AFLP assessment of genetic variability and relationships in an Asian wild germplasm collection of Dactylis glomerata L.

Abstract

Orchardgrass (Dactylis glomerata L.), an excellent perennial and cool season forage species distributed in most temperate regions, has been cultivated widely in Western China. Amplified fragment length polymorphism markers were employed to determine the genetic variability and population structure among 41 indigenous orchardgrass accessions from Central Asia and Western China. On the basis of 531 polymorphic fragments resulted from eight primer combinations, polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.252, 16.34 and 25.27 per primer combination, respectively, demonstrating the high efficiency and reliability of the markers used. We found relatively low differentiation (Fst=0.135) for three geographical groups, where Central Asia (CA) and Southwest China (SWC) group exhibited higher intra-population diversity (He=0.20 and 0.21) than that of the Xinjiang (XJ) group (He=0.14). We also did not detect a clear pattern of isolation by distance with a low value of r=0.301 in the Mantel test. STRUCTURE, FLOCK, UPGMA clustering and PCoA analyses showed that CA group is more related to the SWC Group rather than to the XJ Group. In addition, this study strongly suggests that geographical and ecological environmental factors together could better explain the genetic differentiation between different geographical regions than geographic isolation alone, especially for Xinjiang accessions. The present study also could support that Southwest China might be the internal diversity center of D. glomerata in China. The knowledge about the genetic variability of the Asian accessions examined contributes to rapid characterization, defining gene pools of wild accessions, and selecting appropriate germplasms for plant improvement.

AFLP-based genetic diversity of wild orchardgrass germplasm collections from Central Asia and Western China, and the relation to environmental factors

“…AFLP reactions were performed following Sun et al [ 2 ] with a few minor modifications. Six informative and reliable pairs of Mse I ( ) and Eco RI ( ) primers used in amplification were selected from a set of 100 primer pairs.…”

“…Dactylis glomerata L., a perennial cool-season forage grass, belongs to the monotypic genera Dactylis , known as orchardgrass or cocksfoot [ 1 ]. The basic chromosome number of Dactylis is 2n = 14 and, although the species consists of diploid, tetraploid and hexaploid, the commonly used forage form is tetraploid [ 2 , 3 ]. With agronomically and economically importance, Dactylis is the fourth widely used grass genus following Lolium , Festuca and Phleum in global temperate areas, used as silage, hay or grazing [ 4 – 8 ].…”

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

“…Then, the DNA concentration was quantified using the NanoDrop TM 2000 Spectrophotometers (Thermo Fisher, Waltham, MA, USA). The DNA samples diluted to 100 ng•mL −1 were stored at −20 C. According to Sun et al (2017) with minor modifications, AFLP fingerprinting was performed using six primers (Table S2), and the fragments measuring 60-500 bp with a peak height above or equal to 100 reflective fluorescent units (RFUs) were scored using Genemarker 2.2 (SoftGenetics) as "1" (presence of fragment) or "0" (absence of fragment).…”

“…According to the band frequency less than 95%, number of polymorphic bands (NPB) and the percentage of polymorphic bands (PPB) were calculated. In addition, polymorphic information content (PIC) and Shannon's diversity index (I) were calculated as indicators for estimating the discriminatory power of each primer combination (Sun et al, 2017). The PIC of each primer pair was defined as follows, supposing that p and q represent the frequencies of the marker bands that were present and absent, respectively: -Ruiz et al, 2000).…”

“…Nei's genetic distance (GD) matrix among eleven populations, with 10,000 bootstrap values, was obtained via AFLP-SURV v1.0 (Sun et al, 2017), and the UPGMA dendrogram was constructed via the CONSENSE module in PHYLIP v3.695 (Christensen et al, 2011). The principal coordinate analysis (PCoA) of 81 genotypes was performed by NTSYS v2.2 and R package Scatterplot3d (Ligges & Mächler, 2002) for the depicture of their hierarchical structure to evaluate the genetic homogeneity of the natural populations.…”