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GWAS for main effects and epistatic interactions for grain morphology traits in wheat

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Title GWAS for main effects and epistatic interactions for grain morphology traits in wheat
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Creator Parveen Malik
Jitendra Kumar
Shiveta Sharma
Prabina Kumar Meher
Harindra Singh Balyan
Pushpendra Kumar Gupta
Shailendra Sharma
 
Subject Epistasis interaction
GWAS
Grain morphology
Triticum aestivum L
 
Description Not Available
In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length-width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017-2018, 2018-2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research.
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Date 2022-08-07T05:30:22Z
2022-08-07T05:30:22Z
2022-03-26
 
Type Research Paper
 
Identifier Malik, P., Kumar, J., Sharma, S. et al. (2022). GWAS for main effects and epistatic interactions for grain morphology traits in wheat. Physiol Mol Biol Plants 28, 651–668. https://doi.org/10.1007/s12298-022-01164-w
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http://krishi.icar.gov.in/jspui/handle/123456789/73729
 
Language English
 
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Publisher Not Available