Evolutionary Quantitative Genetics

Walsh, B.

doi:10.1002/9780470061619.ch17

Cited by 10 publications

(9 citation statements)

References 60 publications

(92 reference statements)

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“…Our results contradict the general principles of the infinitesimal model for which allele frequencies are not expected to substantially change during time, as allele effects on complex traits would be infinitesimally small (Walsh ), but they agree with the evolution of this theory that was proposed after the introduction of genomic information in animal breeding (Hill ). In our study, the genome‐wide evaluation of allele frequency shifts was probably limited by the problem of multiple testing that needed stringent thresholds to declare significant or suggestively significant changes (222, 399 and 493 SNPs were below the P Bonferroni = 0.01, 0.05 and 0.10 thresholds respectively).…”

Section: Discussionsupporting

confidence: 61%

“…According to the infinitesimal model underlying quantitative genetics, the genetic structure of quantitative traits is determined by an infinite number of genes, each of them with a very small effect. Therefore, directional selection derived by modern breeding goals is not expected to significantly change allele frequencies at any loci in the population (Barton & Keightley ; Walsh ). However, it is now well known that a detectable part of the genetic variance of complex traits subject to genetic improvement plans is explained by specific loci, as demonstrated by many QTL studies thus far produced in pigs and in several other livestock species (Hu et al .…”

Section: Introductionmentioning

confidence: 99%

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Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

et al. 2015

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In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

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Section: Discussionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

et al. 2015

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“…For most normally distributed phenotypes, fitness is generally greatest around the median value of the phenotype. Hence, individuals with extreme values of the phenotype will be at a selective disadvantage, but in the population as a whole, alleles serving to increase and decrease the trait will both be selected for (Walsh, 2003).…”

Section: Persistence Of Risk Alleles In the Gene Poolmentioning

confidence: 99%

Lifetime reproductive output over two generations in patients with psychosis and their unaffected siblings: the Uppsala 1915–1929 Birth Cohort Multigenerational Study

2009

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“…We used whole-genome SNP and phenotypic data from the UK Biobank (total n ~ 100,000 - 400,000) to address two principal questions: (1) is there evidence consistent with directional dominance on traits related to fitness and health, such that increased F ROH is associated with lower trait values? and (2) do F R0H -trait relationships persist after controlling for multiple background sociodemographic variables? This sample is population-based, reducing concerns about ascertainment-induced confounds, and includes information on multiple relevant sociodemographic control variables and traits previously associated with F ROH (e.g.…”

Section: Introductionmentioning

confidence: 99%

Relationships between estimated autozygosity and complex traits in the UK Biobank

Johnson

Evans

2018

Preprint

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28Inbreeding increases the risk of certain Mendelian disorders in humans but may 29 also reduce fitness through its effects on complex traits and diseases. Such inbreeding 30 depression is thought to occur due to increased homozygosity at causal variants that are 31 recessive with respect to fitness. Until recently it has been difficult to amass large 32 enough sample sizes to investigate the effects of inbreeding depression on complex 33 traits using genome-wide single nucleotide polymorphism (SNP) data in population-34 based samples. Further, it is difficult to infer causation in analyses that relate degree of 35 inbreeding to complex traits because confounding variables (e.g., education) may 36 influence both the likelihood for parents to outbreed and offspring trait values. The 37present study used runs of homozygosity in genome-wide SNP data in up to 400,000 38 individuals in the UK Biobank to estimate the proportion of the autosome that exists in 39 autozygous tracts-stretches of the genome which are identical due to a shared 40 common ancestor. After multiple testing corrections and controlling for possible 41 sociodemographic confounders, we found significant relationships in the predicted 42 direction between estimated autozygosity and three of the 26 traits we investigated: age 43 at first sexual intercourse, fluid intelligence, and forced expiratory volume in 1 second. 44Our findings for fluid intelligence and forced expiratory volume corroborate those of 45 several published studies while the finding for age at first sexual intercourse was novel. 46These results may suggest that these traits have been associated with Darwinian fitness 47 over evolutionary time, although there are other possible explanations for these 48 associations that cannot be eliminated. Some of the autozygosity-trait relationships were 49 attenuated after controlling for background sociodemographic characteristics, suggesting 50 that care needs to be taken in the design and interpretation of ROH studies in order to 51 glean reliable information about the genetic architecture and evolutionary history of 52 complex traits. 53 3 54 Author Summary 55Inbreeding is well known to increase the risk of rare, monogenic diseases, and there has 56 been some evidence that it also affects complex traits, such as cognition and 57 educational attainment. However, difficulties can arise when inferring causation in these 58 types of analyses because of the potential for confounding variables (e.g., 59socioeconomic status) to bias the observed relationships between distant inbreeding and 60 complex traits. In this investigation, we used single-nucleotide polymorphism data in a 61 very large (N > 400,000) sample of seemingly outbred individuals to quantify the degree 62 to which distant inbreeding is associated with 26 complex traits. We found robust 63 evidence that distant inbreeding is inversely associated with fluid intelligence and a 64 measure of lung function, and is positively associated with age at first sex, while other 65 trait associati...

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Evolutionary Quantitative Genetics

Cited by 10 publications

References 60 publications

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

Lifetime reproductive output over two generations in patients with psychosis and their unaffected siblings: the Uppsala 1915–1929 Birth Cohort Multigenerational Study

Relationships between estimated autozygosity and complex traits in the UK Biobank

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