Browsing by Author "Qiu, Yinjie"

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    Hard fescue (Festuca brevipila) reference transcriptome generated by PabBio Isoform sequencing
    (2020-01-31) Qiu, Yinjie; Yang, Ya; Hirsch, Cory D.; Watkins, Eric; qiuxx221@umn.edu; Qiu, Yinjie; University of Minnesota Turfgrass Research Lab
    Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool-season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome of this taxon. Here, we report a reference transcriptome generated from root, crown, leaf, and seed head tissues. We obtained 59,510 full-length transcripts of which 38,595 were non-redundant full-length transcripts, with a N50 of 2,585 bp. The longest and shortest transcripts were 11,487 and 58 bp, respectively. By using the long-read transcriptome assembly to improve the reference de novo short reads assembly we investigated the phylogenetic relationship between selected taxa that were closely related to F. brevipila. Overall, the F. brevipila Pacbio reference transcriptome improved the completeness of the short reads assembly and provided the foundation for genomics studies of this important turfgrass species.
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    Leveraging High Throughput Sequencing For Fine Fescue (Festuca Spp.) Breeding And Genetics
    (2020-03) Qiu, Yinjie
    Fine fescues (Festuca L., Poaceae) are turfgrass species that perform well in low-input environments. Improvement of these grass species through breeding and genetics have been limited due to the difficulty of species identification and lack of genomic resources. The objectives of this dissertation were to develop an improved method for fine fescue species identification, generate the first reference transcriptome for hard fescue, and use the reference transcriptome for transcriptome studies. In my first project, I used flow cytometry, chloroplast genome sequencing, and molecular marker development to provide new fine fescue identification methodology. Next, I used flow cytometry to characterize ploidy level in the USDA F. ovina collection. My third project used PacBio Isoform sequencing to develop the reference transcriptome using four tissue types for hard fescue; by using a phylotranscriptomic approach, the reference transcriptome provided information of the allopolyploid origin of the hexaploid species. Finally, the reference transcriptome was used to study how hard fescue responded to propiconazole fungicide application; in addition, untargeted metabolomics was used to study changes in metabolites caused by fungicide application. This dissertation developed methods for fine fescue by a combination use of flow cytometry and molecular markers. Methods and genomics resources developed in this dissertation will benefit fine fescue breeding and genetics programs.
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    Sustainable Turf Management for City of Watertown Athletic Fields
    (Resilient Communities Project (RCP), University of Minnesota, 2016) Brettingen, Joey; Schwab, Ryan; Lunseth, Shay; Qiu, Yinjie
    This project was completed as part of the 2015-2016 Resilient Communities Project (rcp.umn.edu) partnership with Carver County. The City of Watertown was experiencing increased demand for athletic fields in the community. With no plans to build additional fields, public works staff wanted to identify strategies to better maintain existing playing fields so they could handle increased use. The goal of this project was to develop a set of best management practices for soccer fields in Watertown that would mitigate environmental impacts, reduce maintenance costs, and meet growing demand for fields. Project lead Shane Fineran from the City of Watertown worked with teams of students in HORT 4062: Turfgrass Weed and Disease Science and HORT 4063: Turfgrass Science to develop recommendations, which included increasing aeration to improve drainage and reduce the need for irrigation, eliminating weeds to reduce turf competition, and introducing new nitrogen fertilizer techniques. The students' final report and presentation are available.