Rare and common variants: twenty arguments

Seleccionado por: Daniel

 

Gibson, G. 2012. Rare and common variants: twenty arguments. Nature Reviews Genetics 13:135–145.

 

Absract

Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small effect. Here I review 20 arguments for and against each of these models of the genetic basis of complex traits and conclude that both classes of effect can be readily reconciled.

 

 

Para estimar la heredabilidad (h2) se han usado tradicionalmente dos métodos y mas recientemente uno con un enfoque genómico. El primero de ellos se basa en la correlación entre parientes donde los parámetros de la regression se pueden usar para estimar la heredabilidad. El segundo está basado en los resultados de experimentos de selección artificial donde la respuesta a la selección es product del diferencial de selección y la heredabilidad. Finalmente el tercero se basa en estudios de GWAS (Genome Wide Association Studies) donde se han identificado por ejemplo hasta 90,000 SNPs que explican solo el 10% de la varianza fenotípica asociada con la altura en poblaciones humanas mientras que con el enfoque de correlación entre parientes se ha estimado en un 80%. A esta enorme diferencia se le ha bautizado como el problema de la heredabilidad perdida (missing heritability problem) y se han propuesto varias causas posibles para explicarla como la interacción entre loci o la variación epigenética, entre otras.
En este artículo Gibson presenta cuatro modelos de la arquitectura genetica que han sido propuestos para explicar el problema de la heredabilidad perdida sobre todo en enfermedades de poblaciones humanas que en mi opinion puede extrapolarse a cualquier fenotipo de cualquier especie de interés.

 

 

 

 

Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives

Selecionado por: Laura

Baute, G. J., N. C. Kane, C. J. Grassa, Z. Lai, and L. H. Rieseberg. 2015. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytologist 206:830–838.

 

Abstract

 

The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed.

To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris.

Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line.

Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching.

 

 Lo escogí por los énfasis en los cambios en los patrones de expresión, y la detección de selección en distintos eventos, e hibridización.