Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

ABSTRACT: Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE116423 | GEO | 2018/07/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]

Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

2012-08-10 | GSE39308 | GEO

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

2012-08-10 | GSE39307 | GEO

Gene expression level of six rice lineages

Project description:Towards understanding gene expression variation among related rice lineages on a genome-wide scale, we sought to assess global gene expression in the heading-stage panicle using a whole genome oligonucleotide microarray designed to represent 36,926 annotated indica genes. Using a loop-design, we interrogated gene expression patterns in six related rice lineages, including O. sativa (two Asian cultivars indica and japonica), O. nivara (Asian annual wild rice), O. rufipogon (Asian perennial wild rice) and O. glaberrima (African cultivated rice). Series_sample_order: Sample 1-12 Slide A; Sample 13-24 Slide B

2008-06-10 | E-GEOD-11712 | biostudies-arrayexpress

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]

2012-08-10 | E-GEOD-39308 | biostudies-arrayexpress

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. The 5' end of the 3' degraded mRNAs with polyA tails were collected and generated from seedlings at four-leaves stage of O.rufipogon by degradome highthoughput sequecing using Illumina GAII

2012-08-10 | E-GEOD-39307 | biostudies-arrayexpress

E-GEOD-116423

Project description:Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

2020-04-01 | E-GEOD-116423 | ExpressionAtlas

Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

Project description:Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

| PRJNA478448 | ENA

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

Project description:Rice was domesticated independently in Asia and Africa, leading to two distinct but closely related crop species, Oryza sativa and Oryza glaberrima, respectively. The two domestications lead to morphological changes, in which a higher branching complexity of the panicles, influencing seed production and crop yield. Although much emphasis was placed on changes in transcriptional regulation during rice domestication and improvement, no large-scale study of small RNA regulation changes during domestication has been reported so far. To analyze whether rice domestication has altered the expression of small RNAs, we performed deep sequencing of small RNA transcriptomes from early developmental stages of panicles from 10 genotypes of the cultivated African species and 10 genotypes of its wild-relative O. barthii. Our study shows a drastic expression change of the 21-nucleotide smallRNA population. A total of 29% of these smallRNAs are overexpressed in panicles of O. barthii vs. O. glaberrima, corresponding mainly to 21-nucleotide phased siRNAs (or phasiRNAs). We also show that these changes are associated with a differential expression of a known regulator of phased siRNAs, miR2118 during early panicle development. Finally, these changes are associated to a heterochronic alteration of phasiRNAs and miR2118 expression pattern, during panicle development with a delayed expression in the domesticated species. Our study suggests a major reshaping of the regulation network from a specific class of small RNA during African rice domestication.

2016-04-18 | GSE48346 | GEO

Co-cultivating rice plants with Azolla filiculoides modifies root architecture and timing of developmental stages

Project description:Innovative strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. Traditionally, in Southern-East Asian countries, rice farming benefits from the use of Azolla spp., either as green manure or as co-cultivated plants, for the supply of nitrogen. Azolla spp. are ferns that, in virtue of their symbiosis with the nitrogen-fixing cyanobacterium Trichormus azollae, fix atmospheric nitrogen and release it to the environment upon decomposition of their biomass. However, if and to what extent actively growing Azolla plants impact on the development of co-cultivated rice plantlets remains to be understood. To address this point here we employed an experimental model to follow the growth and development of roots and aerial organs of rice seedlings when co-cultivated with Azolla filiculoides. We show that actively growing A. filiculoides plants alter the architecture of the roots, the transcriptome of the roots, and the hormonal profiles of both roots and leaves.

2024-10-10 | GSE278294 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

Project description:MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

2018-04-25 | GSE111440 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data