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Applications in Plant Sciences

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https://www.readbyqxmd.com/read/28337395/isolation-and-characterization-of-microsatellite-loci-for-smilax-sieboldii-smilacaceae
#1
Yalu Ru, Ruijing Cheng, Jing Shang, Yunpeng Zhao, Pan Li, Chengxin Fu
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. METHODS AND RESULTS: Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337394/chloroplast-microsatellite-markers-for-pseudotaxus-chienii-developed-from-the-whole-chloroplast-genome-of-taxus-chinensis-var-mairei-taxaceae
#2
Qi Deng, Hanrui Zhang, Yipeng He, Ting Wang, Yingjuan Su
PREMISE OF THE STUDY: Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. METHODS AND RESULTS: Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337393/development-and-validation-of-est-ssr-markers-for-fokienia-hodginsii-cupressaceae
#3
Mingyan Ding, Kaikai Meng, Qiang Fan, Weizheng Tan, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Fokienia hodginsii (Cupressaceae) is a Tertiary relict evergreen conifer of the monotypic genus Fokienia. Polymorphic microsatellite markers were developed to investigate its genetic diversity and population structure. METHODS AND RESULTS: RNA transcripts of F. hodginsii were sequenced and de novo assembled into 85,818 unigenes, and 1892 simple sequence repeat (SSR) markers were detected from the unigenes. A total of 273 expressed sequence tag-SSR primer pairs were designed and tested, and 129 successfully amplified...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337392/microsatellite-markers-for-population-studies-of-the-salt-marsh-species-juncus-roemerianus-juncaceae
#4
Hayley R Tumas, Brian M Shamblin, Mark S Woodrey, Campbell J Nairn
PREMISE OF THE STUDY: Juncus roemerianus (Juncaceae) is a foundational species and ecosystem engineer of salt marshes in the Gulf of Mexico. These ecosystems provide coastal flood attenuation, nurseries for important species, and other ecosystem services, but are experiencing significant decline. Nuclear microsatellite markers were developed for J. roemerianus to study genetic diversity and population structure for conservation and restoration efforts. METHODS AND RESULTS: Illumina NextSeq high-throughput sequencing was used to develop a panel of 19 polymorphic microsatellite markers that were tested across individuals from three populations on the Gulf Coast...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337391/an-efficient-field-and-laboratory-workflow-for-plant-phylotranscriptomic-projects
#5
Ya Yang, Michael J Moore, Samuel F Brockington, Alfonso Timoneda, Tao Feng, Hannah E Marx, Joseph F Walker, Stephen A Smith
PREMISE OF THE STUDY: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. METHODS AND RESULTS: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337390/an-rbcl-reference-library-to-aid-in-the-identification-of-plant-species-mixtures-by-dna-metabarcoding
#6
Karen L Bell, Virginia M Loeffler, Berry J Brosi
PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337389/development-of-microsatellite-markers-using-illumina-miseq-sequencing-to-characterize-ephedra-gerardiana-ephedraceae
#7
Ji De, Weidong Zhu, Tianmeng Liu, Zhe Wang, Yang Zhong
PREMISE OF THE STUDY: Ephedragerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. METHODS AND RESULTS: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224061/isolation-and-characterization-of-microsatellite-loci-in-sorbus-porrigentiformis-and-cross-amplification-in-s-aria-and-s-rupicola-rosaceae
#8
Rosalía Piñeiro, Freja Karrman-Bailey, Robyn S Cowan, Michael F Fay
PREMISE OF THE STUDY: Southwestern Britain is an emblematic hotspot of polyploid diversity of whitebeams (Sorbus aria agg.; Rosaceae) with ca. 30 polyploid endemic species. The tetraploid S. porrigentiformis is postulated as one of the parents of most of these endemics, along with the sexual diploid S. aria s. str. and the tetraploid S. rupicola. METHODS AND RESULTS: We isolated 16 nuclear microsatellite loci from S. porrigentiformis and characterized them on 45 trees representing the three putative parental species...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224060/twenty-microsatellite-markers-for-the-endangered-vatica-mangachapoi-dipterocarpaceae
