Genetic diversity and structure of diploid Italian ryegrass (Lolium multiflorum Lam.) cultivars and breeding materials in Japan based on genome-wide allele frequency

Abstract

To reveal the genetic diversity and structure of cultivars and breeding materials of diploid Italian ryegrass (Lolium multiflorum Lam.) in Japan, using genome-wide allele frequency data obtained by genotyping by random amplicon sequencing, direct of pooled DNA, we investigated genetic diversity among and within 89 accessions. We selected 2629 reliable alleles at 456 polymorphic loci to evaluate allele frequency in each accession. Results of hierarchical cluster analysis based on Nei's standard genetic distance and of principal component analysis and nonhierarchical cluster analysis based on the complete set of allele frequencies classified the accessions into a large group including major Japanese cultivars and their ancestral landraces with a wide range of maturity, and a small group with mainly medium maturity, including ‘Gulf’, introduced from overseas. The genetic relationships fully reflected the kinship inferred from the breeding history in Japan. Mean expected heterozygosity (H_E) and number of alleles per locus (A) were evaluated as indices of genetic diversity within each accession. We found a significant negative correlation between the year of application for varietal registration and H_E or A in 14 early-maturing Japanese cultivars. The genetic diversity profile can be used for breeding to maintain or increase the diversity within cultivars or breeding materials.