Dig up tall fescue plastid genomes for the identification of morphotype- specific DNA markers or variants

Abstract Background: Tall fescue ( Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, rhizomatous cv. Torpedo, and Mediterranean cv. Resolute have been sequenced using Illumina MiSeq sequencing platform. Results: Chloroplast DNA was extracted from the tall fescue young leaves and used for genome sequencing. The plastid genomes of Continental-, rhizomatous-, and Mediterranean tall fescue were then assembled into a circular master molecule of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and rhizomatous, and 635 SNPs and 123 InDels between rhizomatous and Mediterranean tall fescue. Only four InDels in four genes ( ccsA , rps18 , accD , and ndhH-p ) were identified, which discriminated Continental and rhizomatous genomes from Mediterranean genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Conclusions: To our knowledge, this is the first report of the assembled plastid genomes of rhizomatous cv. Torpedo and Mediterranean cv. Resolute tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of both lawn and forage type commercial varieties.