 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 04, 2017 |
| Title |
Both maternally and paternally imprinted genes regulate seed development in rice |
| Organism |
Oryza sativa |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
|
| Summary |
Genetic imprinting is an epigenetic phenomenon that describes unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms including mammals and flowering plants. The function of imprinted genes was rarely reported.
We report genome-wide analysis of gene expression, DNA methylation, and small RNAs in the rice endosperm and functional tests of five imprinted genes in seed development using CRISPR/Cas9 editing technology.
We identified 162 maternally expressed genes(MEGs) and 95 paternally expressed genes (PEGs) in the rice endosperm, which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci, and some 21-22-siRNAs and lncRNAs. Remarkably, one-third of MEGs and nearly half of PEGs were associated with grain-yield quantitative trait loci and enriched in the endosperm-expressed genes. Disrupting two MEGs increased the amount of small starch granules and reduced grain size, weight, and embryo size, while mutating three PEGs reduced starch content and seed fertility.
Our data support both MEGs and PEGs in rice are required for starch and nutrient accumulation, mediating offspring fitness and optimal seed size. This imprinting strategy provides potential means for improving grain yield of rice and other cereal crops.
|
| |
|
| Overall design |
We have submitted 14 samples: two resequencing samples of rice cultivars (02428 and Longtefu); two BS-seq libraries of endosperm of reciprocal hybrids; two RNA-seq libraries of endosperm of reciprocal hybrids; 4 small RNA libraries of endosperm of reciprocal hybrids and parents; 4 small RNA libraries of seedling of reciprocal hybrids and parents.
|
| |
|
| Contributor(s) |
Yuan J, Chen S, Jiao W, Wang L, Wang L, Ye W, Lu J, Hong D, You S, Cheng Z, Yang D, Chen ZJ |
| Citation(s) |
28295376 |
| BioProject |
PRJNA309746 |
| |
| Submission date |
Feb 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingya Yuan |
| E-mail(s) |
yjy.906@163.com
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
1 Weigang Road
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platforms (2) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
| GPL19290 |
Illumina HiSeq 2500 (Oryza sativa) |
|
| Samples (14)
|
|
| Relations |
| SRA |
SRP068886 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77710_RAW.tar |
9.9 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...