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The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.

ABSTRACT: A novel approach for dissecting complex traits is to experimentally evolve laboratory populations under a controlled environment shift, resequence the resulting populations, and identify single nucleotide polymorphisms (SNPs) and/or genomic regions highly diverged in allele frequency. To better understand the power and localization ability of such an evolve and resequence (E&R) approach, we carried out forward-in-time population genetics simulations of 1 Mb genomic regions under a large combination of experimental conditions, then attempted to detect significantly diverged SNPs. Our analysis indicates that the ability to detect differentiation between populations is primarily affected by selection coefficient, population size, number of replicate populations, and number of founding haplotypes. We estimate that E&R studies can detect and localize causative sites with 80% success or greater when the number of founder haplotypes is over 500, experimental populations are replicated at least 25-fold, population size is at least 1,000 diploid individuals, and the selection coefficient on the locus of interest is at least 0.1. More achievable experimental designs (less replicated, fewer founder haplotypes, smaller effective population size, and smaller selection coefficients) can have power of greater than 50% to identify a handful of SNPs of which one is likely causative. Similarly, in cases where s ? 0.2, less demanding experimental designs can yield high power.

SUBMITTER: Baldwin-Brown JG

PROVIDER: S-EPMC3969567 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.

Baldwin-Brown James G JG Long Anthony D AD Thornton Kevin R KR

Molecular biology and evolution 20140118 4

A novel approach for dissecting complex traits is to experimentally evolve laboratory populations under a controlled environment shift, resequence the resulting populations, and identify single nucleotide polymorphisms (SNPs) and/or genomic regions highly diverged in allele frequency. To better understand the power and localization ability of such an evolve and resequence (E&R) approach, we carried out forward-in-time population genetics simulations of 1 Mb genomic regions under a large combinat ...[more]

PMID: 24441104

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Project description:Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (B RD) and falling bolt (B FB) in combination with the evaluation of enzymatic discoloration. Because of observed in-practice relationship between bruising susceptibility and tuber starch content (TSC), analysis of starch content-corrected bruising susceptibility (SCB) was performed. QTLs for bruising were detected on chromosomes I, V with both test methods. The rotating drum method enabled the detection of additional QTLs on chromosomes VIII and XII. Analysis of SCB enabled the identification of the major QTL on chromosome V and two weaker QTLs on chromosomes VIII and XII, independently of starch content. The QTL for bruising detected on chromosome I overlapped with the most significant QTL for tuber starch content. This QTL was not significant for starch content-corrected bruising susceptibility, and the effect of the QTL on chromosome V was enhanced for this trait. The QTL analysis of ED revealed the contribution of seven QTLs for the trait, located on six chromosomes, including these detected for the first time: a major locus on chromosome V and minor QTLs on chromosomes VII and X, which were specific for the trait. The QTL for ED on chromosome VIII was co-localized with the marker for polyphenol oxidase (POT32). The phenotypic correlation between bruising and ED was confirmed in QTL analyses of both traits, and the QTLs detected for these traits overlapped on chromosomes I, V, and VIII. Our results should provide a basis for further studies on candidate genes affecting blackspot bruise susceptibility and enzymatic discoloration.

Project description:BACKGROUND: An increasing number of aquaculture species are subjected to artificial selection in systematic breeding programs. Rapid improvements of important commercial traits are reported, but little is known about the effects of the strong directional selection applied, on gene level variation. Large numbers of genetic markers are becoming available, making it feasible to detect and estimate these effects. Here a simulation tool was developed in order to explore the power by which single genetic loci subjected to uni-directional selection in parallel breeding populations may be detected. FINDINGS: Two simulation models were pursued: 1) screening for loci displaying higher genetic differentiation than expected (high-FST outliers), from neutral evolution between a pool of domesticated populations and a pool of wild populations; 2) screening for loci displaying lower genetic differentiation (low-FST outliers) between domesticated strains than expected from neutral evolution. The premise for both approaches was that the isolated domesticated strains are subjected to the same breeding goals. The power to detect outlier loci was calculated under the following parameter values: number of populations, effective population size per population, number of generations since onset of selection, initial FST, and the selection coefficient acting on the locus. Among the parameters investigated, selection coefficient, the number of generation since onset of selection, and number of populations, had the largest impact on power. The power to detect loci subjected to directional in breeding programmes was high when applying the between farmed and wild population approach, and low for the between farmed populations approach. CONCLUSIONS: A simulation tool was developed for estimating the power to detect artificial selection acting directly on single loci. The simulation tool should be applicable to most species subject to domestication, as long as a reasonable high accuracy in input parameters such as effective population size, number of generations since the initiation of selection, and initial differentiation (FST) can be obtained. Identification of genetic loci under artificial selection would be highly valuable, since such loci could be used to monitor maintenance of genetic variation in the breeding populations and monitoring possible genetic changes in wild populations from genetic interaction between escapees and their wild counterpart.

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The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.

Publications

The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.

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