#9
Jun-Jie Guo, Shuai-Bin Shang, Chun-Sheng Wang, Zhi-Gang Zhao, Jie Zeng
PREMISE OF THE STUDY: Microsatellite markers were developed for Vatica mangachapoi (Dipterocarpaceae), an endangered species indigenous to Southeast Asia and southern China. METHODS AND RESULTS: Twenty microsatellite markers, including 12 polymorphic markers, were identified from V. mangachapoi using high-throughput sequencing. Polymorphism at each marker was evaluated using 87 individuals from three natural populations. The number of alleles per polymorphic locus ranged from six to 15, and the observed and expected heterozygosity varied from 0...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224059/identification-of-downy-mildew-resistance-gene-candidates-by-positional-cloning-in-maize-zea-mays-subsp-mays-poaceae
#10
Jae Yoon Kim, Jun-Cheol Moon, Hyo Chul Kim, Seungho Shin, Kitae Song, Kyung-Hee Kim, Byung-Moo Lee
PREMISE OF THE STUDY: Positional cloning in combination with phenotyping is a general approach to identify disease-resistance gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combined strategy to improve the identification of disease-resistance gene candidates. METHODS AND RESULTS: Downy mildew (DM)-resistant maize was selected from five cultivars using a spreader row technique...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224058/characterization-of-microsatellite-markers-in-two-exploited-african-trees-entandrophragma-candollei-and-e-utile-meliaceae
#11
Franck S Monthe, Jérôme Duminil, Félicien Tosso, Jérémy Migliore, Olivier J Hardy
PREMISE OF THE STUDY: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae). METHODS AND RESULTS: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224057/identification-and-characterization-of-microsatellite-markers-in-pinus-kesiya-var-langbianensis-pinaceae
#12
Nian-Hui Cai, Yu-Lan Xu, Da-Wei Wang, Shi Chen, Gen-Qian Li
PREMISE OF THE STUDY: Microsatellite primers were developed in Pinus kesiya var. langbianensis (Pinaceae), a species native to southwestern China, to investigate its genetic diversity and population structure in order to provide information for the conservation and management of this species. METHODS AND RESULTS: Using next-generation sequencing, a total of 2349 putative simple sequence repeat primer pairs were designed. Eighteen polymorphic markers in 60 individuals belonging to four populations of P...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224056/evaluation-and-comparison-of-fta-card-and-ctab-dna-extraction-methods-for-non-agricultural-taxa
#13
Chloe S Siegel, Florence O Stevenson, Elizabeth A Zimmer
PREMISE OF THE STUDY: An efficient, effective DNA extraction method is necessary for comprehensive analysis of plant genomes. This study analyzed the quality of DNA obtained using paper FTA cards prepared directly in the field when compared to the more traditional cetyltrimethylammonium bromide (CTAB)-based extraction methods from silica-dried samples. METHODS: DNA was extracted using FTA cards according to the manufacturer's protocol. In parallel, CTAB-based extractions were done using the automated AutoGen DNA isolation system...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28224055/is-biomass-a-reliable-estimate-of-plant-fitness
#14
Brett S Younginger, Dagmara Sirová, Mitchell B Cruzan, Daniel J Ballhorn
The measurement of fitness is critical to biological research. Although the determination of fitness for some organisms may be relatively straightforward under controlled conditions, it is often a difficult or nearly impossible task in nature. Plants are no exception. The potential for long-distance pollen dispersal, likelihood of multiple reproductive events per inflorescence, varying degrees of reproductive growth in perennials, and asexual reproduction all confound accurate fitness measurements. For these reasons, biomass is frequently used as a proxy for plant fitness...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090413/development-of-microsatellite-markers-in-garcinia-paucinervis-clusiaceae-an-endangered-species-of-karst-habitats
#15
Gang Hu, Zhong-Hua Zhang, Ping Yang, Qi-Wei Zhang, Chang-An Yuan
