Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

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.

ZmMADS69 functions as a flowering activator through the ZmRap2.7‐ZCN8 regulatory module and contributes to maize flowering time adaptation

“…a). To further determine whether the difference in the expression of ZmMADS69 detected between the parents of the maize‐teosinte population is common in maize natural populations, we analyzed the recently published transcriptome data of the leaf tissues of 265 diverse maize inbred lines (Kremling et al ., ). Consistent with the results from NILs and the results from our previously reported eRD‐GWAS, increased expression of ZmMADS69 was significantly associated with earlier flowering in natural populations (Fig.…”

Severe inbreeding depression is predicted by the “rare allele load” inMimulus guttatus*

“…Recently, Kremling et al. () showed that rare alleles per inbred line are correlated with extreme gene expression patterns in maize. They also found fitness consequences to this “dysregulation,” but noted that maize breeding history somewhat confounds this effect.…”

“…Thus, although the rare allele load is not the deleterious allele load, the former may be an indicator of the latter due to LD between neutral and deleterious alleles. Recently, Kremling et al (2018) showed that rare alleles per inbred line are correlated with extreme gene expression patterns in maize. They also found fitness consequences to this "dysregulation," but noted that maize breeding history somewhat confounds this effect.…”

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

“…Total RNA of 73 IBM RILs (one replicate) and the two parental lines (five replicates) were extracted with the Promega SV Total RNA Isolation Kit from another aliquot of the same seedling root tissues used for nontargeted metabolite profiling. mRNA sequencing libraries were prepared robotically on a Biomek NXp with manual post-PCR cleanup using the Lexogen QuantSeq 3 0 mRNA-Seq Library Prep Kits (Kremling et al, 2018). These libraries were pooled into one lane and sequenced with 90 bp single-end reads on an Illumina NextSeq 500 with v2 chemistry at the Cornell Biotechnological Resource Center.…”