Dataset Information

Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass.

ABSTRACT: The molecular basis behind shade tolerance in plants is not fully understood. Previously, we have shown that a connection may exist between shade tolerance and dwarfism, however, the mechanism connecting these phenotypes is not well understood. In order to clarify this connection, we analyzed the transcriptome of a previously identified shade-tolerant mutant of perennial ryegrass (Lolium perenne L.) called shadow-1. shadow-1 mutant plants are dwarf, and are significantly tolerant to shade in a number of environments compared to wild-type controls. In this study, we treated shadow-1 and wild-type plants with 95% shade for 2 weeks and compared the transcriptomes of these shade-treated individuals with both genotypes exposed to full light. We identified 2,200 differentially expressed genes (DEGs) (1,096 up-regulated and 1,104 down-regulated) in shadow-1 mutants, compared to wild type, following exposure to shade stress. Of these DEGs, 329 were unique to shadow-1 plants kept under shade and were not found in any other comparisons that we made. We found 2,245 DEGs (1,153 up-regulated and 1,092 down-regulated) in shadow-1 plants, compared to wild-type, under light, with 485 DEGs unique to shadow-1 plants under light. We examined the expression of gibberellin (GA) biosynthesis genes and found that they were down-regulated in shadow-1 plants compared to wild type, notably gibberellin 20 oxidase (GA20ox), which was down-regulated to 3.3% (96.7% reduction) of the wild-type expression level under shade conditions. One GA response gene, lipid transfer protein 3 (LTP3), was also down-regulated to 41.5% in shadow-1 plants under shade conditions when compared to the expression level in the wild type. These data provide valuable insight into a role that GA plays in dwarfism and shade tolerance, as exemplified by shadow-1 plants, and could serve as a guide for plant breeders interested in developing new cultivars with either of these traits.

SUBMITTER: Li W

PROVIDER: S-EPMC5445233 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass.

Li Wei W Katin-Grazzini Lorenzo L Gu Xianbin X Wang Xiaojing X El-Tanbouly Rania R Yer Huseyin H Thammina Chandra C Inguagiato John J Guillard Karl K McAvoy Richard J RJ Wegrzyn Jill J Gu Tingting T Li Yi Y

Frontiers in plant science 20170526

The molecular basis behind shade tolerance in plants is not fully understood. Previously, we have shown that a connection may exist between shade tolerance and dwarfism, however, the mechanism connecting these phenotypes is not well understood. In order to clarify this connection, we analyzed the transcriptome of a previously identified shade-tolerant mutant of perennial ryegrass (Lolium perenne L.) called shadow-1. shadow-1 mutant plants are dwarf, and are significantly tol ...[more]

PMID: 28603533

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Project description:BACKGROUND: Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influence traits of agricultural importance. Moreover, the DNA sequence of mitochondrial genomes has been established and compared for a large number of species in order to characterize evolutionary relationships. Therefore, it is crucial to understand the organization of the mitochondrial genome and how it varies between and within species. Here, we report the first de novo assembly and annotation of the complete mitochondrial genome from perennial ryegrass. RESULTS: Intact mitochondria from perennial ryegrass leaves were isolated and used for mtDNA extraction. The mitochondrial genome was sequenced to a 167-fold coverage using the Roche 454 GS-FLX Titanium platform, and assembled into a circular master molecule of 678,580 bp. A total of 34 proteins, 14 tRNAs and 3 rRNAs are encoded by the mitochondrial genome, giving a total gene space of 48,723 bp (7.2%). Moreover, we identified 149 open reading frames larger than 300 bp and covering 67,410 bp (9.93%), 250 SSRs, 29 tandem repeats, 5 pairs of large repeats, and 96 pairs of short inverted repeats. The genes encoding subunits of the respiratory complexes - nad1 to nad9, cob, cox1 to cox3 and atp1 to atp9 - all showed high expression levels both in absolute numbers and after normalization. CONCLUSIONS: The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.

Project description:BackgroundSingle nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass.ResultsA perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome.ConclusionsHere, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.

Dataset Information

Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass.

Publications

Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass.

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