Functional markers for gene mapping and genetic diversity studies in sugarcane

<p>Abstract</p> <p>Background</p> <p>The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database).</p> <p>Findings</p> <p>A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process.</p> <p>Conclusions</p> <p>These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.</p

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km 2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km 2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co-occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data. © 2018 by the The Authors. Ecology © 2018 The Ecological Society of Americ

Análise histomorfométrica da matriz extracelular do linfonodo poplíteo de cães naturalmente infectados por Leishmania (L.) chagasi

Nas Américas, a leishmaniose visceral canina é causada por Leishmania (Leishmania) chagasi, um protozoário intracelular obrigatório do sistema fagocítico mononuclear; as principais alterações histológicas associadas a essa doença ocorrem nos em órgãos linfóides. Apesar de o cão ser considerado o principal mantenedor e disseminador da leishmaniose no ambiente urbano, são escassos estudos dos aspectos histopatológicos e histomorfométricos, em cães naturalmente infectados com L. chagasi, que investiguem a interação entre o parasito e a matriz extracelular. Este estudo visou caracterizar e quantificar as alterações dos componentes celulares e da matriz extracelular (colágenos I e III) do linfonodo poplíteo de 22 cães com infecção natural por L. chagasi detectada através da reação de imunofluorescência indireta (RIF) e compará-las com as alterações encontradas no linfonodo poplíteo de 10 cães não-infectados, negativos na RIF e clinicamente saudáveis. Fragmentos dos linfonodos foram seccionados longitudinalmente, processados rotineiramente para exame histológico e corados por hematoxilina-eosina. Cortes adicionais do mesmo linfonodo incluídos em glicol metacrilato foram corados pelo azul de toluidina para histomorfometria. Linfonodos de cães infectados apresentaram linfadenopatia generalizada, aumento do tamanho e do número dos folículos linfóides, hipertrofia da cápsula e hiperplasia linfóide significativa. Nos linfonodos de cães do grupo infectado, a análise quantitativa de fibras colágenas mostrou significativo predomínio do colágeno I sobre o colágeno III. Esses resultados demonstram que cães infectados por L. chagasi apresentam degradação dos constituintes da matriz extracelular e conseqüente destruição do arcabouço linfóide, alterando a morfologia do órgão.<br>In the Americas, canine visceral leishmaniasis is caused by Leishmania (Leishmania) chagasi, an obligatory intracellular parasite of the phagocytic-monocytic system; the main histological changes associated with this disease occur in the lymphoid organs. Although dogs are considered to be the main carriers and disseminators of leishmaniasis in urban areas, there are few studies on the histopathologic and histomorphometric aspects in dogs naturally infected by L.chagasi analyzing the interaction between parasite and extracellular matrix. The current study characterize and quantify changes in the cellular and extracellular matrix (collagens type I and III) components of the popliteal lymph node from of 22 dogs with the natural infection by L. chagasi confirmed by indirect immuno-fluorescence assay (IFA) and compare theses findings with those fund in the popliteal lymph node from 10 non-infected dogs, that reacted negative in the IFA, and were clinically healthy. Lymph node fragments were longitudinally sliced and sections were processed for routine histopathology and stained by hematoxylin and eosin. For histomorphometry, additional sections from the same lymph node were fixed in glycol methacrylate and stained with toluidine blue. Lymph nodes from affected dogs were systemically enlarged, had increased numbers of lymphoid follicles, capsule hyperplasia and hypertrophy, and significant hyperplasia of lymphoid cells. In the lymph nodes from infected dogs, quantitative analyses of collagen fibers revealed predominance of type I collagen over type III fibers. These results demonstrate that dogs infected by L.chagasi experience degradation of the extracellular matrix components and consequently destruction of the lymphoid framework, thus altering nodal morphology