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Series GSE77710 Query DataSets for GSE77710
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
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)
GSM2056922 02428_reseq
GSM2056923 Longtefu_reseq
GSM2056924 LX0_EN_BS-seq
SRA SRP068886

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE77710_RAW.tar 9.9 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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