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Applications in Plant Sciences

Lindsay Chaney, Ryan Mangelson, Thiruvarangan Ramaraj, Eric N Jellen, Peter J Maughan
PREMISE OF THE STUDY: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. METHODS AND RESULTS: A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A...
September 2016: Applications in Plant Sciences
Zheng Chen, Yuncheng Deng, Renchao Zhou, Shaoyun He
PREMISE OF THE STUDY: To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. METHODS AND RESULTS: Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H...
September 2016: Applications in Plant Sciences
Kuniaki Otake, Toshiaki Kondo, Sonoko Watanabe, Ikuko Masumoto, Katsumi Iwahori, Yuji Isagi
PREMISE OF THE STUDY: Adenophora palustris (Campanulaceae) is an endangered wetland plant species in Japan. Although it is widely distributed in East Asia, only six extant populations are known in Japan, with fewer than 1000 individuals in total. We developed 15 microsatellite markers for this species and confirmed their utility for the closely related species A. triphylla var. japonica. METHODS AND RESULTS: Ten polymorphic loci were characterized for genetic variation within three populations of A...
September 2016: Applications in Plant Sciences
Jessica N C Francisco, Alison G Nazareno, Lúcia G Lohmann
PREMISE OF THE STUDY: In this study, we developed chloroplast microsatellite markers (cpSSRs) for Pachyptera kerere (Bignoniaceae) to investigate the population structure and genetic diversity of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the chloroplast genome of P. kerere by a combination of de novo and reference-guided assembly. We then used the chloroplast genome to develop a set of cpSSRs from intergenic regions. Overall, 24 primer pairs were designed, 21 of which amplified successfully and were polymorphic, presenting three to nine alleles per locus...
September 2016: Applications in Plant Sciences
Ayu Narita, Ayako Izuno, Yoshiteru Komaki, Takefumi Tanaka, Jin Murata, Yuji Isagi
PREMISE OF THE STUDY: Microsatellite markers were identified for Melastoma tetramerum var. tetramerum (Melastomataceae), a critically endangered shrub endemic to the Bonin Islands, to reveal genetic characteristics in wild and restored populations. METHODS AND RESULTS: Using next-generation sequencing, 27 microsatellite markers were identified. Twenty of these markers were polymorphic in M. tetramerum var. tetramerum, with two to nine alleles per locus and expected heterozygosity ranging from 0...
September 2016: Applications in Plant Sciences
Tetiana Lutsak, Fernando Fernández-Mendoza, Bastian Greshake, Francesco Dal Grande, Ingo Ebersberger, Sieglinde Ott, Christian Printzen
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure. METHODS AND RESULTS: Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0...
September 2016: Applications in Plant Sciences
Takashi Yamamoto, Yoshiaki Tsuda, Gustavo Maruyama Mori, Mariana Vargas Cruz, Yoshimi Shinmura, Alison K S Wee, Koji Takayama, Takeshi Asakawa, Takeru Yamakawa, Monica Suleiman, Juan Núñez-Farfán, Edward L Webb, Yasuyuki Watano, Tadashi Kajita
PREMISE OF THE STUDY: Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant. METHODS AND RESULTS: Fifty-six A. aureum individuals from three populations were sampled and genotyped to characterize the 27 loci. The number of alleles and expected heterozygosity ranged from one to 15 and 0.000 to 0.893, respectively...
September 2016: Applications in Plant Sciences
Mitchell B Cruzan, Ben G Weinstein, Monica R Grasty, Brendan F Kohrn, Elizabeth C Hendrickson, Tina M Arredondo, Pamela G Thompson
PREMISE OF THE STUDY: Low-elevation surveys with small aerial drones (micro-unmanned aerial vehicles [UAVs]) may be used for a wide variety of applications in plant ecology, including mapping vegetation over small- to medium-sized regions. We provide an overview of methods and procedures for conducting surveys and illustrate some of these applications. METHODS: Aerial images were obtained by flying a small drone along transects over the area of interest. Images were used to create a composite image (orthomosaic) and a digital surface model (DSM)...
September 2016: Applications in Plant Sciences
Morgan R Gostel, Carol Kelloff, Kyle Wallick, Vicki A Funk
PREMISE OF THE STUDY: Internationally, gardens hold diverse living collections that can be preserved for genomic research. Workflows have been developed for genomic tissue sampling in other taxa (e.g., vertebrates), but are inadequate for plants. We outline a workflow for tissue sampling intended for two audiences: botanists interested in genomics research and garden staff who plan to voucher living collections. METHODS AND RESULTS: Standard herbarium methods are used to collect vouchers, label information and images are entered into a publicly accessible database, and leaf tissue is preserved in silica and liquid nitrogen...
September 2016: Applications in Plant Sciences
Oliver W White, Bethany Doo, Mark A Carine, Mark A Chapman
PREMISE OF THE STUDY: Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asteraceae], Descurainia bourgaeana [Brassicaceae], and Echium wildpretii [Boraginaceae]) that are representative of lineages that have radiated in the region...
August 2016: Applications in Plant Sciences
Marion Nachtigall, Lorenz Bülow, Jörg Schubert, Lothar Frese
PREMISE OF THE STUDY: Microsatellite primers were developed to promote studies on the patterns of genetic diversity within Patellifolia patellaris (Chenopodiaceae) and the relationship between the three species of the genus Patellifolia. METHODS AND RESULTS: The genomic sequence from P. procumbens was screened for simple sequence repeats (SSRs), and 3648 SSRs were identified. A subset of 53 SSR markers was validated, of which 25 proved to be polymorphic in the three species except for the P...
