…”

Section: Methodsmentioning

confidence: 99%

Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia

Bakoev

Kolosov

Bakoev

et al. 2021

Life

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Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.

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“…The pig ear samples (ear pluck) were obtained as a general breeding monitoring procedure or during the slaughter. The collection of ear samples is a standard practice in pig breeding (Kunhareang, Zhou & Hickford, 2010). Previously collected historic tissue samples of the Soviet-bred pigs were obtained from breeding farms in Russia between 2006 and 2010.…”

Section: Animals and Sample Collectionmentioning

confidence: 99%

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Bakoev

Getmantseva

Kostyunina

et al. 2021

PeerJ

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Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.

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Rapid DNA extraction of pig ear tissues

Cited by 8 publications

References 5 publications

Diferenciación genética de tilapia roja y gris (Oreochromis niloticus) mediante microsatélites y marcadores SCAR como indicadores del sexo genético

Diferenciación genética de tilapia roja y gris (Oreochromis niloticus) mediante microsatélites y marcadores SCAR como indicadores del sexo genético

Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

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