Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection

Wheat ( Triticum aestivum L .) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associat...

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Published in:Frontiers in plant science Vol. 14; p. 1148658
Main Authors: Kumari, Jyoti, Lakhwani, Deepika, Jakhar, Preeti, Sharma, Shivani, Tiwari, Shailesh, Mittal, Shikha, Avashthi, Himanshu, Shekhawat, Neelam, Singh, Kartar, Mishra, Kaushlesh Kumar, Singh, Rakesh, Yadav, Mahesh C., Singh, Gyanendra Pratap, Singh, Amit Kumar
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media SA 28.06.2023
Frontiers Media S.A
Subjects:
ABC transporter
Agricultural production
Gene mapping
Genes
Genetic testing
genome wide association studies
Genomes
Genomics
Genotype & phenotype
Germplasm
Grain size
Human populations
mrMLM
Nucleotides
Particle size
Plant breeding
Plant Science
Population
Principal components analysis
QTN
Quantitative trait loci
Seeds
Single-nucleotide polymorphism
Software
Thioredoxin
thousand grain weight
Wheat
QTN
wheat
thousand grain weight
genome wide association studies
mrMLM
ISSN:1664-462X, 1664-462X
Online Access:Get full text
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Summary:Wheat ( Triticum aestivum L .) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E 1 , E 2 , E 3 , E 4 , E 5 , E 5 , E 6 , and E 7 ). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.
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Edited by: Shouvik Das, Regional Centre for Biotechnology (RCB), India
These authors have contributed equally to this work
Reviewed by: Revathi Ponnuswamy, Indian Institute of Rice Research (ICAR), India; Kumar Paritosh, University of Delhi, India
ISSN:1664-462X
1664-462X
DOI:10.3389/fpls.2023.1148658