Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
Data files
Jan 29, 2024 version files 2.35 MB
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Genotypic_Data.csv
2.30 MB
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Phenotypic_Data.csv
36.18 KB
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README.md
7.88 KB
Abstract
The mapping population consists of 166 recombinant inbred lines (RILs) derived from a cross between HD3086 and HI1500.
Phenotypic data
The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance.
Genotypic data
DNA was extracted from 21 days old seedlings using CTAB method (Murray and Thompson, 1980). Genomic DNA quality was determined using 0.8% agarose gel electrophoresis with λ DNA as the standard and quantified using nanodrop. The 35K SNP Axiom breeders’ array was used for genotyping of parents and the RILs population.
https://doi.org/10.5061/dryad.zpc866tfw
Author/Principal Investigator Information
Name: Dr Harikrishna
ORCID: https://orcid.org/0000-0002-7563-8362
Institution: ICAR-Indian Agricultural Research Institute, New Delhi, India
Address: ICAR-Indian Agricultural Research Institute, New Delhi, India-110012
Email: harikrishna.agri@gmail.com
Date of data collection: 2022-08-01 TO 2022-08-31
Geographic location of data collection: ICAR-Indian Agricultural Research Institute, New Delhi (28°38′30.5″N, 77°09′58.2″E, 228 m AMSL)
Information about funding sources that supported the collection of the data: Part of the research supported by a grant from Bill & Melinda Gates Foundation (Grant number # OPP1215722) sub grant to India for Zn mainstreaming project and National Innovations on Climate Resilient Agriculture (NICRA) a network project of the Indian Council of Agricultural Research (ICAR).
Description of the data and file structure
File List:
Phenotype_Data, have the phenotypic values of 168 genotypes for Thousand Grain Weight, Grain Iron Concentration, Grain Zinc Concentration from Foir different treatments viz., TSIR (Timely Sown Irrigated), TSRI (Timely Sown Restricted Irrigated), LSIR (Late Sown Irrigated) and LSRI (Late sown Restricted Irrigated) trials, SNP_data, contains processed SNP genotypic information obtained through Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States)
Relationship between files, if important: Genotypic and Phenotypic information or files developed with the same set of bread wheat recombinant inbred lines.
Additional related data collected that was not included in the current data package: Nil
Are there multiple versions of the dataset?
If yes, name of file(s) that was updated: Nil
Why was the file updated?
When was the file updated?
METHODOLOGICAL INFORMATION
Description of methods used for collection/generation of data: Around 20 g of grain sample from each of 166 RILs and 2 parents under all the four conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance. The genotypes were genotyped using Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs.
Methods for processing the data: The RILs and Parents consisting of 168 genotypes were genotyped using Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. A total of 4106 SNP markers were polymorphic between the two parents.
Instrument- or software-specific information needed to interpret the data: MetaRv6.0 (Multi Environment Trial Analysis with R) software (Alvarado et al., 2020) was used for calculating best linear unbiased predictors (BLUPs) for the individual conditions and combined across all production conditions.
Standards and calibration information, if appropriate: Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values.
Environmental/experimental conditions: TSIR (Timely Sown Irrigated), TSRI (Timely Sown Restricted Irrigated), LSIR (Late Sown Irrigated) and LSRI (Late sown Restricted Irrigated)
Describe any quality-assurance procedures performed on the data: Nil
People involved with sample collection, processing, analysis and/or submission: Karthik Kumar Manjunath, Hari Krishna, Narayana Bhat Devate, Sunil kumar VP, Divya Chauhan, Shweta Singh, C N Mishra, J B Singh, Nivedita Sinha, Neelu Jain, G P Singh and P K Singh.
DATA-SPECIFIC INFORMATION FOR: [Phenotypic_Data]
Number of variables: 18 (Multiple of 3 variables under different condition)
Number of cases/rows: 168
Variable List: GFeC - Grain Fe Concentration (in mg/kg), FZnc - Grain Zinc Concentration (in mg/kg), TGW- Thousand grain weight (in grams)
TSIR (Timely Sown Irrigated), TSRI (Timely Sown Restricted Irrigated), LSIR (Late Sown Irrigated) and LSRI (Late sown Restricted Irrigated)
BLUP- Best linear Unbiased Predictor of 2 year data.
Pooled - Combined BLUP Across 4 environments.
