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Genetic diversity, selection gains and genome wide selection in the Coffea canephora species
No full textA presença de variabilidade genética associada a estratégias mais eficientes de seleção são imprescindíveis para se obter sucesso nos programas de melhoramento. Nesse sentido, o uso de marcadores moleculares em estudos de diversidade, bem como a seleção baseada em dados fenotípicos por meio do uso de procedimentos genético-estatísticos mais refinados têm se mostrado ferramentas úteis nos programas de melhoramento. Além disso, com o avanço das plataformas de NGS (Next Generation Sequencing), um novo método de seleção, que visa utilizar dados fenótipos e moleculares, denominado Seleção Genômica Ampla foi proposto. O objetivo do trabalho foi identificar marcadores SNP (Single Nucleotide Polymorphism) e validá-los em estudos de diversidade genética; estimar os parâmetros genéticos e os ganhos com a seleção utilizando a metodologia de modelos mistos (REML/BLUP); aplicar o princípio da GWS (Genome Wide Selection) e avaliar sua eficiência em população de C. canephora. A população em estudo, inicialmente, foi composta por 72 genótipos nos quais os marcadores SNP foram identificados e validados. A seleção fenotípica, por meio do procedimento REML/BLUP, foi realizada em 192 genótipos de cafeeiros. Por fim, a população avaliada por meio da GWS foi composta por 165 genótipos. Utilizando a plataforma de sequenciamento da empresa RAPiD Genomics foram identificados 117.450 SNP em 72 indivíduos de C. canephora. Após análises de qualidade, 33.485 SNP foram selecionados e validados em análises de diversidade e estrutura genética de populações. Os marcadores foram eficientes na avaliação da diversidade e estrutura genética de C. canephora e com base em nessas análises foi possível selecionar possíveis cruzamentos promissores dentro e entre os grupos varietais e Híbridos geneticamente mais distantes. Com base nas análises utilizando o método REML/BLUP foi possível selecionar genótipos Conilon e Robusta promissores por serem geneticamente divergentes pela análise de agrupamento e por proporcionarem ganhos elevados com a seleção. Estes podem ser intercruzados para obter cultivares dentro de cada grupo varietal e/ou como genitores em cruzamentos interpopulacionais. Além disso, foi possível selecionar famílias híbridas que se destacaram nas análises. Estas podem ser testadas em diferentes regiões e as promissoras utilizadas como variedade propagada por semente. As famílias híbridas selecionadas podem também ser intercruzadas (cruzamento intrapopulacional) para avanço da seleção recorrente. Por fim, a GWS mostrou-se ferramenta útil para o melhoramento de C. canephora, por predizer com alta acurácia os valores genéticos genômicos dos indivíduos e possibilitar a redução no tempo necessário para completar o ciclo de seleção, proporcionando ganhos significativos em eficiência seletiva por unidade de tempo.The presence of genetic variability associated with more efficient selection strategies is essential for success in breeding programs. In this sense, the use of molecular markers in diversity studies, as well as selection based on phenotypic data through the use of more refined genetic-statistical procedures have been shown to be useful tools in breeding programs. In addition, with the advancement of NGS (Next Generation Sequencing) platforms, a new selection method, which aims to use phenotype and molecular data, called the Genome Wide Selection was proposed. The objective of this work was to identify SNP markers (Single Nucleotide Polymorphism) and to validate them in studies of genetic diversity; to estimate genetic parameters and selection gains using the mixed model methodology (REML/BLUP); to apply the principle of GWS (Genome Wide Selection) and to evaluate its efficiency in C. canephora population. The study population was initially composed of 72 genotypes in which the SNP markers were identified and validated. Phenotypic selection, using the REML/BLUP procedure, was performed on 192 coffee genotypes. Finally, the population evaluated through GWS consisted of 165 genotypes. Using the RAPiD Genomics company sequencing platform, 117,450 SNPs were identified in 72 C. canephora individuals. After quality analyzes, 