Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate...

Area of Science:

• Plant breeding
• Genetics
• Bioinformatics

Background:

• Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing species vital for forage and crop improvement.
• Polycrossing is a common breeding strategy but lacks precise pollen-parent tracking.
• Self-incompatibility (SI) genes are hypothesized to influence mating patterns and limit cross diversity.

Purpose of the Study:

• To investigate the utility of next-generation sequencing for paternity assignment in intermediate wheatgrass.
• To identify potential self-incompatibility (SI) loci influencing mating success in a breeding program.
• To assess the impact of paternity data on optimizing polycross breeding strategies.

Main Methods:

• Developed a reference population from controlled crosses for paternity assignment validation.
• Applied Cervus software for paternity assignment in a large polycross population.
• Conducted a genome-wide association study (GWAS) to identify genetic loci associated with progeny number.

Main Results:

• Achieved 92% paternity assignment accuracy in the reference population.
• Successfully assigned paternity for 80% of progeny in a large polycross, identifying 82 out of 89 pollen parents.
• Identified marker loci near putative SI genes associated with non-random mating and varying progeny success.

Conclusions:

• Next-generation sequencing-based paternity assignment is effective for intermediate wheatgrass breeding.
• Genetic factors, including SI genes, significantly influence the diversity of crosses achieved in polycrosses.
• Incorporating paternity data can enhance breeding program efficiency, genetic diversity, and understanding of mating patterns.