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

BMC Genomics

Research

Konstantin Chekhovskiy¹  Malay C. Saha¹  Md. Shofiqul Islam² 

[1] Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, 73401, Ardmore, OK, USA;Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, 73401, Ardmore, OK, USA;Genetics Laboratory, Indiana Crop Improvement Association, 7700 Stockwell Road, 47909, Lafayette, IN, USA;Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, 47906, West Lafayette, IN, USA;

关键词: Chloroplast genome;    Festuca;    Genomic divergence;    InDels;    Morphotype;    SNPs;    Tall fescue;   

DOI  :  10.1186/s12864-023-09631-8

 received in 2023-05-10, accepted in 2023-08-28,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundTall 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 it being 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.ResultsThe plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules 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 plastid genomes from the Mediterranean plastid 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. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya.ConclusionsTo our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023. corrected publication 2023

【 图 表 】

Fig. 2

12936_2023_4742_Article_IEq20.gif

Fig. 8

Fig. 4

12888_2023_5283_Article_IEq1.gif

Fig. 2

Fig. 5