Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both
Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (
- NSF-PAR ID:
- 10044525
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 92
- Issue:
- 4
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 624-637
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Summary cis‐ andtrans‐ regulatory features. In order to study the variability in transcriptome response to abiotic stress,RNA sequencing was performed using 14‐day‐old maize seedlings of inbreds B73, Mo17, Oh43,PH 207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified.RNA sequencing was also performed on similar tissues of theF 1hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele‐specific transcript abundance in theF 1hybrids, we were able to measure the abundance ofcis‐ andtrans‐ regulatory variation between genotypes for both steady‐state and stress‐responsive expression differences. Although examples oftrans‐ regulatory variation were observed,cis‐ regulatory variation was more common for both steady‐state and stress‐responsive expression differences. The genes withcis‐ allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity. -
Lasky, Jesse R. (Ed.)more » « less
Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of
Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05). cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTLs make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of “gene expression modules,” which has important implications for the evolution of gene expression and how it is studied by geneticists. -
more » « less
SUMMARY Single‐parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non‐presence/absence (non‐PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse
Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non‐PAV SPE genes are mainly regulated bycis effects, with a small fraction undertrans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level ofcis regulation for PAV SPE and non‐PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non‐PAV SPE genes. The expression of parentally silent alleles in hybrids of non‐PAV SPE genes was relatively rare but occurred in most hybrids. Non‐PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non‐additive expression. This study provides a comprehensive understanding of the nature of non‐PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids. -
more » « less
Abstract The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds in
Arabidopsis thaliana -
more » « less
Abstract Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based on single-molecule, full-length cDNA sequencing. To phase and analyze transcripts between hybrids and parents, we developed IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data from embryo, endosperm and root tissues, and identified allele-specific, gene-level and isoform-level differential expression between the inbred parental lines and hybrid offspring. After phasing 6907 genes in the reciprocal hybrids, we annotated the SNPs and identified large-effect genes. In addition, we identified parent-of-origin isoforms, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.
