Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties.

ABSTRACT: The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties. The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits. Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.

SUBMITTER: Zainal-Abidin RA

PROVIDER: S-EPMC7298397 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties.

Zainal-Abidin Rabiatul-Adawiah RA Zainal Zamri Z Mohamed-Hussein Zeti-Azura ZA Sew Yun Shin YS Simoh Sanimah S Ab Razak Shahril S Abu-Bakar Norliza N

Data in brief 20200603

The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties ...[more]

PMID: 32566707

Similar Datasets

RNA-seq data from whole rice grains of pigmented and non-pigmented Malaysian rice varieties.

Project description:Pigmented rice is enriched with antioxidants, macro- and micronutrients. A comprehensive investigation of the gene expression patterns among the pigmented rice varieties would help to understand the cellular mechanism and biological processes of rice grain pigmentation. Hence, we performed RNA sequencing and analysis on the whole grain of dehusked mature seeds of selected six Malaysian rice varieties with varying grain pigmentations. These varieties were black rice (BALI and Pulut Hitam 9), red rice (MRM16 and MRQ100) and white rice (MR297 and MRQ76). Illumina HiSeq™ 4000 sequencer was used to generate total raw nucleotides of approximately 53 Gb in size. From 353,937,212 total paired-end raw reads, 340,131,496 total clean reads were obtained. The raw reads were deposited into European Nucleotide Archive (ENA) database and can be accessed via accession number PRJEB34340. This dataset allows us to identify and profile all expressed genes with functions related to nutritional traits (i.e. antioxidants, folate and amylose content) and quality trait (i.e. aroma) across both pigmented and non-pigmented rice varieties. In addition, the transcriptome data obtained will be valuable for discovery of potential gene markers and functional SNPs related to functional traits to assist in rice breeding programme.

| S-EPMC7138961 | biostudies-literature

Genome resequencing of pigmented rice varieties

Project description:Leaves from four pigmented rice varieties were sequenced using Illumina Hi-seq 4000 sequencing technology. Approximately 30x depth of sequencing for each varieties.

| PRJEB29070 | ENA

Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.

Project description:Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.

| S-EPMC6811786 | biostudies-literature

SWATH-based quantitative proteomics data derived from whole grain of Malaysian local pigmented and non-pigmented rice varieties

Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.

2020-04-27 | PXD018338 | Pride

Comprehensive proteomics data on whole rice grain of selected pigmented and non-pigmented rice varieties using SWATH-MS approach.

Project description:The proteome data of whole rice grain is considerably limited particularly for rice with pigmentations such as black and red rice. Hence, we performed proteome analysis of two black rice varieties (BALI and Pulut Hitam 9), two red rice varieties (MRM16 and MRQ100) and two white rice varieties (MR297 and MRQ76) using label-free liquid chromatography Triple TOF 6600 tandem mass spectrometry (LC-MS/MS). Our aim was to profile and identify proteins related to nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits based on peptide-centric scoring from the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) approach. Both information dependent acquisition (IDA) and SWATH-MS run were performed in this analysis. Raw data was then processed using ProteinPilot software to identify and compare proteins from the six different varieties. In future, this proteomics data will be integrated with previously obtained genomics [1] and transcriptomics [2] data focusing on the above nutritional and quality traits, with an ultimate aim to develop a panel of functional biomarkers related to those traits for future rice breeding programme. The raw MS data of the pigmented and non-pigmented rice varieties have been deposited to ProteomeXchange database with accession number PXD018338.

| S-EPMC7334386 | biostudies-literature

Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data.

Project description:Genome comparisons provide information on the nature of genetic change, but such comparisons are challenged to differentiate the importance of the actual sequence change processes relative to the role of selection. This problem can be overcome by identifying changes that have not yet had the time to undergo millions of years of natural selection. We describe a strategy to discover accession-specific changes in the rice genome using an abundant resource routinely provided for many genome analyses, resequencing data. The sequence of the fully sequenced rice genome from variety Nipponbare was compared to the pooled (∼114×) resequencing data from 126 japonica rice accessions to discover "Nipponbare-specific" sequences. Analyzing nonrepetitive sequences, 8504 "candidate" Nipponbare-specific changes were detected, of which around two-thirds are true novel sequence changes and the rest are predicted genome sequencing errors. Base substitutions outnumbered indels in this data set by > 28:1, with ∼8:5 bias toward transversions over transitions, and no transposable element insertions or excisions were observed. These results indicate that the strategy employed is effective for finding recent sequence changes, sequencing errors, and rare alleles in any organism that has both a reference genome sequence and a wealth of resequencing data.

| S-EPMC5972431 | biostudies-literature

Whole genome resequencing of MR297 and MRQ76 rice varieties.

Project description:Whole genome resequencing of MR297 and MRQ76 rice varieties using Illumina HiSeq 4000 sequencing technology.

| PRJEB32344 | ENA

Expression data from non-pigmented and pigmented mouse melanocytes

Project description:Immortalized, amelanotic melanocytes isolted from skin of Balb/c express enzymatically-inactive tyrosinase due to a homozygous point mutation (TGT->TCT) in tyrosinase gene, resulting in a lack of melanin . To serve as a control cell line, pigmentation was restored in these cells by correcting the point mutation using an RNA-DNA oligonucleotide (kingly gift from Dr. Alexeev Y. Vitali). We used microarray to detail the effect of tyrosinase mutation on gene expression in normal versus mutant melanocytes.

2013-09-21 | GSE51073 | GEO

Mapping of Rice Varieties and Sowing Date Using X-Band SAR Data.

Project description:Rice is a major staple food for nearly half of the world's population and has a considerable contribution to the global agricultural economy. While spaceborne Synthetic Aperture Radar (SAR) data have proved to have great potential to provide rice cultivation area, few studies have been performed to provide practical information that meets the user requirements. In rice growing regions where the inter-field crop calendar is not uniform such as in the Mekong Delta in Vietnam, knowledge of the start of season on a field basis, along with the planted rice varieties, is very important for correct field management (timing of irrigation, fertilization, chemical treatment, harvest), and for market assessment of the rice production. The objective of this study is to develop methods using SAR data to retrieve in addition to the rice grown area, the sowing date, and the distinction between long and short cycle varieties. This study makes use of X-band SAR data from COSMO-SkyMed acquired from 19 August to 23 November 2013 covering the Chau Thanh and Thoai Son districts in An Giang province, Viet Nam, characterized by a complex cropping pattern. The SAR data have been analyzed as a function of rice parameters, and the temporal and polarization behaviors of the radar backscatter of different rice varieties have been interpreted physically. New backscatter indicators for the detection of rice paddy area, the estimation of the sowing date, and the mapping of the short cycle and long cycle rice varieties have been developed and assessed. Good accuracy has been found with 92% in rice grown area, 96% on rice long or short cycle, and a root mean square error of 4.3 days in sowing date. The results have been discussed regarding the generality of the methods with respect to the rice cultural practices and the SAR data characteristics.

| S-EPMC5795876 | biostudies-other

Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield.

Project description:Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.

| S-EPMC5513431 | biostudies-other

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