Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Feb 10;9(2):e85050.
doi: 10.1371/journal.pone.0085050. eCollection 2014.

Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir

Andrea Giordano  1 , Noel O I Cogan  2 , Sukhjiwan Kaur  3 , Michelle Drayton  2 , Aidyn Mouradov  2 , Stephen Panter  2 , Gustavo E Schrauf  4 , John G Mason  5 , German C Spangenberg  1
Affiliations

Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir

Andrea Giordano et al. PLoS One. .

Abstract

Background: Paspalum dilatatum Poir. (common name dallisgrass) is a native grass species of South America, with special relevance to dairy and red meat production. P. dilatatum exhibits higher forage quality than other C4 forage grasses and is tolerant to frost and water stress. This species is predominantly cultivated in an apomictic monoculture, with an inherent high risk that biotic and abiotic stresses could potentially devastate productivity. Therefore, advanced breeding strategies that characterise and use available genetic diversity, or assess germplasm collections effectively are required to deliver advanced cultivars for production systems. However, there are limited genomic resources available for this forage grass species.

Results: Transcriptome sequencing using second-generation sequencing platforms has been employed using pooled RNA from different tissues (stems, roots, leaves and inflorescences) at the final reproductive stage of P. dilatatum cultivar Primo. A total of 324,695 sequence reads were obtained, corresponding to c. 102 Mbp. The sequences were assembled, generating 20,169 contigs of a combined length of 9,336,138 nucleotides. The contigs were BLAST analysed against the fully sequenced grass species of Oryza sativa subsp. japonica, Brachypodium distachyon, the closely related Sorghum bicolor and foxtail millet (Setaria italica) genomes as well as against the UniRef 90 protein database allowing a comprehensive gene ontology analysis to be performed. The contigs generated from the transcript sequencing were also analysed for the presence of simple sequence repeats (SSRs). A total of 2,339 SSR motifs were identified within 1,989 contigs and corresponding primer pairs were designed. Empirical validation of a cohort of 96 SSRs was performed, with 34% being polymorphic between sexual and apomictic biotypes.

Conclusions: The development of genetic and genomic resources for P. dilatatum will contribute to gene discovery and expression studies. Association of gene function with agronomic traits will significantly enable molecular breeding and advance germplasm enhancement.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Frequency histograms showing the distribution of contigs compared to sequence read length (A), the distribution of the number of reads per contig (B), and distribution of singletons compared to read length (bp) (C).
Figure 2
Figure 2. Sequence analysis of the generated P. dilatatum contigs compared to the reference grass genomes.
The P. dilatatum contigs were compared using BLASTn with an e value threshold of 10−10 and significant matches were identified and totaled and presented as a Venn diagram.
Figure 3
Figure 3. Assignment of putative function and gene ontology (GO) annotations to P. dilatatum sequence contigs based on Biological process classification (A), Molecular function (B) and Cellular components (C).
Figure 4
Figure 4. Distribution and frequency of different SSR repeat motifs identified from the P. dilatatum contig dataset.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Christin PA, Samaritani E, Petitpierre B, Salamin N, Besnard G (2009) Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics. Genome Biol Evol 1: 221–230. - PMC - PubMed
    1. Clayton WD (1983) Tropical grasses. In: McIvor JG, Bray RA, editors. Genetic Resources of Forage Plants. Melbourne: CSIRO. pp 39–46.
    1. Harlan JR (1983) The scope for collection and improvement if forage plants. In: McIvor JG, Bray RA, editors. Genetic Resources of Forage Plants. Melbourne: CSIRO.pp3–14.
    1. Holt EC (1956) Dallisgrass. Texas Agricultural Experiment Station EUA Bulletin 829: 14.
    1. Hutton EM, Nelson CJ (1968) Plant breeding and genetics. In: Commonwealth Agricultural Bureaux, editors. Some concepts and methods in sub-tropical pasture research. Brisbane: CSIRO. pp 79–92

Publication types

Grants and funding

This work was supported by funding from the Victorian Department of Primary Industries, the Dairy Futures Cooperative Research Centre and the Molecular Plant Breeding Cooperative Research Centre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.