Dataset Information

Global Genetic Heterogeneity in Adaptive Traits.

ABSTRACT: Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS in the model plant species Arabidopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, whereas others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis-regulated, whereas the latter are predominately affected by trans-acting variants. Our result illustrate that conclusions about genetic architecture can be extremely sensitive to sampling and population structure.

SUBMITTER: Lopez-Arboleda WA

PROVIDER: S-EPMC8557469 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Global Genetic Heterogeneity in Adaptive Traits.

Lopez-Arboleda William Andres WA Reinert Stephan S Nordborg Magnus M Korte Arthur A

Molecular biology and evolution 20211001 11

Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results m ...[more]

PMID: 34240182

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Project description:Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (V a ) and coefficient of variation (CV a %), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CV a %) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (Q ST ). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (F ST ). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.

Dataset Information

Global Genetic Heterogeneity in Adaptive Traits.

Publications

Global Genetic Heterogeneity in Adaptive Traits.

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