Candidate genes for stem rust resistance in Italian ryegrass revealed by nested association mapping

Area of Science:

• Plant Pathology
• Agronomy
• Genetics

Background:

• Stem rust, caused by Puccinia graminis ssp. graminicola, significantly reduces seed yield in Italian ryegrass (Lolium multiflorum Lam.).
• Genetic control of stem rust resistance in Italian ryegrass is poorly understood, with limited knowledge from biparental mapping populations.

Purpose of the Study:

• To discover novel sources of stem rust resistance in Italian ryegrass.
• To identify candidate genes associated with stem rust resistance using advanced genomic tools.
• To provide selection criteria for breeding programs aimed at enhancing disease resistance.

Main Methods:

• Utilized a large F2 nested association mapping (NAM) population (708 individuals from 24 founders) with high variation in stem rust resistance.
• Conducted field phenotyping under natural inoculation across multiple location-year combinations.
• Integrated reduced-representation sequencing and whole-genome sequencing to identify 3,199,253 SNP markers for association mapping.

Main Results:

• Identified four novel candidate genes associated with stem rust resistance.
• Discovered two candidate genes encoding receptor-like serine/threonine kinases on chromosomes 6 and 7.
• Found two superior haplotypes within the Chr7.32208 gene, suitable for direct implementation in breeding.

Conclusions:

• Field phenotyping and high-density genotyping in a NAM population successfully identified novel stem rust resistance sources in Italian ryegrass.
• The identified candidate genes, particularly serine/threonine kinases, offer promising targets for functional validation and breeding.
• The superior haplotypes provide valuable tools for marker-assisted selection to improve stem rust resistance in Italian ryegrass breeding programs.