Detecting major introgressions in wheat and their putative origins using coverage analysis

Area of Science:

• Plant genetics
• Crop improvement
• Genomic analysis

Background:

• Introgressions from crop wild relatives (CWRs) enhance cultivated plants with beneficial traits.
• Traditional detection methods like cytological analysis are limited for unknown genetic material.
• Single nucleotide polymorphism (SNP)-based methods exist but require known parental lines.

Purpose of the Study:

• To develop a novel method for detecting introgressions in unknown plant samples.
• To identify the putative donor species responsible for these introgressions.
• To analyze the historical and current impact of introgressions in wheat breeding.

Main Methods:

• Development of a new bioinformatics method for introgression detection.
• Application of the method to 10 publicly available wheat genome sequences.
• Analysis of introgression patterns and their origins.

Main Results:

• Identification of nine major introgressions in the analyzed wheat genomes.
• Demonstration of the method's ability to differentiate multiple introgressions at the same locus.
• Tracing introgressions to early wheat cultivars, highlighting their historical use in breeding.
• Evidence of introgressions containing valuable resistance genes.

Conclusions:

• The developed method effectively detects introgressions and predicts donor species in unknown genetic material.
• Natural introgressions have played a significant role in wheat's breeding history and continue to impact elite lines.
• These introgressions represent a valuable genetic resource, particularly for disease resistance.