Chromosome-Scale Genome Assembly and Annotation of Allotetraploid Annual Bluegrass (Poa annua L.).

Poa annua L. is a globally distributed grass with economic and horticultural significance as a weed and as a turfgrass. This dual significance, and its phenotypic plasticity and ecological adaptation, have made P. annua an intriguing plant for genetic and evolutionary studies. Because of the lack of genomic resources and its allotetraploid (2n = 4x = 28) nature, a reference genome sequence would be a valuable asset to better understand the significance and polyploid origin of P. annua. Here we report a genome assembly with scaffolds representing the 14 haploid chromosomes that are 1.78 Gb in length with an N50 of 112 Mb and 96.7% of BUSCO orthologs. Seventy percent of the genome was identified as repetitive elements, 91.0% of which were Copia- or Gypsy-like long-terminal repeats. The genome was annotated with 76,420 genes spanning 13.3% of the 14 chromosomes. The two subgenomes originating from Poa infirma (Knuth) and Poa supina (Schrad) were sufficiently divergent to be distinguishable but syntenic in sequence and annotation with repetitive elements contributing to the expansion of the P. infirma subgenome.

Screening Tall Fescue for Resistance to Rhizoctonia solani and Rhizoctonia zeae Using Digital Image Analysis.

Brown patch, caused by Rhizoctonia solani, is a destructive disease on tall fescue. Compared with R. solani, Rhizoctonia zeae causes indistinguishable symptoms in the field but varies in geographic distribution. This may contribute to geographic variability observed in the resistance response of improved brown patch-resistant cultivars. This study examined R. solani and R. zeae susceptibility of four cultivars, selected based on brown patch performance in the National Turfgrass Evaluation Program (NTEP), and nine plant introductions (PIs). Twenty genotypes per PI/cultivar were evaluated by using four clonal replicates in a randomized complete block design. Plants were inoculated under controlled conditions with two repetitions per pathogen. Disease severity was assessed digitally in APS Assess, and analysis of variance and correlations were performed in SAS 9.3. Mean disease severity was higher for R. solani (65%) than for R. zeae (49%) (P = 0.0137). Interaction effects with pathogen were not significant for PI (P = 0.0562) but were for genotype (P < 0.001). Moderately to highly resistant NTEP cultivars compared with remaining PIs exhibited lower susceptibility to R. zeae (P < 0.0001) but did not differ in susceptibility to R. solani (P = 0.7458). Correlations between R. solani and R. zeae disease severity were not significant for either PI (R = 0.06, P = 0.8436) or genotype (R = 0.11, P = 0.09). Breeding for resistance to both pathogens could contribute to a more geographically stable resistance response. Genotypes were identified with improved resistance to R. solani (40), R. zeae (122), and both pathogens (26).

Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress.

BACKGROUND: Kentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green colour under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues. RESULTS: Sample replicates grouped tightly by tissue and treatment, and fewer differentially expressed transcripts were detected in the tolerant PI 372742 samples compared to the susceptible PI 368233 samples, and in root tissues compared to shoot tissues. A de novo assembly resulted in 388,764 transcripts, with 36,587 detected as differentially expressed. Approximately 75 % of transcripts had homology based annotations, with several differences in GO terms enriched between the PI 368233 and PI 372742 samples. Gene expression profiling identified salt-responsive gene families that were consistently down-regulated in PI 372742 and unlikely to contribute to salt tolerance in Kentucky bluegrass. Gene expression profiling also identified sets of transcripts relating to transcription factors, ion and water transport genes, and oxidation-reduction process genes with likely roles in salt tolerance. CONCLUSIONS: The transcript assembly represents the first such assembly in the highly polyploidy, facultative apomictic Kentucky bluegrass. The transcripts identified provide genetic information on how this plant responds to and tolerates salt stress in both shoot and root tissues, and can be used for further genetic testing and introgression.

Association of simple sequence repeat (SSR) markers with submergence tolerance in diverse populations of perennial ryegrass.

Submergence stress can cause the death of grass plants. Identification of the association between molecular markers and submergence tolerance-related traits facilitates an efficient selection of the tolerant cultivars for commercial production. A global collection of 99 diverse perennial ryegrass (Lolium perenne L.) accessions was evaluated for submergence tolerance and analyzed with 109 simple sequence repeat (SSR) markers. Submergence significantly reduced leaf color, chlorophyll fluorescence (F(v)/F(m)), maximum plant height (HT), and relative growth rate (RGR). Significant variations in these trait values were observed among the accessions under submerged conditions. Rapid linkage-disequilibrium (LD) decay was identified within 4cM. The analysis of population structure (Q) identified four subpopulations in the collection, but no obvious relative kinship (K) was found. The Q model was the best to describe associations between SSR and traits, compared to the simple linear, K, and Q + K models. Fifteen SSR markers were associated with a reduction in leaf color, F(v)/F(m), HT, and RGR under submergence stress using the Q model. These markers can be used for genetic improvement of submergence tolerance of perennial ryegrass after further validation. The diverse populations of perennial ryegrass is a valuable resource for association mapping of stress tolerance-related physiological traits.

Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses.

Advances in plant genomics have permitted the analysis of several members of the grass family, including the major domesticated species, and provided new insights into the evolution of the major crops on earth. Two members, colonial bentgrass (Agrostis capillaris L.) and creeping bentgrass (A. stolonifera L.) have only recently been domesticated and provide an interesting case of polyploidy and comparison to crops that have undergone human selection for thousands of years. As an initial step of characterizing these genomes, we have sampled roughly 10% of their gene content, thereby also serving as a starting point for the construction of their physical and genetic maps. Sampling mRNA from plants subjected to environmental stress showed a remarkable increase in transcription of transposable elements. Both colonial and creeping bentgrass are allotetraploids and are considered to have one genome in common, designated the A2 genome. Analysis of conserved genes present among the ESTs suggests the colonial and creeping bentgrass A2 genomes diverged from a common ancestor approximately 2.2 million years ago (MYA), thereby providing an enhanced evolutionary zoom in respect to the origin of maize, which formed 4.8 MYA, and tetraploid wheat, which formed only 0.5 MYA and is the progenitor of domesticated hexaploid wheat.