DOI: 10.5061/dryad.3n5tb2rs1
title: Unlocking the grain quality enigma: A KASP-driven voyage through bread wheat's quantitative trait nucleotides under heat adversity

description: 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.
description: 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](mailto: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 (&lt;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