Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture

Abstract

The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic diversity.

The Effects of the Sex Chromosomes on the Inheritance of Species Specific Traits of the Shape of the Copulatory Organ in Drosophila virilis and Drosophila lummei

“…An analysis of QTLs for commercially valuable traits in farm animals supports well the conclusion that recessive variation maintained in a population plays an important role [73][74][75]. The majority of the traits are related to morphological and physiological characteristics affected by stabilizing selection.…”

The Role of the Sex Chromosomes in the Inheritance of Species Specific Traits of the Shape of the Copulatory Organ in Drosophila

“…Modeling of ample experimental data has shown that well reproducible results are obtained with both of the models, none of them is possible to prefer over the other (Zhang, Hill, 2005). An analysis of QTLs for commercially valuable traits in farm animals supports well the conclusion that recessive variation maintained in a population plays an important role (Andersson, Georges, 2004;Hill, 2014;Zan et al, 2017). The majority of the traits are related to morphological and physiological characteristics affected by stabilizing selection.…”

A multi-locus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild-collectedArabidopsis thaliana

“…We have earlier developed a multi locus approach to explore the genetic architecture of 326 highly polygenic traits and a detailed description of the approach is available in (Sheng et al 327 2015;Brandt et al 2017;Lillie et al 2017). In short, the method was designed to study traits 328 where earlier data suggest them to be polygenic in the analysed population.…”

“…The additional burden of corrections also for 57 population structure decreases power further. By making combined use of powerful model 58 populations, and new analytical approaches accounting for the polygenic nature of complex 59 adaptive traits, it is possible to dissect polygenic genetic architecture with greater sensitivity 60 in order to facilitate deeper insights to the genetic basis of adaptive traits (Sheng,Pettersson,61 Honaker, Siegel, & Carlborg, 2015; Zan et al, 2017). These potent statistical methods have 62 so far not been adapted to analyses of natural populations, but could be useful also for 63 identifying the genetic mechanisms that govern adaptation for polygenic traits in nature.…”