Revealing the genetic architecture of soybean resistance to the stink bug complex

Detalhes bibliográficos
Autor(a) principal: Martins, Emanoel Sanches
Data de Publicação: 2021
Tipo de documento: Tese
Idioma: eng
Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
Texto Completo: https://www.teses.usp.br/teses/disponiveis/11/11137/tde-11112021-112335/
Resumo: Damage caused by the stink bug complex in soybean has exceeded the figure of millions of dollars annually. Cultivating extensive areas, the damage due to these insects has increased, reducing the gains in production. Among the insects control, resistant cultivars to the stink bug complex may be an alternative to the use of insecticides. It is known that this resistance has a quantitative nature and is thus controlled by several genes. In this way, strategies that aim to clarify the control of these insects become overpowering for the future of soybeans. To this end, the objective of this project was to identify and elucidate the genetic architecture of soybean resistance to the stink bug complex. In the first study, we seek to map regions of resistance and elucidate the interactions between QTLs and environments involved in resistance to the stink bug complex on soybean, in a population of recombinant inbred lines (RILs). For this purpose, a population of 256 RILs were used, developed from the cross between IAC-100 (resistant) and CD-215 (susceptible). The experiments were carried out at the ESALQ experimental area in the city of Piracicaba, SP, during the seasons 2012/2013, 2013/2014, 2014/2015, 2015/2016, 2016/2017, 2017/2018, and 2018/2019. We use an alpha-lattice 10 x 26, with three replications as the experimental design. Nine traits associated with resistance to the stink bug complex and agronomic performance were evaluated. For genotyping of RILs, the genotyping technique by sequencing (Genotyping-by- Sequencing) was used. Subsequently, with the data obtained and the analyzes carried out, we found a total of seven significant QTLs, 5 of which were considered as stable QTLs and with potential for use in marker assisted selection. Additionally, in this first study, we developed an epistasis study using the SPAEML software, in which we conclude that the size of the studied population (n = 256) is too small to quantify epistatic effects. In the second study, we developed a work aimed to validate the regions found by the QTL mapping through a genomic wide association study. A soybean breeding panel composed of 299 lines, obtained from a multiparental crossing, was evaluated. This population was evaluated during the years 2018/2019 and 2019/2020, in the experimental area of ESALQ in a 16x19 alpha-lattice design with three replications. We evaluated traits that had significant QTLs in the QTL mapping. Genotypic data were obtained by genotyping by sequencing. With the data obtained, we calculated the means adjusted through mixed models and subsequently performed the GWAS to validate the regions of resistance to the stinkbug complex. A total of 22 QTNs were found, with three regions validating the QTLs found in the previous mapping. For our studies, chromosomes 1, 6, and 15 appear as regions with possible candidate resistance genes and with great potential to assist breeding programs to decide for resistant cultivars.
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spelling Revealing the genetic architecture of soybean resistance to the stink bug complexRevelando a arquitetura genética da resistência da soja ao complexo de percevejoGlycine maxGlycine maxGWASGWASMapeamento de QTLsQTL mappingQTL validationResistance to insectsResistência a insetosValidação de QTLsDamage caused by the stink bug complex in soybean has exceeded the figure of millions of dollars annually. Cultivating extensive areas, the damage due to these insects has increased, reducing the gains in production. Among the insects control, resistant cultivars to the stink bug complex may be an alternative to the use of insecticides. It is known that this resistance has a quantitative nature and is thus controlled by several genes. In this way, strategies that aim to clarify the control of these insects become overpowering for the future of soybeans. To this end, the objective of this project was to identify and elucidate the genetic architecture of soybean resistance to the stink bug complex. In the first study, we seek to map regions of resistance and elucidate the interactions between QTLs and environments involved in resistance to the stink bug complex on soybean, in a population of recombinant inbred lines (RILs). For this purpose, a population of 256 RILs were used, developed from the cross between IAC-100 (resistant) and CD-215 (susceptible). The experiments were carried out at the ESALQ experimental area in the city of Piracicaba, SP, during the seasons 2012/2013, 2013/2014, 2014/2015, 2015/2016, 2016/2017, 2017/2018, and 2018/2019. We use an alpha-lattice 10 x 26, with three replications as the experimental design. Nine traits associated with resistance to the stink bug complex and agronomic performance were evaluated. For genotyping of RILs, the genotyping technique by sequencing (Genotyping-by- Sequencing) was used. Subsequently, with the data obtained and the analyzes carried out, we found a total of seven significant QTLs, 5 of which were considered as stable QTLs and with potential for use in marker assisted selection. Additionally, in this first study, we developed an epistasis study using the SPAEML software, in which we conclude that the size of the studied population (n = 256) is too small to quantify epistatic effects. In the second study, we developed a work aimed to validate the regions found by the QTL mapping through a genomic wide association study. A soybean breeding panel composed of 299 lines, obtained from a multiparental crossing, was evaluated. This population was evaluated during the years 2018/2019 and 2019/2020, in the experimental area of ESALQ in a 16x19 alpha-lattice design with three replications. We evaluated traits that had significant QTLs in the QTL mapping. Genotypic data were obtained by genotyping by sequencing. With the data obtained, we calculated the means adjusted through mixed models and subsequently performed the GWAS to validate the regions of resistance to the stinkbug complex. A total of 22 QTNs were found, with three regions validating the QTLs found in the previous mapping. For our studies, chromosomes 1, 6, and 15 appear as regions with possible candidate resistance genes and with great potential to assist breeding programs to decide for resistant cultivars.Danos causados pelo complexo de percevejos na soja têm ultrapassado a cifra de milhões de dólares anuais. Com extensas áreas de cultivo, o prejuízo devido a estes insetos tem aumentado, reduzindo os ganhos na produção. Dentre as alternativas de controle, as cultivares resistentes ao complexo de percevejo podem ser uma alternativa ao uso de inseticidas. Sabe-se que tal resistência é de natureza quantitativa e, portanto, controlada por diversos genes. Desta maneira, estratégias que visam esclarecer o controle destas pragas se tornam preponderantes para o futuro da soja. Mediante tal fato, o objetivo deste trabalho consistiu em identificar e elucidar a arquitetura genética da resistência da soja ao complexo de percevejos. No primeiro estudo, buscamos mapear regiões de resistência e elucidar as interações entre QTLs e ambientes envolvidas na resistência ao complexo de percevejos da soja, por meio de uma população de linhagens recombinantes endogâmicas (RILs). Para tanto, foi utilizado uma população de 256 RILs desenvolvida a partir do cruzamento entre os genótipos IAC-100 (resistente) e CD-215 (suscetível). Os experimentos foram realizados na área experimental da ESALQ no município de Piracicaba, SP, durante as safras 2012/2013, 2013/2014, 2014/2015, 2015/2016, 2016/2017, 2017/2018 e 2018/2019, em um delineamento experimental de alfa-látice 10 x 26, com três repetições. Foram avaliadas 9 características associados a resistência ao complexo de percevejos e ao desempenho agronômico. Para genotipagem das RILs, foi utilizada a técnica de genotipagem por sequenciamento (Genotyping-by-Sequencing). Posteriormente, com os dados obtidos e as análises realizadas, encontramos um total de sete QTLs significativos sendo 5 deles considerados como QTLs estáveis e com potencial para uso na seleção assistida por marcadores. Adicionalmente, neste primeiro capítulo desenvolvemos um estudo de epistasia utilizando o software SPAEML, onde concluímos que o tamanho da população estudada (n=256) é muito pequena para quantificar efeitos epistáticos. No segundo estudo, desenvolvemos um trabalho com objetivo de validar as regiões encontradas pelo mapeamento de QTL por meio de um estudo de associação genômica ampla. Foi avaliado um painel de melhoramento de soja composto de 299 linhagens, obtido de um cruzamento multiparental. Essa população foi avalida durante os anos de 2018/2019 e 2019/2020, na área experimental da ESALQ em um delineamento de alfa-látice 16x19 com três repetições. Foram avaliados caracteres que tiveram QTLs significativos no mapeamento. Os dados genotípicos foram obtidos via genotipagem por sequenciamento. Com os dados obtidos, obtivemos as médias ajustadas via modelos mistos e posteriormente realizamos GWAS para validação das regiões de resistência ao complexo de percevejos. Foi encontrado um total de 22 QTNs sendo três regiões validando os QTLs encontrados no mapeamento anterior. Para os nossos estudos, os cromossomos 1, 6 e 15 aparecem como regiões com possíveis candidatos genes de resistência e com grande potencial de auxiliarem os programas de melhoramento na tomada de decisões quanto a busca de cultivares resistentes.Biblioteca Digitais de Teses e Dissertações da USPPinheiro, Jose BaldinMartins, Emanoel Sanches2021-08-27info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttps://www.teses.usp.br/teses/disponiveis/11/11137/tde-11112021-112335/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2021-11-12T14:12:02Zoai:teses.usp.br:tde-11112021-112335Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212021-11-12T14:12:02Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false
dc.title.none.fl_str_mv Revealing the genetic architecture of soybean resistance to the stink bug complex
