QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat
Data files
Jan 29, 2024 version files 1.61 MB
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Genotypic_Data.csv
1.49 MB
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Phenotypic_Data.csv
85.62 KB
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README.md
14.50 KB
Abstract
The mapping population comprises of 180 RILs developed from a cross between GW322 and KAUZ.
Phenotypic data
Phenotypic evaluation was conducted across two consecutive crop seasons (2021-22 and 2022-23) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at ICAR-IARI, New Delhi. Various physiological and agronomic traits of importance were measured. The component traits of yield including days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY) were measured under heat and combined stress conditions.
Genotypic data
DNA was isolated from 21-day-old seedlings using the CTAB method (Murray and Thompson, 1980). DNA quality check was done using 0.8% agarose gel electrophoresis. The Axiom Breeders' array containing 35K Single Nucleotide Polymorphism (SNP) was employed for the genotyping of RILs and parents.
README: QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat
https://doi.org/10.5061/dryad.0rxwdbs7b
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: 2021-12-01 TO 2023-07-31
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 was 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 182 genotypes for days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY) were measured under heat and combined stress conditions from two different treatments viz., LSIR (Late Sown Irrigated) and LSRI (Late sown Restricted Irrigated) trials in two seasons 2021-22 and 2022-23, 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.
METHODOLOGICAL INFORMATION
Description of methods used for collection/generation of data: SPAD values were recorded at the anthesis stage using SPAD-502Plus (Konica Minolta). The instrument GreenSeeker™ was used to record NDVI. NDVI was measured at four stages: at anthesis, 10 days after anthesis, 20 days after anthesis and 30 days after anthesis. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance. Days to heading is the number of days from sowing to 50% heading is recorded for each genotype. Plant height is measured from the base of the ground to the tip of the plants. It’s measured using a measuring scale and the unit of measurement is cm. Spike length is measured from the base to the tip of the spikelets excluding awns. It’s measured using a measuring scale and the unit of measurement is cm. 20 random spikes were harvested from each plot. The harvested spikes from each plot were threshed and cleaned separately. The weight of seeds from 20 spikes was recorded with an electronic balance. The weight of 20 spikes was divided by 20 to obtain individual spike weight and the unit of measurement is gm. After the crop attained harvest maturity the crop was cut to the base using a sickle and the weight of the entire biological yield was measured using a hand-held mechanical balance. The unit of measurement is kg. Spikes from each plot were threshed separately using a full man thresher and seeds were cleaned to remove chaffy material. The seed yield from each plot was measured using a mechanical balance. The unit of measurement is kg. 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 182 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 2476 SNP markers were polymorphic between the two parents.
Instrument- or software-specific information needed to interpret the data: PBTools v1.4 software (PBTools, version 1.4, 2014) 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: Nil
Environmental/experimental conditions: 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, Sahana Police Patil, Divya Chauhan, Shweta Singh, Sudhir Kumar, Neelu Jain, G P Singh and P K Singh.
DATA-SPECIFIC INFORMATION FOR: [Phenotypic_Data]
Number of variables: 88 (Multiple of 11 variables under different conditions)
Number of cases/rows: 182
Variable List: days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY)
LSIR1 (Late Sown Irrigated condition in 2021-22), LSRI1 (Late sown Restricted Irrigated condition in 2021-22), LSIR2 (Late Sown Irrigated condition in 2022-23) and LSRI2 (Late sown Restricted Irrigated condition in 2022-23)
H- Combined BLUP Across 2 seasons under LSIR
DH- Combined BLUP Across 2 seasons under LSRI
Pooled - Combined BLUP Across treatments and seasons.
