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Applications in Plant Sciences

Jun-Wei Ye, Qin Li, Xiang-Yu Tian, Lei Bao, Hong-Fang Wang, Jian-Ping Ge
Premise of the study: To investigate a more detailed evolutionary history of Lindera obtusiloba (Lauraceae) and other Lindera species, polymorphic low-copy nuclear primers were developed. Methods and Results: Unigenes of the L. obtusiloba transcriptome greater than 800 bp in length were randomly chosen for initial design of 168 primers. Agarose gel electrophoresis and Sanger sequencing were used to select low-copy nuclear genes. Twenty-seven primers were obtained and were used to investigate genetic diversity in 90 individuals from 24 populations...
December 2017: Applications in Plant Sciences
Shuai Yuan, Gui Zeng, Miaomiao Shi, Dianxiang Zhang
Premise of the study: Microsatellite primers were developed for Primula ovalifolia , a member of Primula section Petiolares (Primulaceae), to study the population genetics and species delimitation in this section. Methods and Results: A total of 4753 markers were successfully designated from 5139 putative simple sequence repeat loci. We isolated 38 expressed sequence tag-simple sequence repeat markers from 220 selected marker sites and tested polymorphism in three populations of P...
December 2017: Applications in Plant Sciences
Catherine L Simmons, Robert W Lamont, Alison Shapcott
Premise of the study: The swamp orchid, Phaius australis (Orchidaceae), is nationally endangered due to illegal collection and habitat loss and fragmentation, resulting in a disjunct distribution in spring and coastal wetland ecotones along Australia's east coast. Polymorphic microsatellite markers were developed to study genetic diversity and population structure for conservation and restoration purposes. Methods and Results: Illumina HiSeq high-throughput sequencing was used to develop 15 nuclear microsatellite markers, including 10 polymorphic markers for P...
December 2017: Applications in Plant Sciences
Jing Li, Yibo Luo, Lingling Xu
Premise of the study: To investigate genetic diversity and structure, microsatellite markers were developed and characterized for Cypripedium tibeticum , an endangered orchid species, and their utility tested in two relatives: C. flavum and C. bardolphianum . Methods and Results: Candidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of C. tibeticum ...
December 2017: Applications in Plant Sciences
Maria L Kuzmina, Thomas W A Braukmann, Aron J Fazekas, Sean W Graham, Stephanie L Dewaard, Anuar Rodrigues, Bruce A Bennett, Timothy A Dickinson, Jeffery M Saarela, Paul M Catling, Steven G Newmaster, Diana M Percy, Erin Fenneman, Aurélien Lauron-Moreau, Bruce Ford, Lynn Gillespie, Ragupathy Subramanyam, Jeannette Whitton, Linda Jennings, Deborah Metsger, Connor P Warne, Allison Brown, Elizabeth Sears, Jeremy R Dewaard, Evgeny V Zakharov, Paul D N Hebert
Premise of the study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region...
December 2017: Applications in Plant Sciences
Xi-Qiong Liu, Cheng-Yu Yu, Jun-Gang Dong, Ai-Xia Xu, Sheng-Wu Hu
Premise of the study: SP2S is a spontaneous thermo-sensitive genic male sterility (TGMS) mutation that facilitates two-line hybrid breeding in Brassica napus (Brassicaceae). De novo assembly of the floral bud transcriptome of SP2S can provide a foundation for deciphering the transcriptional regulation of SP2S in response to temperature change. Methods: mRNAs of the young floral buds of SP2S and its near-isogenic line SP2F grown under cool (16°C)/warm (22°C) conditions were sequenced on an Illumina Solexa platform, producing 239...
December 2017: Applications in Plant Sciences
Janet M Anthony, Richard J N Allcock, Mark P Dobrowolski, Siegfried L Krauss
Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S...
November 2017: Applications in Plant Sciences
Eva Kondrysová, Karol Krak, Bohumil Mandák
Premise of the study: Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. Methods and Results: Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0...
November 2017: Applications in Plant Sciences
Zhi-Zhong Li, Meng-Xue Lu, Josphat K Saina, Andrew W Gichira, Qing-Feng Wang, Jin-Ming Chen
Premise of the study: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis . One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively...
November 2017: Applications in Plant Sciences
Zuo-Zhou Li, Hua Tian, Jin-Ju Zhang
Premise of the study: Polymorphic microsatellite markers were developed to reveal the genetic diversity of extant populations and the mating system of Sinowilsonia henryi (Hamamelidaceae). Methods and Results: In this study, nuclear simple sequence repeat (SSR) markers were developed using the Illumina high-throughput sequencing technique (RNA-Seq). The de novo-assembled transcriptome generated a total of 64,694 unique sequences with an average length of 601 bp...
November 2017: Applications in Plant Sciences
Jenna L Wingfield, Lauren G Ruane, Joshua D Patterson
Premise of the study: The three-dimensional structure of tree canopies creates environmental heterogeneity, which can differentially influence the chemistry, morphology, physiology, and/or phenology of leaves. Previous studies that subdivide canopy leaves into broad categories (i.e., "upper/lower") fail to capture the differences in microenvironments experienced by leaves throughout the three-dimensional space of a canopy. Methods: We use a three-dimensional spatial mapping approach based on spherical polar coordinates to examine the fine-scale spatial distributions of photosynthetically active radiation (PAR) and the concentration of ultraviolet (UV)-absorbing compounds ( A 300 ) among leaves within the canopies of black mangroves ( Avicennia germinans )...
