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      Development of microsatellite markers for Fargesia denudata (Poaceae), the staple-food bamboo of the giant panda 1

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          Abstract

          Premise of the study:

          There is a need for microsatellite primers to analyze genetic parameters of Fargesia denudata (Poaceae), the staple-food bamboo of the giant panda ( Ailuropoda melanoleuca).

          Methods and Results:

          Using next-generation sequencing technology, we obtained a 75-Mb assembled sequence of F. denudata and identified 182 microsatellites. Primer pairs for 70 candidate microsatellite markers were selected and validated in four individuals, and 42 primer pairs generated reliable amplicons. Fourteen of 16 tested markers were found to be polymorphic in 72 individuals from four F. denudata populations. The number of alleles ranged from two to 19 per locus; the observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.87, respectively. The transferability of these 16 novel microsatellite markers was validated in five related species.

          Conclusions:

          These markers will be useful for examining the genetic diversity, genetic structure, and cloning of F. denudata, the staple-food bamboo of the giant panda, and related bamboo species.

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          Most cited references 4

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          Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

          A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
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            Giant panda conservation science: how far we have come.

            The giant panda is a conservation icon, but science has been slow to take up its cause in earnest. In the past decade, researchers have been making up for lost time, as reflected in the flurry of activity reported at the symposium Conservation Science for Giant Pandas and Their Habitat at the 2009 International Congress for Conservation Biology (ICCB) in Beijing. In reports addressing topics ranging from spatial ecology to molecular censusing, from habitat recovery in newly established reserves to earthquake-induced habitat loss, from new insights into factors limiting carrying capacity to the uncertain effects of climate change, this symposium displayed the vibrant and blossoming application of science to giant panda conservation. Collectively, we find that we have come a long way, but we also reach an all-too-familiar conclusion: the more we know, the more challenges are revealed. While many earlier findings are supported, many of our assumptions are debatable. Here we discuss recent advancements in conservation science for giant pandas and suggest that the way forward is more direct application of emerging science to management and policy.
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              Exploiting the Transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to Develop and Characterize New EST-SSR Markers and Construct an EST-SSR Database

              Background Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. Methodology/Principal Findings A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). Conclusions The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
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                Author and article information

                Journal
                Appl Plant Sci
                Appl Plant Sci
                apps
                Applications in Plant Sciences
                Botanical Society of America
                2168-0450
                June 2016
                1 June 2016
                : 4
                : 6
                Affiliations
                [2 ]College of Forestry, Key Laboratory for Forest Resources and Ecosystem Processes of Beijing, Beijing Forestry University, Beijing 100083, People’s Republic of China
                [3 ]College of Life Science, Lanzhou University, Lanzhou 730000, Gansu, People’s Republic of China
                Author notes
                [1]

                This research was supported by the Fundamental Research Funds for the Central Universities (grant no. 2015ZCQ-LX-03), National Natural Science Foundation of China (grant nos. 41201051, 41430749), and the Beijing Nova Program (grant no. Z151100000315056) to F.K.D.

                [4 ]Authors for correspondence: dufang325@ 123456bjfu.edu.cn and lijq@ 123456bjfu.edu.cn
                Article
                apps1600005
                10.3732/apps.1600005
                4915919
                27347452
                © 2016 Lv et al. Published by the Botanical Society of America

                This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA).

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