TSIR_GFeC_BLUP- Grain Fe Concentration under TSIR in mg/kg
TSRI_GFeC_BLUP- Grain Fe Concentration under TSRI in mg/kg
LSIR_GFeC_BLUP- Grain Fe Concentration under LSIR in mg/kg
LSRI_GFeC_BLUP- Grain Fe Concentration under LSRI in mg/kg
I_TSRI_GFeC_BLUP- Grain Fe Concentration under TSRI at Indore in mg/kg
Pooled_GFeC- Grain Fe Concentration Pooled over 4 treatments in mg/kg
TSIR_GZnC_BLUP- Grain Zn Concentration under TSIR in mg/kg
TSRI_GZnC_BLUP- Grain Zn Concentration under TSRI in mg/kg
LSIR_GZnC_BLUP- Grain Zn Concentration under LSIR in mg/kg
LSRI_GZnC_BLUP- Grain Zn Concentration under LSRI in mg/kg
I_TSRI_GZnC_BLUP- Grain Zn Concentration under tSRI at Indore in mg/kg
Pooled_GZnC- Grain Zn Concentration Pooled over 4 treatments in mg/kg
TSIR_TKW_BLUP- Thousand Grain Weight under TSIR in g
TSRI_TKW_BLUP- Thousand Grain Weight under TSRI in g
LSIR_TKW_BLUP- Thousand Grain Weight under LSIR in g
LSRI_TKW_BLUP- Thousand Grain Weight under LSRI in g
I_TSRI_TKW_BLUP- Thousand Grain Weight under TSRI at Indore in g
Poooled_TKW- Thousand Grain Weight Pooled over 4 treatments in g
Missing data codes: Nil
Specialized formats or other abbreviations used: TGW - Thousand Grain weight, GFeC - Grain Iron Concentration, GZnC - Grain Zinc Concentration
DATA-SPECIFIC INFORMATION FOR: [Genotypic_Data]
Number of variables: 4106
Number of cases/column: 11 identifier + 168 genotypes
Variable List: 4106 SNP markers
Missing data codes: NA
Specialized formats or other abbreviations used: A - Adinine, G - Guanine, C - Cytosine, T - Thymine, NA - Missing
SNP Data format: HapMap format - The Hapmap file format is a table which consists of 11 columns plus one column for each sample genotyped. The first row contains the header labels of samples, and each additional row contains all the information associated with a single SNP.
first 11 column contains details of -
1 : rs# : contains the SNP identifier;
2 : alleles : contains SNP alleles according to NCBI database dbSNP;
3 : chrom : contains the chromosome that the SNP was mapped;
4 : pos : contains the respective position of this SNP on chromosome;
5 : strand : contains the orientation of the SNP in the DNA strand. Thus, SNPs could be in the forward (+) or in the reverse (-) orientation relative to the reference genome;
6 : assembly# : contains the version of reference sequence assembly (from NCBI);
7 : center : contains the name of genotyping center that produced the genotypes;
8 : protLSID contains the identifier for HapMap protocol;
9 : assayLSID contain the identifier HapMap assay used for genotyping;
10 : panelLSID contains the identifier for panel of individuals genotyped;
11 : QCcode contains the quality control for all entries
Sharing/Access information
Licenses/restrictions placed on the data: Nil
Links to publications that cite or use the data: DOI:
Links to other publicly accessible locations of the data:
Links/relationships to ancillary data sets: Nil
Was data derived from another source?
If yes, list source(s): Nil
Recommended citation for this dataset: Manjunath et al., 2023, Data from: Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers, Dryad, Dataset
Code/Software
n/a
The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. Two irrigations were given in TSRI, one at germination and other at 21 days after sowing; six irrigations were provided during cropping period in irrigated condition (TSIR). Late sown trials (LSIR and LSRI) were planted in second fortnight of December to expose plants to heat stress, and under LSRI condition irrigation was withheld to expose plants to both terminal heat and drought stress. The genotypes were evaluated in an alpha-lattice design with two replications. Each genotype was sown in 3 rows of 1 m each with 22.5 cm distance between rows and 10 cm distance between plants. Uniform agronomic practises were practiced for proper establishment of crop stand.
Phenotyping
From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance. MetaRv6.0 (Multi Environment Trial Analysis with R) software (Alvarado et al., 2020) was used to calculate best linear unbiased predictors (BLUPs).