The first Nested Association Mapping (NAM) population for Italian ryegrass reveals genomic regions associated with seed shattering

Abstract Background Nested association mapping (NAM) populations are a powerful tool for investigating the genetic control of agronomically important traits and have been successfully used in self-pollinating crop species. Here, we present the first NAM population established in the outcrossing forage grass species Italian ryegrass ( Lolium multiflorum Lam.), to dissect the genetic control of seed shattering. High and stable seed yields are essential for the commercial success of new cultivars. Seed shattering strongly reduces seed yield in Italian ryegrass, but has so far not been targeted in Italian ryegrass breeding programs. Results The NAM population was based on one common and 23 diverse founder plants and consisted of 708 F 2 individuals. Reduced-representation sequencing (ddRAD) of the 708 F 2 individuals, combined with whole genome sequencing data of the 24 founder plants, yielded a total of 3,199,253 SNPs that were used for population structure analysis, parentship analysis and genome-wide association studies. Phenotypic data for seed shattering and seed yield-related traits, collected in three field trials, showed high phenotypic variance within the NAM population. A total of seven quantitative trait loci (QTL) were identified for seed shattering, seed yield, spike length, flag leaf length and flowering time. Within these QTL regions, one putative candidate gene for seed shattering and three putative candidate genes for flowering time were identified. For seed shattering, the significantly associated SNP within the gene chr7.26897 , known to be involved in ripening-related pathways, explained 10.03% of the phenotypic variance. Conclusions The identified loci provide valuable resources for breeding. The QTL regions containing putative candidate genes identified within these loci offer promising targets for functional validation and demonstrate the effectiveness of NAM populations for elucidating the genetic architecture of complex traits in outcrossing forage grasses.