Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance

Urochloa decumbens (Stapf) R. D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in defense against biotic stresses. We used the Setaria viridis genome a reference to align GBS reads and selected 4,240 high-quality SNP markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66 and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to defense against biotic stresses. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle

A reatividade negativa oriunda da poliquimioterapia imposta na Hanseníase

Introdução: A hanseníase é uma doença infectocontagiosa, que devido às repercussões clínicas e aos dados epidemiológicos é considerada de notificação compulsória. Contudo, esse transtorno quando é precocemente identificado e adequadamente manejado, evita consideravelmente o círculo vicioso de contágio e as manifestações clínicas que tornam a doença tão alvo de estigma. Objetivo: Descrever a reação negativa oriunda da poliquimioterapia imposta na hanseníase. Metodologia: Trata-se de uma revisão narrativa de literatura, fundamentada nas plataformas do Scielo, Pubmed, Lilacs e demais literaturas pertinentes ao tema, utilizando-se os seguintes descritores: Reação Hansênica, Efeitos Adversos e Poliquimioterapia, no período de janeiro de 2023. Resultados e Discussão:  Atualmente, o protocolo terapêutico voltado para a Hanseníase é a poliquimioterapia e possui boa eficácia e tolerância pela maioria dos pacientes.  No advém, a minoria destes apresenta reações adversas que variam de leve a exacerbadas e que devem ser devidamente classificados e orientados para outras opções farmacológica, objetivando impedir que o paciente abandone o tratamento, junto às enormes repercussões oriundas deste, e propiciar melhor qualidade de vida. Conclusão: Estima-se que o tratamento da Hanseníase é algo importante e indispensável para evitar problemas de saúde pública, mas este se baseia em uma alta carga associada de remédios potentes, a qual alguns portadores possuem sensibilidade e se orientados, podem continuar o tratamento até o alcance da cura.&nbsp

Modelos genéticos-estatísticos para seleção genômica em Panicum maximum com informação de dosagem alélica

