DOI: 10.5061/dryad.zpc866tfw
title: Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers

description: The mapping population consists of 166 recombinant inbred lines (RILs)
 derived from a cross between HD3086 and HI1500. Phenotypic dataThe 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 dataDNA 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.
description: 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.
 <strong>Phenotyping</strong><br>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). 
description: # Mapping of the QTLs governing grain micronutrients and thousand kernel
 weight in wheat (Triticum aestivum L.) using high density SNP markers
 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: 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