33,485 SNPs were selected and validated in analyzes of diversity and genetic structure of populations. The markers were efficient in evaluating the genetic diversity and structure of C. canephora and based on these analyzes, it was possible to select possible promising crosses within and among the genetically distant varietal and hybrid groups. Based on the analyzes using the REML/BLUP method, it was possible to select promising Conilon and Robusta genotypes because they are genetically divergent by cluster analysis and because they provide high gains with selection. These can be cross-linked to obtain cultivars within each varietal group and/or as parents at interpopulation crossings. In addition, it was possible to select hybrid families that stood out in the analyzes. These can be tested in different regions and the promising ones used as seed propagated variety. Selected hybrid families can also be cross-linked (intrapopulation cross) to advance recurrent selection. Finally, the GWS proved to be a useful tool for the improvement of C. canephora, by accurately predicting the genomic genetic values of the individuals and allowing the reduction in the time needed to complete the selection cycle, providing significant gains in selective efficiency by unit of time.Conselho Nacional de Desenvolvimento Científico e Tecnológic
Molecular marker assisted selection for multiple resistance to rust and anthracnose in coffee fruits
No full textMarcadores moleculares intimamente ligados a dois genes maiores (SH3 e SH?) que conferem resistência à ferrugem, e marcadores moleculares ligados ao gene Ck-1 que confere resistência à antracnose dos frutos do cafeeiro também conhecida por Coffee Berry Disease (CBD), foram previamente identificados. Estes marcadores apresentam potencial para serem usados em programas de melhoramento visando
identificar e monitorar genótipos contendo genes de resistência a esses patógenos (Hemileia vastatrix e Colletotrichum kahawae). Dessa forma, o objetivo do trabalho foi utilizar a estratégia de seleção assistida por marcadores moleculares associados aos genes SH3 (proveniente de Coffea liberica), SH? (proveniente do Híbrido de Timor-UFV 443-03) e Ck-1, no programa de melhoramento do cafeeiro da Empresa de Pesquisa Agropecuária de Minas Gerais (Epamig)/Universidade Federal de Viçosa (UFV). Inicialmente os marcadores moleculares disponíveis na literatura foram validados e então utilizados na seleção assistida de 160 genótipos. Esses cafeeiros fazem parte do germoplasma da UFV/Epamig e foram introduzidos do CIFC por serem potencialmente portadores de resistência à ferrugem. Por meio dos marcadores validados foi possível identificar onze indivíduos resistentes
homozigotos para o gene SH3, UFV311-48 (F2), UFV311-49 (F2), UFV 311-56 (F2), UFV313-133 (F2), UFV329-72 (F2), UFV329-78 (F2), UFV334-65 (F2), UFV335-12 (F2), UFV335-77 (F2), UFV399-45 (F2) e UFV409-08 (F2). O gene SH3 confere resistência a diferentes raças de H. vastatrix e a sua incorporação em variedades de interesse tem sido sugerida como importante estratégia para obter resistência à ferrugem. Também foram identificados cafeeiros que além se serem portadores do
gene SH3 em homozigose, apresentaram o gene SH? proveniente do Híbrido de Timor (UFV443-03). Tais genótipos são o UFV311-48 (F2), UFV311-49 (F2), UFV 311-56 (F2), UFV313-133 (F2), UFV334-65 (F2), UFV399-45 (F2) e UFV409-08 (F2). Para o gene Ck-1 que confere resistência à CBD, foi observado que o genótipo UFV328-60 (F2) foi homozigoto resistente quando analisado com os dois marcadores apesar de não apresentar bandas ligadas aos genes SH3 e SH?. Entretanto UFV317-12 (F1) se viimostrou resistente heterozigoto com o marcador CBD-Sat235 (marcador do Ck-1) e resistente homozigoto com o marcador CBD-Sat207 (outro marcador do Ck-1), e portador do gene SH? que confere resistência à ferrugem. Logo, por meio da Seleção
Assistida por Marcadores Moleculares foram identificados cafeeiros portadores de diferentes genes de resistência à ferrugem e à CBD. Esse germoplasma, apesar de ser derivado de C. liberica, apresentou além do gene SH3 o gene SH?, até então identificado apenas em genótipos derivados de C. canephora. Os cafeeiros identificados poderão ser utilizados em cruzamentos para a introdução desses genes em outros materiais genéticos de interesse nos programas de melhoramento. A