November 2017: Applications in Plant Sciences
Brendan F Kohrn, Jessica M Persinger, Mitchell B Cruzan
Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure...
November 2017: Applications in Plant Sciences
Theresa M Culley
We are now in an era where sharing and making data widely accessible are not only expected within many disciplines, but also required by federal granting agencies and many scientific journals. In addition, there are practical reasons why authors should deposit their data into permanent data repositories: (1) it prevents data loss due to accidents, theft, or death of the researcher; (2) it enables published research to be reproduced by others; (3) publications associated with accessible data sets can have higher citation rates; (4) deposited data sets are increasingly recognized for scholarly recognition and professional advancement; and (5) stored and accessible data can be used in the future for projects that are unanticipated today...
October 2017: Applications in Plant Sciences
Lijing Sun, Kaikai Meng, Boyong Liao, Chunmei Li, Yue Zhang, Wenbo Liao, Sufang Chen
Premise of the study: The genus Anneslea (Pentaphylacaceae) contains four species and six varieties, most of which are locally endemic. Here, simple sequence repeat (SSR) markers were developed for the conservation of these species. Methods and Results: The genome of A. fragrans was sequenced and de novo assembled into 445,162 contigs, of which 30,409 SSR loci were detected. Primers for 100 SSR loci were validated with PCR amplification in three populations of A...
October 2017: Applications in Plant Sciences
Ping Wang, Karin Tremetsberger, Estrella Urtubey, Karl-Georg Bernhardt
Premise of the study: We developed microsatellite markers to study clonal growth and interspecific hybridization in the Patagonian and subantarctic plant Hypochaeris incana (Asteraceae) and its closest relatives. Methods and Results: We developed primers for microsatellite loci from 454 sequence reads of genomic DNA of H. incana . We tested them on individuals of H. acaulis , H. hookeri , H. incana , H. palustris , and H. tenuifolia . We selected 15 polymorphic microsatellite loci, which delivered clearly scorable fragments in most or all species...
October 2017: Applications in Plant Sciences
Haijun Liu, Zhihua Yan, Hualing Xu, Chunmei Li, Qiang Fan, Wenbo Liao, Boyong Liao
Premise of the study: Brainea insignis (Aspleniaceae) is an endangered tree fern in China whose wild populations have been seriously damaged due to overexploitation. Expressed sequence tag-simple sequence repeat (EST-SSR) primers were developed to investigate its genetic diversity and provide resources for future conservation studies. Methods and Results: We obtained 72,897 unigenes of B. insignis using transcriptome sequencing and detected 15,006 SSRs in 12,058 unigenes...
October 2017: Applications in Plant Sciences
Maila Beyer, Alison G Nazareno, Lúcia G Lohmann
Premise of the study: We developed chloroplast microsatellite markers (cpSSRs) to be used to study the patterns of genetic structure and genetic diversity of populations of Stizophyllum riparium (Bignonieae, Bignoniaceae). Methods and Results: We used genomic data obtained through an Illumina HiSeq sequencing platform to develop a set of cpSSRs for S. riparium . A total of 36 primer pairs were developed, of which 28 displayed polymorphisms across 59 individuals from three populations...
October 2017: Applications in Plant Sciences
Brent A Berger, Jiahong Han, Emily B Sessa, Andrew G Gardner, Kelly A Shepherd, Vincent A Ricigliano, Rachel S Jabaily, Dianella G Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA ( CYC )-like genes...
October 2017: Applications in Plant Sciences
Yueqin Cheng, Pingping Li, Yi Yang, Jianhang Zhang, Fengming Yan, Hongwei Wang
Premise of the study: Phytolacca acinosa (Phytolaccaceae) is a traditional Chinese herb with multiple medicinal uses and is an important pigment source. Due to excessive human harvesting, the population numbers and sizes have decreased dramatically. Methods and Results: Using an enriched genomic library, we developed and characterized 15 microsatellite primers for P. acinosa , 13 of which were polymorphic. The number of alleles varied from two to seven. The observed heterozygosity and expected heterozygosity per locus ranged from 0...
October 2017: Applications in Plant Sciences
Si-Si Wang, Yang Zhang, De-Chen Liu, Xiao-Wei Sun, Rong Wang, Yuan-Yuan Li
PREMISE OF THE STUDY: To quantify the population-level genetic characteristics of Cunninghamia lanceolata (Taxodiaceae), an important timber conifer, we developed 30 pairs of microsatellite primers based on the nuclear genome. METHODS AND RESULTS: Using the streptavidin-biotin capture system, we developed 14 polymorphic and 16 monomorphic microsatellites. Polymorphisms were detected in 14 loci using 94 individual trees that were collected from three C. lanceolata populations in Hubei and Zhejiang provinces and in Chongqing Municipality, China...
September 2017: Applications in Plant Sciences
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