Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers

Abstract

BackgroundGenetic diversity of 19 forage-type and 2 turf-type cultivars of tall fescue (Festuca arundinacea Schreb.) was revealed using SSR markers in an attempt to explore the genetic relationships among them, and examine potential use of SSR markers to identify cultivars by bulked samples.ResultsA total of 227 clear band was scored with 14 SSR primers and out of which 201 (88.6 %) were found polymorphic. The percentage of polymorphic bands (PPB) per primer pair varied from 62.5 to 100 % with an average of 86.9 %. The polymorphism information content (PIC) value ranged from 0.116 to 0.347 with an average of 0.257 and the highest PIC value (0.347) was noticed for primer NFA040 followed by NFA113 (0.346) whereas the highest discriminating power (D) of 1 was shown in NFA037 and LMgSSR02-01C. A Neighbor-joining dendrogram and the principal component analysis identified six major clusters and grouped the cultivars in agreement with their breeding histories. STRUCTURE analysis divided these cultivars into 3 sub-clades which correspond to distance based groupings.ConclusionThese findings indicates that SSR markers by bulking strategy are a useful tool to measure genetic diversity among tall fescue cultivars and could be used to supplement morphological data for plant variety protection.

Genetic variability and structure of an important wild steppe grass Psathyrostachys juncea (Triticeae: Poaceae) germplasm collection from north and central Asia

“…At the population's level, the descriptive statistics, including number of polymorphic loci (NPL), percentage of polymorphic loci (PPL), Nei's gene diversity (H j ), and Shannon diversity index (H o ), were calculated by AFLP-SURV v1.0 (Zhang et al, 2018). The observed number of alleles per locus (N a ) and the effective number of alleles per locus (N e ) were computed by POPGENE v1.31 (Fu et al, 2016), assuming populations under Hardy-Weinberg equilibrium (HWE).…”

Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses

“…Illumina reads were trimmed for adapters and for quality using FASTX-toolkit [-q 20 -p 90] (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Detailed characterization of repeat families was performed using stand-alone version of RepeatExplorer pipeline [36] running on IBM server with 16 processors, 100Gb of RAM and 17Tb of disk space. In the first step, comparative analysis of repetitive parts of the genomes was performed using the RepeatExplorer pipeline according to Novák et al [48].…”

“…In addition to understanding the molecular organization of chromosome domains, characterization of repetitive parts of nuclear genomes helps to develop cytogenetic markers [20,34,35]. Repetitive DNA sequences are also used extensively in studies of genetic diversity and to study processes of genome evolution and speciation [36][37][38][39].…”

Comparative analysis of DNA repeats and identification of a Fesreba centromeric element in fescues and ryegrasses

“…A putative LTR element, which localized preferentially to centromeric regions was identified in F. pratensis [29]. In addition to understanding the molecular organization of chromosome domains, the knowledge of repetitive parts of nuclear genomes helps to develop cytogenetic markers [15,[29][30][31]. Repetitive DNA sequences are widely used also in the studies of genetic diversity and to study processes of genome evolution and speciation [32][33][34].…”