August 2016: Applications in Plant Sciences
Florent Martos, Gérard Lebreton, Eric Rivière, Laurence Humeau, Marie-Hélène Chevallier
PREMISE OF THE STUDY: Polymorphic markers were required for a native tree of the Mascarene Islands, Foetidia mauritiana (Lecythidaceae), to investigate the effects of fragmentation of lowland tropical habitats on tree mating systems and on gene flow. METHODS AND RESULTS: Using microsatellite enrichment and next-generation sequencing, we identified 13 microsatellite loci (dinucleotide repeats). They were highly polymorphic in 121 trees sampled in the largest three populations on Réunion, revealing 2-17 different alleles per locus...
August 2016: Applications in Plant Sciences
Jacob J Hadle, Lauren A Konrade, Rochelle R Beasley, Stacey L Lance, Kenneth L Jones, James B Beck
PREMISE OF THE STUDY: Buchloë dactyloides (Poaceae) is an important component of Great Plains prairies and a popular drought-tolerant turfgrass alternative in North America. This species comprises an autopolyploid series, and microsatellite primers were developed to understand the distribution of genetic variation among cytotypes and across its large geographic range. METHODS AND RESULTS: Fifteen microsatellite loci were designed and successfully amplified in six B...
August 2016: Applications in Plant Sciences
Hana Park, Changkyun Kim, You-Mi Lee, Joo-Hwan Kim
PREMISE OF THE STUDY: Ten polymorphic chloroplast microsatellite (cpSSR) markers were developed and characterized in an endemic and endangered herb, Maianthemum bicolor (Asparagaceae s.l.), for use in conservation genetics. METHODS AND RESULTS: Primer sets flanking each of the 10 cpSSR loci in noncoding regions of the chloroplast genome of M. bicolor were designed. These cpSSR markers were tested on a total of 33 adult individuals from three natural populations in South Korea...
August 2016: Applications in Plant Sciences
Craig H Carlson, Lawrence B Smart
PREMISE OF THE STUDY: Root biomass is an important trait often disregarded in woody perennial selection due to the challenge and expense of accurately and efficiently measuring large populations. In this study, we aim to develop a simple method that can predict root dry weight within a diverse shrub willow (Salix) breeding population representing species hybrids and their parents using root electrical capacitance (REC). METHODS: The REC method was tested on plants started from cuttings and grown in pots with potting mix in the greenhouse for 11 wk to assess the relationship of REC with 24 biomass traits and its usefulness in allometric models for root and stem dry biomass...
August 2016: Applications in Plant Sciences
Xin Yin, Yunqiang Yang, Yongping Yang
PREMISE OF THE STUDY: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using Illumina sequencing for further genetic diversity studies of Stipa purpurea (Poaceae). METHODS AND RESULTS: Twenty-nine polymorphic and eight monomorphic EST-SSR loci were developed and characterized in 90 individuals from nine S. purpurea populations. The number of alleles per locus ranged from two to 13, and heterozygosity within populations and total heterozygosity ranged from 0...
August 2016: Applications in Plant Sciences
Fabien De Bellis, Roger Malapa, Valérie Kagy, Stéphane Lebegin, Claire Billot, Jean-Pierre Labouisse
PREMISE OF THE STUDY: Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. METHODS AND RESULTS: A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A...
August 2016: Applications in Plant Sciences
Katlego B Riet, Nombuso Ndlovu, Lizelle A Piater, Ian A Dubery
PREMISE OF THE STUDY: Simultaneous analysis of defense-related phytohormones can provide insights into underlying biochemical interactions. Ultra-high-performance liquid chromatographic (UHPLC) techniques hyphenated to electrospray ionization mass spectrometry (ESI-MS) are powerful analytical platforms, suitable for quantitative profiling of multiple classes of metabolites. METHODS: An efficient and simplified extraction method was designed followed by reverse-phase UHPLC for separation of seven phytohormones: salicylic acid, methyl salicylate, jasmonic acid, methyl jasmonate, absiscic acid, indole acetic acid, and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid...
August 2016: Applications in Plant Sciences
Virginia K Duwe, Ludo A H Muller, Thomas Borsch, Sascha A Ismail
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for the threatened species Crepis mollis (Asteraceae) to investigate population and conservation genetics. METHODS AND RESULTS: Illumina sequencing was conducted on pooled genomic DNA from 10 individuals of two populations. Ten polymorphic and 10 monomorphic microsatellite loci with di-, tri-, tetra-, penta-, and hexanucleotide repeat motifs were developed and characterized in C. mollis. In the polymorphic markers, up to 17 alleles per locus were detected with an observed and expected heterozygosity ranging from 0...
July 2016: Applications in Plant Sciences
Bo Zhao, Yun-Qian Du, Jing-Jian Li, Wen-Xiu Tang, Shu-Hua Zhong
PREMISE OF THE STUDY: Begonia fimbristipula (Begoniaceae) is a medicinal herb distributed in the Chinese provinces of Fujian, Guangdong, Guangxi, Hainan, Hunan, Jiangxi, and Zhejiang, and it is on the verge of extinction due to habitat destruction and deterioration of its ecosystem. Here we developed a set of highly polymorphic microsatellite markers for population genetic and conservation studies of this endangered medicinal plant. METHODS AND RESULTS: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 18 polymorphic microsatellite markers were identified within 48 individuals from two geographic locations...
July 2016: Applications in Plant Sciences
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