Several species of economic interest are autotetraploid, such as the forage Panicum maximum, which is responsible for high productivity and quality of tropical pastures. The main accessions in nature are autotetraploid apomictic plants, on the other hand, diploid sexual plants may also be found. Although apomixis is advantageous because it fixes hybrid vigor, sexual reproduction is fundamental to allow genetic recombination by crossing among superior genotypes. Thus, genetic breeding consists of crossing apomictic plants with tetraploidized sexual plants. In these crosses, the use of superior sexual parents allows to increase the frequency of favorable alleles in the progeny. Therefore, recurrent selection programs in tetraploid sexual populations are fundamental to P. maximum breeding programs and strategies such as genomic selection can increase the accuracy of selection, allowing shorter breeding cycles and release cultivars in the market in the short term when compared to conventional programs. As P. maximum is a perennial crop, genotypes are evaluated in sucessive harvests. Thus, the study goals are to evaluate nutritional, structural, and yield traits in a sexual tetraploid population of P. maximum, investigating different classes of linear mixed models applied to longitudinal data, as well as to develop genomic selection models which consider tetraploid allelic dosage. This work was split into two chapters. In the first chapter, three classes of models were analyzed: i) Class A consists in modeling the interaction of genotypes and harvests with homogeneous correlations, genotypes were assumed not correlated, and residual effects were assumed homocedastic and not correlated; ii) Class B consists of groups of models in which genetic and residual effects were fitted with different variance and covariance (VCOV) structures and genotypes were not correlated; and iii) Class C is similar to Class B, however genotypes were correlated by an additive relationship matrix based on pedigree values. For all traits, Class C models performed better based on goodness of fit of the models. Therefore, we recommend to incorporate additive relationship matrix besides to model harvests with different levels of correlations over time. In the second chapter, SNP markers, obtained by genotyping-by-sequencing (GBS) technique, were used to develop Bayesian and GBLUP models that consider tetraploid allelic dosage. Bayesian models accuracies did not differ from the accuracy of GBLUP model and, we recommend the latter because it requires less computational time. The accuracy of genomic selection models reinforces the advantage of implementing this strategy in P. maximum breeding programs.Diversas espécies de interesse econômico são autotetraploides, como a forrageira Panicum maximum, a qual proporciona alta produtividade e qualidade para pastagens tropicais. Os principais acessos na natureza são plantas apomíticas tetraploides, no entanto pode-se encontrar também plantas sexuais diploides. Embora a apomixia seja vantajosa pela facilidade em fixar o vigor híbrido, a reprodução sexual é fundamental por permitir recombinação genética a partir de cruzamentos entre genótipos superiores. Desta forma, o melhoramento nesta espécie consiste em cruzar plantas apomíticas com plantas sexuais tetraploidizadas. A utilização de parentais sexuais superiores nestes cruzamentos permite aumentar a frequência de alelos favoráveis na progênie. Portanto, programas de seleção recorrente intrapopulacional em populações sexuais tetraploides são fundamentais para programas de melhoramento em P. maximum. Além disto, a utilização de estratégias como seleção genômica são promissoras para aumentar os ganhos de seleção, permitindo avançar ciclos de seleção recorrente e lançar cultivares no mercado em menor prazo, quando comparados a programas convencionais. Como P. maximum é uma cultura perene, os genótipos são avaliados em sucessivos cortes. Assim, este estudo tem como finalidade avaliar caracteres de produtividade, estruturais e nutricionais em uma população sexual tetraploide de P. maximum, investigando diferentes classes de modelos lineares mistos aplicados a dados longitudinais, além de desenvolver modelos de seleção genômica que considerem a natureza tetraploide da população. Este trabalho foi dividido em dois capítulos. No primeiro capítulo, três classes de modelos foram analisados: i) Classe A consiste em modelar a interação genótipos por cortes com correlações homogêneas, genótipos não correlacionados entre si e os efeitos residuais são ajustados com homocedasticidade e ausência de correlação; ii) Classe B consiste em grupos de modelos com diferentes estruturas de variância e covariância (VCOV) para efeitos genéticos e residuais e genótipos não correlacionados; iii) Classe C é similar à Classe B, no entanto os genótipos são correlacionados por uma matriz de parentesco aditivo calculado por pedigree. Para todos os caracteres, os modelos da Classe C tiveram melhor ajuste. Portanto, recomenda-se testar matrizes de VCOV que permitam modelar cortes com diferentes níveis de correlações ao longo do tempo bem como incluir informação de parentesco aditivo e, se disponível, matriz de parentesco genômico. No segundo capítulo, marcadores SNPs, obtidos via genotipagem por sequenciamento, foram aplicados em modelos Bayesianos e GBLUP os quais foram desenvolvidos para incorporar informação de dosagem alélica tetraploide. Uma vez que as acurácias dos modelos Bayesianos não diferiram das acurácias do modelo GBLUP com dosagem alélica, recomenda-se o uso do segundo por requerer menos tempo computacional. A acurácia dos modelos preditivos reforça a vantagem em implementar seleção genômica em programas de melhoramento de P. maximum

SELEÇÃO ASSISTIDA POR MARCADORES DE DNA EM RETROCRUZAMENTO VISANDO RESISTÊNCIA AO MOFO BRANCO EM FEIJOEIRO

The present study aimed to use DNA markers to select plants for the first and second backcross (BC) of two distinct populations of common bean, carrying the QTL for resistance to white mold and RAPD and microsatellite markers to identify the plants of the BC population more similar to their recurrent parent. For this, it was used the lines G122 (resistant - P1) as donor parent and VC3 (susceptible - P2) as recurrent parent for generation of the population F1RC1-GV evaluated for resistance to white mold by means of the SCAR Phs and genotyped with RAPD primers. In the F1RC2-EM population were used the lines Ex Rico 23 (resistant) as donor parent and M20 (susceptible) as recurrent parent evaluated for resistance to white mold, by means of RAPD primers O12.1600 and O15.1800 and genotyped with microsatellite (SSR) primers. Genetic similarity (sgij) between each BC plant and the recurrent parent was estimated using the Sorensen-Dice coefficient. The proportion of the SSR alleles derived from the recurrent parent was also estimated and, simultaneously, genetic similarity and the proportion of SSR alleles were efficient for identifying plants more similar to the recurrent parent. It was found that marker assisted selection (MAS) contributes to reducing the number of BC in at least a generation

A joint learning approach for genomic prediction in polyploid grasses

Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora