Unlocking the grain quality enigma: A KASP-driven voyage through bread wheat's quantitative trait nucleotides under heat adversity
Data files
May 15, 2024 version files 7.79 MB
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data_set.zip
7.78 MB
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README.md
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Abstract
Heat stress is a critical factor affecting global wheat production and productivity. In this study, out of 500 studied accessions a diverse panel of 126 wheat genotypes grown under twelve distinct environmental conditions was analyzed. Using 35K single-nucleotide polymorphism (SNP) genotyping assays and trait data on five biochemical parameters, including grain protein content (GPC), grain amylose content (GAC), grain total soluble sugars (TSS), grain iron (Fe), and zinc (Zn) content, six multi-locus GWAS models were employed for association analysis. This revealed 67 significantly associated QTNs linked to grain quality parameters, explaining phenotypic variations ranging from 3% to 44% under heat stress conditions. By considering the results in consensus to at least three GWAS models and three locations, the final QTNs were reduced to 17, with 14 being novel findings. Notably, two novel markers, AX-94461119 (chromosome 6A) and AX-95220192 (chromosome 7D), associated with grain iron and zinc, respectively, were validated through KASP approach. Candidate genes, such as chaperonin Cpn60/GroEL/TCP-1 family, P-loop containing nucleoside triphosphate hydrolases (NTPases), Bowman-Birk type proteinase inhibitor (BBI), and NPSN13 protein, were identified from the associated genomic regions, which could be potentially targeted for improving quality traits and heat tolerance in wheat.
This readme file was generated on [2024-08-05] by [Sundeep Kumar]
GENERAL INFORMATION
Title of Dataset: Data from: Unlocking the Grain Quality Enigma: A KASP-Driven Voyage Through Bread Wheat's Quantitative Trait Nucleotides Under Heat Adversity
Author/Principal Investigator Information
Name: Dr Sundeep Kumar
Institution:ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi-110012
Address: ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi-110012
Email: Sundeep.Kumar@icar.gov.in
Date of data collection: 2021-11-01 to 2022-11-01
Geographic location of data collection: BISA farm at Pusa, Bihar, falling under the North East Plain Zones (NEPZ); BISA Jabalpur, situated in the Central Zone (CZ); and BISA Ludhiana, located in the North West Plain Zones (NWPZ)
Information about funding sources that supported the collection of the data: ICAR-National Bureau of Plant Genetic Resources
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: Nil
Links to publications that cite or use the data: Nil
Links to other publicly accessible locations of the data: Nil
Links/relationships to ancillary data sets: Nil
Was data derived from another source?
If yes, list source(s): Nil
DATA & FILE OVERVIEW
File List: Phenotype data S2 a&b, Phenotype data S3 a&b,Phenotype data S4 a&b, have the phenotypic values of 126 genotypes for grain protein content (GPC), grain amylose content (GAC), grain total soluble sugars (TSS), and the grain iron and zinc content, Final SNP data, contains processed SNP genotypic information obtained through Axiom® Wheat Breeders’ Array (Thermo Fisher Scientific, Wilmington, DE, USA)
Relationship between files, if important: Genotypic and Phenotypic information or files developed with the same set of germplasm lines of bread wheat
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: Standard procedure for data collection was followed as given in manual ‘Wheat Physiological Breeding II: A Field Guide to Wheat Phenotyping’ (Pask et al., 2012). Data was collected on traits like grain protein content (GPC), grain amylose content (GAC), grain total soluble sugars (TSS), and the grain iron and zinc content. The genotypes were genotyped using Axiom® Wheat Breeders’ Array (Thermo Fisher Scientific, Wilmington, DE, USA)having35,143 SNPs genome-wide SNPs.
Methods for processing the data: The GWAS panel of 126 genotypes were genotyped using Axiom® Wheat Breeders’ Array (Thermo Fisher Scientific, Wilmington, DE, USA)having35,143 SNPs genome-wide SNPs.. The monomorphic, markers with Minor allele frequency (<10%), genotype missing and monomorphic SNPs were further filtered as a quality control step, and as a final number 15805 polymorphic SNPs (44.97%) were used for association mapping
Instrument- or software-specific information needed to interpret the data: R package mrMLM v3.1 ’, Trait Analysis by aSSociation Evolution and Linkage (TASSEL) version 5.0, STRUCURE, STRUCTURE HARVESTER
Standards and calibration information, if appropriate: NIL
Environmental/experimental conditions: Timely sown (TS) and Late sown (LS)
Describe any quality-assurance procedures performed on the data: near-infrared spectroscopy (NIRS) for biochemical analysis
People involved with sample collection, processing, analysis and/or submission: Latief Bashir, Neeraj Budhlakoti, Anjan Kumar Pradhan, Divya Sharma, Antil Jain, Saman Saim Rehman , Vishal Kondal, Sherry R Jacob, Rakesh Bhardwaj, Kiran Gaikwad, Dwijesh Chandra Mishra, Abhishek Pandey, Satinder Kaur, Pradeep Kumar Bhati, Rakesh Singh, Gyanendra Pratap Singh, Sundeep Kumar
DATA-SPECIFIC INFORMATION FOR: [ Phenotype data S2 a&b, Phenotype data S3 a&b,Phenotype data S4 a&b]
Number of variables: 10 in each spread sheet
Number of cases/rows: 126
Variable List: grain protein content (GPC), grain amylose content (GAC), grain total soluble sugars (TSS), and the grain iron and zinc content
JB_TS for Jabalpur timely sown, JB_LS for Jabalpur late sown, PB_TS for Punjab timely sown, PB_LS for Punjab late sown, SM_TS for Samastipur timely sown, SM_LS for Samastipur late sownRI for restricted irrigated
2020 for data collected on 2020 rabi season. rest are 2021 rabi season
Missing data codes: Nil
Specialized formats or other abbreviations used: Nil
DATA-SPECIFIC INFORMATION FOR: [Final SNP]
Number of variables: 15806
Number of cases/rows: 137
Variable List: 15806 SNP markers
Missing data codes: NA
Specialized formats or other abbreviations used: A - Adinine, G - Guanine, C - Cytosine, T - Thymine, NA - Missing