utilização dos marcadores moleculares validados, nos programas de melhoramento, serão imprescindíveis para monitoramento dos genes nas diferentes gerações e cruzamentos.Molecular markers closely linked to two major genes (SH3 and SH?) that confer resistance to rust, and molecular markers linked to the gene Ck-1, which confers resistance to anthracnose in coffee fruits, also known as Coffee berry disease (CBD), were previously identified. These markers have potential to be used in breeding programs aiming to identify and monitor genotypes containing genes resistant to these pathogens (Hemileia vastatrix and Colletotrichum kahawae). Thus, the present work aimed to use molecular marker assisted selection associated with genes SH3 (from Coffea liberica), SH? (from the Timor Hybrid UFV443-03 ) and Ck-1 , in a coffee breeding program of the Agricultural Research Company of Minas Gerais (Epamig)/Universidade Federal de Viçosa (UFV). Initially, the molecular markers available in the literature were validated and then used in marker assisted selection of 160 genotypes. These coffee plants are part of the UFV/Epamig coffee germplasm bank and were introduced by the CIFC because they are potential carriers of rust resistance. The validated markers allowed identifying eleven resistant individuals homozygous for the gene SH3 UFV311- 48 (F2), UFV311-49 (F2), UFV311-56 (F2), UFV313-133 (F2), UFV329-72 (F2) UFV329-78 (F2) UFV334-65 (F2) UFV335-12 (F2) UFV335-77 (F2) UFV399-45 (F2) and UFV409-08 (F2). The gene SH3 confers resistance to different races of H. vastatrix and its incorporation in varieties of interest has been suggested as an important strategy for rust resistance. There was also identification of coffee plants that carry the gene SH3 in homozigosity that presented gene SH? from the Timor Hybrid (UFV443-03). These genotypes are UFV311-48 (F2) UFV311-49 (F2), UFV311-56 (F2) UFV313-133 (F2) UFV334-65 (F2) UFV399-45 (F2) and UFV409-08 (F2). For gene Ck-1, which confers resistance to CBD, it was observed that the genotype UFV328-60 (F2) was resistant homozygous when tested with the two markers, although presenting no bands related to the genes SH3 and SH?. However, UFV317-12 (F1) was resistant heterozygous with marker CBD-Sat235 (marker Ck-1) and resistant homozygous with marker CBD-Sat207 (another Ck-1 marker) and carried the gene SH?, which confers ixresistance to rust. Therefore, Molecular Marker Assisted Selection allowed identifying coffee plants carrying different genes resistant to rust and CBD. This germplasm, although derived from C. liberica, presented both the gene SH3 and gene
SH?, hitherto only identified in genotypes derived from C. canephora. The coffee plants identified may be used in crosses for the introduction of these genes in other genetic materials of interest in breeding programs. The use of validated molecular markers in breeding programs will be invaluable for monitoring genes in different generations and crosses.Conselho Nacional de Desenvolvimento Científico e Tecnológic
Genome-wide association Study (GWAS) in Coffea canephora
No full textEstudos de associação genômica ampla (GWAS) tem sido tradicionalmente utilizados para a identificação de locos de interesse responsáveis pela variação fenotípica. A utilização desse tipo de metodologia explora as ligações mais próximas existentes entre os marcadores moleculares e regiões cromossômicas de interesse para um maior entendimento das características fenotípicas da espécie em estudo, propiciando a identificação de marcas a serem utilizadas em seleções assistidas por marcadores moleculares (SAM) nos programas de melhoramento. Nesse contexto, a utilização dessa metodologia visando um maior entendimento de caracteres morfoagronomicos em um menor período de tempo se mostra uma solução viável para programas de melhoramento de espécies com longo ciclo de vida (plantas perenes) como o café. Assim, o objetivo do trabalho foi identificar regiões cromossômicas com associações significativas em populações de C. canephora em melhoramento para as principais características fenotípicas de importância para essa espécie, através da metodologia de Associação Genômica Ampla (GWAS). A população em estudo foi composta por 165 genótipos contendo