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Dysregulation of expression correlates with rare-allele burden and fitness loss in maize
- Source :
- Nature. 555:520-523
- Publication Year :
- 2018
- Publisher :
- Springer Science and Business Media LLC, 2018.
-
Abstract
- Here we report a multi-tissue gene expression resource that represents the genotypic and phenotypic diversity of modern inbred maize, and includes transcriptomes in an average of 255 lines in seven tissues. We mapped expression quantitative trait loci and characterized the contribution of rare genetic variants to extremes in gene expression. Some of the new mutations that arise in the maize genome can be deleterious; although selection acts to keep deleterious variants rare, their complete removal is impeded by genetic linkage to favourable loci and by finite population size. Modern maize breeders have systematically reduced the effects of this constant mutational pressure through artificial selection and self-fertilization, which have exposed rare recessive variants in elite inbred lines. However, the ongoing effect of these rare alleles on modern inbred maize is unknown. By analysing this gene expression resource and exploiting the extreme diversity and rapid linkage disequilibrium decay of maize, we characterize the effect of rare alleles and evolutionary history on the regulation of expression. Rare alleles are associated with the dysregulation of expression, and we correlate this dysregulation to seed-weight fitness. We find enrichment of ancestral rare variants among expression quantitative trait loci mapped in modern inbred lines, which suggests that historic bottlenecks have shaped regulation. Our results suggest that one path for further genetic improvement in agricultural species lies in purging the rare deleterious variants that have been associated with crop fitness.
- Subjects :
- Crops, Agricultural
0301 basic medicine
Linkage disequilibrium
Genotype
Quantitative Trait Loci
Biology
Zea mays
Genome
Linkage Disequilibrium
03 medical and health sciences
Inbred strain
Gene Expression Regulation, Plant
Genetic linkage
Allele
Alleles
Population Density
Regulation of gene expression
Genetics
Multidisciplinary
Sequence Analysis, RNA
Genetic Variation
Phenotype
030104 developmental biology
RNA, Plant
Seeds
Expression quantitative trait loci
Genetic Fitness
Genome, Plant
Subjects
Details
- ISSN :
- 14764687 and 00280836
- Volume :
- 555
- Database :
- OpenAIRE
- Journal :
- Nature
- Accession number :
- edsair.doi.dedup.....9173df278fca6299a2ef407b518deeb7
- Full Text :
- https://doi.org/10.1038/nature25966