A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep

Pasandideh, M.; Rahimi-Mianji, Ghodrat; Gholizadeh, Mohsen

doi:10.1007/s12041-018-0941-9

“…ADG was previously reported as a selection criteria in a breeding program for Nile tilapia, which has been applying selection for at least five generations [46]. We found a lead SNP associated with ADG on chromosome LG15, located in an intronic region of the FUT8 gene, which has been associated with ADG (from birth to six months-age) in a sheep population from Irian [47].…”

Section: Discussionmentioning

confidence: 67%

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Yoshida¹,

Yáñez²

2020

Preprint

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Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

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“…LG15, located in an intronic region of the FUT8 gene, which has been associated with ADG (from birth to six months-age) in a sheep population from Irian [48]. In mice, the disruption of the FUT8 gene induces severe growth retardation and early mortality during postnatal development [49][50][51][52].…”

Section: Discussionmentioning

confidence: 99%

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Yoshida

¹

,

Yáñez

²

2020

Preprint

View full text Add to dashboard Cite

Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

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“…Los GWAS son una metodología relativamente nueva en ovinos, puesto que estos surgieron inicialmente en medicina y genómica de humanos, como una herramienta para caracterizar y encontrar variantes asociadas a patologías o predisponentes al desarrollo de las mismas (39) ; también para conocer las interacciones existentes entre genes, la modificación de éstas y para detectar haplotipos de alto riesgo o combinaciones de múltiples SNP dentro de un único gen (40) . Gracias a la popularidad de este tipo de estudios en humanos, su uso se extendió al campo de la medicina y producción animal (41) , siendo una herramienta útil para la identificación de genes o regiones genómicas que causan la variación genética en los rasgos más importantes de interés productivo (10,19,40,42) .…”

Section: Estudios De Asociación Genómica Gwas Y Su Aplicación En Ovinosunclassified

Estudios de asociación genómica en ovinos de América Latina. Revisión

Tobar

¹

,

Álvarez

²

,

Franco

³

2020

Rev. Mex. Cienc. Pecu.

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Los ovinos, son una de las especies domésticas más importantes a nivel mundial, debido al potencial productivo y reproductivo que poseen. En este sentido, identificar los mejores animales para características productivas de interés económico, es el objetivo principal en los programas de selección y mejoramiento genético de los rebaños. Sin embargo, en la mayoría de los países de América Latina la selección de los animales no es eficiente, debido a la elección subjetiva de los mismos y a la naturaleza compleja de estas características, ya que, al ser de carácter cuantitativo, su expresión involucra la interacción de múltiples genes con el ambiente. En la actualidad, gracias a los avances en las tecnologías de nueva secuenciación, genotipado y análisis de asociación genómica (GWAS), se han podido identificar numerosas variaciones en el ADN de los animales, principalmente polimorfismos de nucleótido simple (SNP) que pueden encontrarse en genes que afectan la expresión de rasgos económicos de interés. Esta revisión presenta los avances de la implementación de los análisis de asociación genómica (GWAS), en América Latina, su aplicación en los sistemas productivos de ovinos y los resultados que se han obtenido al indagar en características de tipo productivo, reproductivo, funcional o de calidad.

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A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep

Cited by 19 publications

References 60 publications

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Estudios de asociación genómica en ovinos de América Latina. Revisión

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