os dois grupos varietais Conilon e Robusta além dos Híbridos provenientes desse cruzamento. Foram avaliadas oito características morfoagronomicas sendo elas altura da planta, vigor vegetativo, incidência a cercosporiose, incidência a ferrugem, diâmetro da copa, produtividade, época de maturação dos frutos e tamanho dos frutos. Os cafeeiros foram genotipados com marcadores SNP, distribuídos em todo o genoma. Foram realizadas análises de qualidade (MAF ≥0,01 e CR ≥ 90%) que resultaram em 17.885 SNP. Após a aplicação da metodologia de GWAS, foram identificados marcadores SNP com associações significativas para cinco características (altura da planta, diâmetro da copa, vigor vegetativo, incidência a ferrugem e a cercoporiose). As análises também permitiram a identificação de genes candidatos, nos quais, os marcadores SNP estavam inseridos. Foi possível também relacionar a função dos genes candidatos a característica nos quais esses se encontravam inseridos. Foi possível a identificação da presença dos genes 08-g11560, 10-g16500, 11-g17430, 00-g17460 e 02- g38180 nas duas principais doenças do cafeeiro. Os marcadores SNP com associações significativas se mostraram distribuídos em todo o genoma da espécie e estavam presentes em todos os cromossomos. Com destaque para os cromossomos 0,2,6,9 e 11. Por fim, a metodologia se mostrou eficiente em populações C.canephora, os genes candidatos encontrados inseridos nos marcadores SNP com associações significativas poderão ser avaliados com maior detalhamento e posteriormente poderão ser usados em seleções assistidas por marcadores moleculares (SAM) auxiliando programas de melhoramento da espécie.Genome-wide Association Study (GWAS) have traditionally been used to identify loci of interest responsible for the phenotypic variation. The use of this type of methodology explores the closer links between molecular markers and chromosomal regions of interest for a better understanding of the phenotypic characteristics of the species under study, favoring the identification of markers to be used in selections assisted by molecular markers (SAM) in breeding programs. In this context, the use of this methodology aiming at a greater understanding of morphoagronomic characters in a shorter period of time is a viable solution for breeding programs of species with a long life cycle (perennial plants) such as coffee. Thus, the objective of this work was to identify chromosomal regions with significant associations in C. canephora populations in breeding for the main phenotypic characteristics of importance for this species, through the GWAS methodology. The study population consisted of 165 genotypes containing the two Conilon and Robusta varietal groups in addition to the hybrids from that cross. Eight morphoagronomic characteristics were evaluated: plant height, vegetative vigor, incidence of cercosporiae, incidence of rust, canopy diameter, productivity, fruit maturation time and fruit size. The coffee trees were genotyped with SNP markers, distributed throughout the genome. Quality analyzes (MAF ≥0.01 and CR ≥ 90%) were performed, resulting in 17,885 SNPs. After application of the GWAS methodology, SNP markers were identified with significant associations for five characteristics (plant height, crown diameter, vegetative vigor, incidence of rust and cercoporiosis). The analyzes also allowed the identification of candidate genes in which the SNP markers were inserted. It was also possible to relate the function of the candidate genes to the characteristic in which they were inserted. It was possible to identify the presence of genes 08-g11560, 10-g16500, 11-g17430, 00-g17460 and 02-g38180 in the two major diseases of coffee. The SNP markers with significant associations were shown to be distributed throughout the genome of the species and were present on all chromosomes. Finally, the methodology was efficient in populations C.canephora, the candidate genes found inserted in the SNP markers with significant associations can be evaluated in greater detail and later can be used in molecular marker assisted selections (SAM) to support species breeding programs.Conselho Nacional de Desenvolvimento Científico e Tecnológic
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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