Genome wide association study and transcriptome analysis identify candidate genes regulating wheat coleoptile length

Area of Science:

• Plant Genetics and Breeding
• Agronomy
• Molecular Biology

Background:

• Coleoptile length is a vital agronomic trait in wheat, influencing seedling establishment and yield, particularly in arid environments.
• Understanding the genetic basis of coleoptile development is crucial for improving wheat varieties.
• Current knowledge on genes regulating wheat coleoptile length requires further investigation.

Purpose of the Study:

• To identify quantitative trait loci (QTLs) and candidate genes associated with wheat coleoptile length using genome-wide association study (GWAS).
• To explore the genetic regulatory network and molecular mechanisms underlying coleoptile elongation.
• To develop molecular markers for marker-assisted breeding of wheat with enhanced coleoptile length.

Main Methods:

• Genome-wide association study (GWAS) using a 660K SNP array on 150 wheat varieties.
• Linkage disequilibrium (LD) and haplotype analyses to identify core QTLs.
• Gene expression analysis (RNA-Seq) and functional annotation.
• Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction prediction.
• Development of Kompetitive Allele Specific PCR (KASP) markers.

Main Results:

• 353 significantly associated SNPs and 23 stable QTLs for coleoptile length were detected across environments.
• Identification of two candidate genes (TraesCS2B02G423500, TraesCS2B02G449200) regulating wheat coleoptile length.
• Differential expression analysis revealed thousands of genes involved in coleoptile development at different stages.
• WGCNA and protein interaction analysis highlighted 19 interacting genes involved in hormone signaling and cell elongation.
• Two KASP markers were successfully developed for potential use in breeding programs.

Conclusions:

• The study successfully identified major QTLs and candidate genes controlling wheat coleoptile length.
• A network of interacting genes involved in hormone signaling and cell processes contributes to coleoptile elongation.
• The identified genetic resources, including QTLs, candidate genes, and KASP markers, provide a valuable foundation for enhancing wheat coleoptile length and improving crop yield.