Show simple item record

dc.contributor.authorHuang, Xiu
dc.contributor.authorYan, Hai-Dong
dc.contributor.authorZhang, Xin-Quan
dc.contributor.authorZhang, Jian
dc.contributor.authorFrazier, Taylor P.
dc.contributor.authorHuang, De-Jun
dc.contributor.authorLu, Lu
dc.contributor.authorHuang, Lin-Kai
dc.contributor.authorLiu, Wei
dc.contributor.authorPeng, Yan
dc.contributor.authorMa, Xiao
dc.contributor.authorYan, Yan-Hong
dc.date.accessioned2019-04-29T13:01:15Z
dc.date.available2019-04-29T13:01:15Z
dc.date.issued2016-04-18
dc.identifier.other496
dc.identifier.urihttp://hdl.handle.net/10919/89250
dc.description.abstractHemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yawn" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.en
dc.description.sponsorshipNational Basic Research Program of China (973 Program) [2014CB138705]
dc.description.sponsorshipStrategic Planning and Management Innovation of Science and Technology Support Demonstration Project of Chongqing Modern Cattle and Sheep Industry [cstc2014zktjccxbx0021]
dc.description.sponsorshipModern Agro-industry Technology Research System [CARS-35-05]
dc.description.sponsorshipSichuan Agricultural University Excellent Master's Degree Papers Breeding [YS2014003]
dc.format.mimetypeapplication/pdf
dc.language.isoen
dc.publisherFrontiers
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectde novo assemblyen
dc.subjectmarker developmenten
dc.subjectHemarthria R. Br.en
dc.subjectRNA-Seqen
dc.subjecttranscriptomeen
dc.titleDe novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Speciesen
dc.typeArticle - Refereed
dc.contributor.departmentSchool of Plant and Environmental Sciencesen_US
dc.description.notesThis work was supported by National Basic Research Program of China (973 Program) (2014CB138705), Strategic Planning and Management Innovation of Science and Technology Support Demonstration Project of Chongqing Modern Cattle and Sheep Industry (cstc2014zktjccxbx0021), Modern Agro-industry Technology Research System (CARS-35-05), and the Sichuan Agricultural University Excellent Master's Degree Papers Breeding (YS2014003).
dc.title.serialFrontiers In Plant Science
dc.identifier.doihttps://doi.org/10.3389/fpls.2016.00496
dc.identifier.volume7
dc.type.dcmitypeText
dc.identifier.pmid27148320
dc.identifier.eissn1664-462X


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International