DOI: 10.5061/dryad.0rxwdbs7b
title: QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat

description: The mapping population comprises of 180 RILs developed from a cross
 between GW322 and KAUZ. Phenotypic dataPhenotypic 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 dataDNA 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.
description: 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.
 <strong>Phenotyping:</strong><br>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.
description: # QTL mapping: insights into genomic regions governing component traits of
 yield under combined heat and drought stress in wheat
 Author/Principal
 Investigator Information Name: Dr Harikrishna ORCID:
 Institution: ICAR-Indian
 Agricultural Research Institute, New Delhi, India Address: ICAR-Indian
 Agricultural Research Institute, New Delhi, India-110012 Email:
 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