Revelando a arquitetura genética da resistência da soja ao complexo de percevejo
title Revealing the genetic architecture of soybean resistance to the stink bug complex
spellingShingle Revealing the genetic architecture of soybean resistance to the stink bug complex
Martins, Emanoel Sanches
Glycine max
Glycine max
GWAS
GWAS
Mapeamento de QTLs
QTL mapping
QTL validation
Resistance to insects
Resistência a insetos
Validação de QTLs
title_short Revealing the genetic architecture of soybean resistance to the stink bug complex
title_full Revealing the genetic architecture of soybean resistance to the stink bug complex
title_fullStr Revealing the genetic architecture of soybean resistance to the stink bug complex
title_full_unstemmed Revealing the genetic architecture of soybean resistance to the stink bug complex
title_sort Revealing the genetic architecture of soybean resistance to the stink bug complex
author Martins, Emanoel Sanches
author_facet Martins, Emanoel Sanches
author_role author
dc.contributor.none.fl_str_mv Pinheiro, Jose Baldin
dc.contributor.author.fl_str_mv Martins, Emanoel Sanches
dc.subject.por.fl_str_mv Glycine max
Glycine max
GWAS
GWAS
Mapeamento de QTLs
QTL mapping
QTL validation
Resistance to insects
Resistência a insetos
Validação de QTLs
topic Glycine max
Glycine max
GWAS
GWAS
Mapeamento de QTLs
QTL mapping
QTL validation
Resistance to insects
Resistência a insetos
Validação de QTLs
description Damage caused by the stink bug complex in soybean has exceeded the figure of millions of dollars annually. Cultivating extensive areas, the damage due to these insects has increased, reducing the gains in production. Among the insects control, resistant cultivars to the stink bug complex may be an alternative to the use of insecticides. It is known that this resistance has a quantitative nature and is thus controlled by several genes. In this way, strategies that aim to clarify the control of these insects become overpowering for the future of soybeans. To this end, the objective of this project was to identify and elucidate the genetic architecture of soybean resistance to the stink bug complex. In the first study, we seek to map regions of resistance and elucidate the interactions between QTLs and environments involved in resistance to the stink bug complex on soybean, in a population of recombinant inbred lines (RILs). For this purpose, a population of 256 RILs were used, developed from the cross between IAC-100 (resistant) and CD-215 (susceptible). The experiments were carried out at the ESALQ experimental area in the city of Piracicaba, SP, during the seasons 2012/2013, 2013/2014, 2014/2015, 2015/2016, 2016/2017, 2017/2018, and 2018/2019. We use an alpha-lattice 10 x 26, with three replications as the experimental design. Nine traits associated with resistance to the stink bug complex and agronomic performance were evaluated. For genotyping of RILs, the genotyping technique by sequencing (Genotyping-by- Sequencing) was used. Subsequently, with the data obtained and the analyzes carried out, we found a total of seven significant QTLs, 5 of which were considered as stable QTLs and with potential for use in marker assisted selection. Additionally, in this first study, we developed an epistasis study using the SPAEML software, in which we conclude that the size of the studied population (n = 256) is too small to quantify epistatic effects. In the second study, we developed a work aimed to validate the regions found by the QTL mapping through a genomic wide association study. A soybean breeding panel composed of 299 lines, obtained from a multiparental crossing, was evaluated. This population was evaluated during the years 2018/2019 and 2019/2020, in the experimental area of ESALQ in a 16x19 alpha-lattice design with three replications. We evaluated traits that had significant QTLs in the QTL mapping. Genotypic data were obtained by genotyping by sequencing. With the data obtained, we calculated the means adjusted through mixed models and subsequently performed the GWAS to validate the regions of resistance to the stinkbug complex. A total of 22 QTNs were found, with three regions validating the QTLs found in the previous mapping. For our studies, chromosomes 1, 6, and 15 appear as regions with possible candidate resistance genes and with great potential to assist breeding programs to decide for resistant cultivars.
publishDate 2021
dc.date.none.fl_str_mv 2021-08-27
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/doctoralThesis
format doctoralThesis
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language eng
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dc.rights.driver.fl_str_mv Liberar o conteúdo para acesso público.
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Liberar o conteúdo para acesso público.
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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dc.publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
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reponame:Biblioteca Digital de Teses e Dissertações da USP
instname:Universidade de São Paulo (USP)
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