LSIR1_NDVI1- normalized difference vegetation index at anthesis under LSIR condition in 2021-22
LSIR2_NDVI1- normalized difference vegetation index at anthesis under LSIR condition in 2022-23
H_NDVI1- normalized difference vegetation index at anthesis under LSIR condition pooled over 2 seasons
LSRI1_NDVI1- normalized difference vegetation index at anthesis under LSRI condition in 2021-22
LSRI2_NDVI1- normalized difference vegetation index at anthesis under LSRI condition in 2022-23
DH_NDVI1- normalized difference vegetation index at anthesis under LSRI condition pooled over 2 seasons
Pooled_NDVI1- normalized difference vegetation index at anthesis pooled over treatments and seasons
LSIR1_NDVI2- normalized difference vegetation index at 10 days after anthesis under LSIR condition in 2021-22
LSIR2_NDVI2- normalized difference vegetation index at 10 days after anthesis under LSIR condition in 2022-23
H_NDVI2- normalized difference vegetation index at 10 days after anthesis punder LSIR condition pooled over 2 seasons
LSRI1_NDVI2- normalized difference vegetation index at 10 days after anthesis at anthesis under LSRI condition in 2021-22
LSRI2_NDVI2- normalized difference vegetation index at 10 days after anthesis under LSRI condition in 2022-23
DH_NDVI2- normalized difference vegetation index at 10 days after anthesis under LSRI condition pooled over 2 seasons
Pooled_NDVI2- normalized difference vegetation index at 10 days after anthesis pooled over treatments and seasons
LSIR1_NDVI3- normalized difference vegetation index at 20 days after anthesis under LSIR condition in 2021-22
LSIR2_NDVI3- normalized difference vegetation index at 20 days after anthesis under LSIR condition in 2022-23
H_NDVI3- normalized difference vegetation index at 20 days after anthesis under LSIR condition pooled over 2 seasons
LSRI1_NDVI3- normalized difference vegetation index at 20 days after anthesis at anthesis under LSRI condition in 2021-22
LSRI2_NDVI3- normalized difference vegetation index at 20 days after anthesis under LSRI condition in 2022-23
DH_NDVI3- normalized difference vegetation index at 20 days after anthesis under LSRI condition pooled over 2 seasons
Pooled_NDVI3- normalized difference vegetation index at 20 days after anthesis pooled over treatments and seasons
LSIR1_NDVI4- normalized difference vegetation index at 30 days after anthesis under LSIR condition in 2021-22
LSIR2_NDVI4- normalized difference vegetation index at 30 days after anthesis under LSIR condition in 2022-23
H_NDVI4- normalized difference vegetation index at 30 days after anthesis under LSIR condition pooled over 2 seasons
LSRI1_NDVI4- normalized difference vegetation index at 30 days after anthesis at anthesis under LSRI condition in 2021-22
LSRI2_NDVI4- normalized difference vegetation index at 30 days after anthesis under LSRI condition in 2022-23
DH_NDVI4- normalized difference vegetation index at 30 days after anthesis under LSRI condition pooled over 2 seasons
Pooled_NDVI4- normalized difference vegetation index at 30 days after anthesis pooled over treatments and seasons
LSIR1_PH- plant height under LSIR condition in 2021-22
LSIR2_PH- plant height under LSIR condition in 2022-23
H_PH- plant height under LSIR condition pooled over 2 seasons
LSRI1_PH- plant height under LSRI condition in 2021-22
LSRI2_PH- plant height under LSRI condition in 2022-23
DH_PH- plant height under LSRI condition pooled over 2 seasons
Pooled_PH- plant height pooled over treatments and seasons
LSIR1_DFH- days to fifty percent heading under LSIR condition in 2021-22
LSIR2_DFH- days to fifty percent heading under LSIR condition in 2022-23
H_DFH- days to fifty percent heading under LSIR condition pooled over 2 seasons
LSRI1_DFH- days to fifty percent heading under LSRI condition in 2021-22
LSRI2_DFH- days to fifty percent heading under LSRI condition in 2022-23
DH_DFH- days to fifty percent heading under LSRI condition pooled over 2 seasons
Pooled_DFH- days to fifty percent heading pooled over treatments and seasons
LSIR1_GWPS- grain weight per spike under LSIR condition in 2021-22
LSIR2_GWPS- grain weight per spike under LSIR condition in 2022-23
H_GWPS- grain weight per spike under LSIR condition pooled over 2 seasons
LSRI1_GWPS- grain weight per spike under LSRI condition in 2021-22
LSRI2_GWPS- grain weight per spike under LSRI condition in 2022-23
DH_GWPS- grain weight per spike under LSRI condition pooled over 2 seasons
Pooled_GWPS- grain weight per spike pooled over treatments and seasons
LSIR1_TGW- thousand grain weight under LSIR condition in 2021-22
LSIR2_TGW- thousand grain weight under LSIR condition in 2022-23
