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Integrated IBD Analysis, GWAS Analysis and Transcriptome Analysis to Identify the Candidate Genes for White Spot
Dong Wang1,2, Yue He1,2, Lei Nie1,2
1College of Agriculture, Guizhou University, Guiyang 550006, China.
International Journal of Molecular Sciences
|June 28, 2023
Summary
Foundation parents are crucial for maize breeding. This study identifies genetic markers linked to maize white spot resistance, aiding in developing more resilient crops for Southwest China.
Area of Science:
- Plant Genetics
- Crop Breeding
- Agricultural Science
Background:
- Foundation parents (FPs) are vital in maize breeding.
- Maize white spot (MWS) significantly reduces crop yield in Southwest China.
- Genetic mechanisms underlying MWS resistance are not well understood.
Purpose of the Study:
- To identify genetic factors associated with MWS resistance in elite maize lines.
- To integrate genome-wide association studies (GWAS) and transcriptome analysis for functional insights.
- To explore the role of identity-by-descent (IBD) segments in MWS resistance.
Main Methods:
- Genotyping of 143 elite maize lines using the MaizeSNP50 chip (~60,000 SNPs).
- Phenotypic evaluation of MWS resistance across three environments.
- Integrated GWAS and transcriptome analysis to identify candidate genes and regions.
Main Results:
- Identified 225, 192, and 197 unique IBD segments in FPs QB512, QR273, and HCL645, respectively.
- Detected 15 quantitative trait nucleotides (QTNs) associated with MWS, with SYN10137-PZA00131.14 found in QB512's IBD segments and prevalent in QR273's descendants.
- Located candidate gene Zm00001d031875 within the significant SYN10137-PZA00131.14 region through integrated analysis.
Conclusions:
- The study provides novel insights into the genetic basis of MWS resistance in maize.
- Identified specific IBD segments and QTNs that can be utilized for marker-assisted selection in breeding programs.
- The candidate gene Zm00001d031875 warrants further investigation for its role in MWS resistance.