PREMISE OF THE STUDY: Microsatellite markers were developed for Garcinia paucinervis (Clusiaceae), an endangered and endemic tree species of karst habitats, to analyze its genetic diversity and genetic structure. METHODS AND RESULTS: Using shotgun sequencing on an Illumina MiSeq platform, a total of 22 microsatellite primer sets were characterized, of which 17 were identified as polymorphic. For these polymorphic loci, the total number of alleles per locus ranged from two to 12 across 54 individuals from three populations...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090412/development-characterization-and-cross-amplification-of-microsatellite-markers-in-the-understudied-african-genus-anthonotha-fabaceae
#16
Boris B Demenou, Olivier J Hardy
PREMISE OF THE STUDY: Anthonotha macrophylla (Fabaceae) is a common tree species throughout the Guineo-Congolian forest that is sometimes confounded with other congeneric species; it is expected to be an interesting phylogeographical model to infer the history of the African dense forests. We developed 18 microsatellite markers from this species and tested their transferability in 15 congeneric species. METHODS AND RESULTS: A genomic library was obtained using the Illumina platform, and 18 polymorphic microsatellite loci were developed...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090411/development-of-ssr-markers-by-454-sequencing-in-the-endemic-species-gentianella-praecox-subsp-bohemica-gentianaceae
#17
Mária Šurinová, Jiří Brabec, Zuzana Münzbergová
PREMISE OF THE STUDY: Polymorphic microsatellite loci were developed and used to genotype individuals of Gentianella praecox subsp. bohemica (Gentianaceae), a highly protected taxon in Europe, to study the genetic structure of the remaining populations. METHODS AND RESULTS: Thirty-eight primer pairs were successfully amplified; of these, 12 polymorphic microsatellite loci were developed using a 454 sequencing approach and used to genotype 180 individuals of G. praecox subsp...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090410/retrospective-analysis-of-heavy-metal-contamination-in-rhode-island-based-on-old-and-new-herbarium-specimens
#18
Sofia M Rudin, David W Murray, Timothy J S Whitfeld
PREMISE OF THE STUDY: Herbarium specimens may provide a record of past environmental conditions, including heavy metal pollution. To explore this potential, we compared concentrations of copper, lead, and zinc in historical and new collections from four sites in Rhode Island, USA. METHODS: We compared historical specimens (1846 to 1916) to congener specimens collected in 2015 at three former industrial sites in Providence, Rhode Island, and one nonindustrial site on Block Island...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090409/development-and-characterization-of-23-microsatellite-loci-for-rhododendron-ovatum-ericaceae
#19
De-Chen Liu, Yang Zhang, Si-Si Wang, Meng-Yu Liao, Xin-Yu Fan, Yuan-Yuan Li, Rong Wang
PREMISE OF THE STUDY: To estimate the genetic variation of Rhododendron ovatum (Ericaceae), a monoecious evergreen shrub, 23 microsatellite markers were identified from its nuclear genome. METHODS AND RESULTS: We developed 16 polymorphic and seven monomorphic microsatellite primers using the biotin-streptavidin capture method. The 16 polymorphic loci were investigated further using 89 individuals sampled from three populations in China. The number of alleles per locus ranged from four to 30, indicating a high level of polymorphism...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090408/development-of-microsatellite-markers-for-viscum-coloratum-santalaceae-and-their-application-to-wild-populations
#20
Bo-Yun Kim, Han-Sol Park, Soonok Kim, Young-Dong Kim
PREMISE OF THE STUDY: Microsatellite primers were developed for Viscum coloratum (Santalaceae), a semiparasitic medicinal plant that is known for its anticancer properties. Due to excessive human harvesting and loss of suitable habitat of its populations, it has become a potentially threatened species requiring immediate conservation efforts. METHODS AND RESULTS: Based on transcriptome data for V. coloratum, 124 primer pairs were randomly selected for initial validation, of which 19 yielded polymorphic microsatellite loci, with two to six alleles per locus...
January 2017: Applications in Plant Sciences
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