H_TGW- thousand grain weight under LSIR condition pooled over 2 seasons
LSRI1_TGW- thousand grain weight under LSIR condition in 2021-22
LSRI2_TGW- thousand grain weight under LSIR condition in 2022-23
DH_TGW- thousand grain weight under LSIR condition pooled over 2 seasons
Pooled_TGW- thousand grain weight pooled over treatments and seasons
LSIR1_BM- biomass under LSIR condition in 2021-22
LSIR2_BM- biomass under LSIR condition in 2022-23
H_BM- biomass under LSIR condition pooled over 2 seasons
LSRI1_BM- biomass under LSRI condition in 2021-22
LSRI2_BM- biomass under LSRI condition in 2022-23
DH_BM- biomass under LSRI condition pooled over 2 seasons
Pooled_BM- biomass pooled over treatments and seasons
LSIR1_PY- plot yield under LSIR condition in 2021-22
LSIR2_PY- plot yield under LSIR condition in 2022-23
H_PY- plot yield under LSIR condition pooled over 2 seasons
LSRI1_PY- plot yield under LSRI condition in 2021-22
LSRI2_PY- plot yield under LSRI condition in 2022-23
DH_PY- plot yield under LSRI condition pooled over 2 seasons
Pooled_PY- plot yield pooled over treatments and seasons
LSIR1_CT- canopy temperature under LSIR condition in 2021-22
LSRI1_CT- canopy temperature under LSRI condition in 2021-22
LSIR2_SN- number of spikelets under LSIR condition in 2022-23
LSRI2_SN- number of spikelets under LSRI condition in 2022-23
LSIR1_SPAD- spad value under LSIR condition in 2021-22
LSIR2_SPAD- spad value under LSIR condition in 2022-23
H_SPAD- spad value under LSIR condition pooled over 2 seasons
LSRI1_SPAD- spad value under LSRI condition in 2021-22
LSRI2_SPAD- spad value under LSRI condition in 2022-23
DH_SPAD- spad value under LSRI condition pooled over 2 seasons
POOLED_SPAD- spad value pooled over treatments and seasons
LSIR1_SL- spike length under LSIR condition in 2021-22
LSIR2_SL- spike length under LSIR condition in 2022-23
H_SL- spike length under LSIR condition pooled over 2 seasons
LSRI1_SL- spike length under LSRI condition in 2021-22
LSRI2_SL- spike length under LSRI condition in 2022-23
DH_SL- spike length under LSRI condition pooled over 2 seasons
POOLED_SL- spike length pooled over treatments and seasons
Missing data codes: Nil
Specialized formats or other abbreviations used: Nil
DATA-SPECIFIC INFORMATION FOR: [Genotypic_Data]
Number of variables: 2476
Number of cases/column: 11 identifier + 182 genotypes
Variable List: 2476 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 contain 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., 2024, Data from: QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat, Dryad, Dataset
Code/Software
n/a
Methods
The experiment was carried out at ICAR-IARI, New Delhi (28.6550° N, 77.1888° E, MSL 228.61 m) over two consecutive crop seasons (2021-22 and 2022-23). The study involved the evaluation of RILs developed from GW322/KAUZ along with their parents under two distinct conditions: heat stress (late sown irrigation; LSIR) and combined drought and heat stress (late sown restricted irrigation; LSRI) in augmented design (Federer, 1956; Federer, 1961; Searle, 1965). The experimental field was divided into four blocks, with four checks utilized in the study. Each check was replicated three times.
Phenotyping:
The instrument GreenSeeker™ was used to record NDVI. NDVI was measured at four stages: at anthesis, 10 days after anthesis, 20 days after anthesis and 30 days after anthesis. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance. Days to heading is the number of days from sowing to 50% heading is recorded for each genotype. Plant height is measured from the base of the ground to the tip of the plants. It’s measured using a measuring scale and the unit of measurement is cm. Spike length is measured from the base to the tip of the spikelets excluding awns. It’s measured using a measuring scale and the unit of measurement is cm. 20 random spikes were harvested from each plot. The harvested spikes from each plot were threshed and cleaned separately. The weight of seeds from 20 spikes was recorded with an electronic balance. The weight of 20 spikes was divided by 20 to obtain individual spike weight and the unit of measurement is gm. After the crop attained harvest maturity the crop was cut to the base using a sickle and the weight of the entire biological yield was measured using a hand-held mechanical balance. The unit of measurement is kg. Spikes from each plot were threshed separately using a full man thresher and seeds were cleaned to remove chaffy material. The seed yield from each plot was measured using a mechanical balance. The unit of measurement is kg.