GWAS reveals potential candidate gene(s) associated with markers linked to tiller production, regrowth rate, and seed shattering in Italian ryegrass ( <i>Lolium perenne</i> ssp. <i>multiflorum</i> )

Abstract Italian ryegrass [ Lolium perenne (L.) ssp. multiflorum (Lam.) Husnot], a cool-season forage crop in temperate countries, is also a major weed problem in winter crops, especially wheat ( Triticum aestivum L.). Understanding the molecular mechanisms underlying its adaptive traits is crucial for managing L. perenne ssp . multiflorum as both a crop and a weed species. Genome-wide association studies (GWAS) were performed using single nucleotide polymorphism (SNP) data from double-digest restriction site associated DNA (ddRAD) sequencing to assess the genetic diversity and identify the genetic region(s) associated with key adaptive traits, namely tillering ability, regrowth rate, and seed shattering in this species. A collection of 56 wild/weedy populations, 25 half-sib breeding lines, four commercial cultivars, and one reference sample each of L. perenne ssp . multiflorum , perennial ryegrass ( Lolium perenne (L.), rigid ryegrass ( Lolium rigidum Gaudin), and poison ryegrass ( Lolium temulentum L.) obtained from the USDA-GRIN were used for the study. About 3,079 SNPs were used for principal component and marker-trait association analyses. In the principal component analysis, the half-sibs, cultivars, and wild populations clustered separately; however, a few wild populations were mixed with the half-sibs. Sequence annotation of the flanking sequences of significant SNPs identified in GWAS with the NCBI database revealed potential candidate genes underlying the traits, including Ethylene receptor2 promoting regrowth in common barley ( Hordeum vulgare L.) and other species; an auxin-responsive protein SAUR36-like controlling tiller production in Tausch’s goatgrass ( Aegilops tauschii Coss.) and river wheat ( Triticum turgidum L.; syn. Triticum dicoccoides Koern. Ex. Schwinf.); and 4-coumarate-coenzyme A ligase for reduced seed shattering in L. perenne and L. rigidum . This information on marker-trait associations for these traits in L. perenne ssp . multiflorum will aid in manipulating the traits in crop breeding and weed management programs.