In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

Background: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was~88 kbp, while for the Andean gene pool was~395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches

Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean

Genes related to the response to drought stress in leaf and root tissue of drought-susceptible (DS) and tolerant (DT) genotypes were characterized by RNA-Seq. In total, 54,750 transcripts, representative of 28,590 genes, were identified; of these, 1,648 were of high-fidelity (merge of 12 libraries) and described for the first time in the Andean germplasm. From the 1,239 differentially expressed genes (DEGs), 458 were identified in DT, with a predominance of genes in categories of oxidative stress, response to stimulus and kinase activity. Most genes related to oxidation-reduction terms in roots were early triggered in DT (T75) compared to DS (T150) suggestive of a mechanism of tolerance by reducing the damage from ROS. Among the KEGG enriched by DEGs up-regulated in DT leaves, two related to the formation of Sulfur-containing compounds, which are known for their involvement in tolerance to abiotic stresses, were common to all treatments. Through qPCR, 88.64% of the DEGs were validated. A total of 151,283 variants were identified and functional effects estimated for 85,780. The raw data files were submitted to the NCBI database. A transcriptome map revealed new genes and isoforms under drought. These results supports a better understanding of the drought tolerance mechanisms in beans

KirstLab/scrnaseq_medicago_A17_sunn4

<p>Source code to reproduce the analysis described by Pereira et al., 2023 in the paper " The Interplay of Auxin and Cytokinin Gene Activation and Degradation Directs Cell Lineage Transitions in Nodule Development of <em>Medicago truncatula</em> ".</p&gt

Transcriptome analysis and gene expression of common bean (Phaseolus vulgaris L.) under abiotic stress

Submitted by Marlene Santos ([email protected]) on 2019-08-20T17:06:15Z No. of bitstreams: 2 Dissertação - Wendell Jacinto Pereira - 2016.pdf: 4635252 bytes, checksum: 0d54265ef07d542384b6eb5a558dd96e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Approved for entry into archive by Luciana Ferreira ([email protected]) on 2019-08-21T10:26:04Z (GMT) No. of bitstreams: 2 Dissertação - Wendell Jacinto Pereira - 2016.pdf: 4635252 bytes, checksum: 0d54265ef07d542384b6eb5a558dd96e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Made available in DSpace on 2019-08-21T10:26:04Z (GMT). No. of bitstreams: 2 Dissertação - Wendell Jacinto Pereira - 2016.pdf: 4635252 bytes, checksum: 0d54265ef07d542384b6eb5a558dd96e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-03-08OutroThe common bean (Phaseolus vulgaris L.) is an important foodstuff strongly associated with an issue if global food security. Among the factors that affect their agricultural production, abiotic stress episodes listed as high risk and impact, can restrict the area under cultivation and crop yields. The characterization of high-throughput differential gene expression involved in plant response to abiotic stresses enables profile the genes, and the metabolic pathways, involved in the mechanisms of tolerance to abiotic stresses. In this study, the expression of genes related to response to drought stress in leaf and root tissue of two contrasting common bean genotypes for stress tolerance was evaluated by RNA-Seq. A new Phaseolus vulgaris transcriptome was built featuring 1,668 new loci and 23,169 new isoforms. In all, 54,807 transcripts were identified, found being distributed in 28,640 genes. Through the edgeR package (Bioconductor), they determined by differential expression analysis of leaf and root 1,242 differentially expressed genes. Of these, 458 genes had different expression in tolerant genotype (191 up-regulates and 267 down-regulated) when compared to the sensitive genotype. Functional annotation revealed in tolerant genotype predominance of genes in the categories enriched oxidoreductase activity, oxidation-reduction process, regulation of gene expression, regulation of macromolecule metabolic process and dioxygenase activity. By qPCR, of the 15 DEGs identified via RNA-Seq and selected for characterization, 74.42% were validated for differential expression. Additionally, a total of 151,283 variants were identified, of which 135,167 are SNPs and 16,115 are indels. Through functional annotation, performed in SnpEff v.4.2, were identified 330,378 effects caused by variants. The data used in this study were deposited in the Sequence Read Archive (NCBI) and will be available. The results of this study contribute to the expansion of knowledge about the gene mechanisms, as well as their functional variants, related to abiotic stresses tolerance in beans.O feijoeiro comum (Phaseolus vulgaris L.) é um gênero alimentício de primeira necessidade fortemente associado à segurança alimentar mundial. Dos fatores que afetam a sua produção, episódios de estresses abióticos, como a seca, figuram como de grande risco e impacto, podendo restringir as áreas de cultivo e o rendimento das lavouras. A caracterização em larga escala da expressão diferencial de genes envolvidos na resposta da planta aos estresses abióticos possibilita traçar o perfil dos genes, bem como das rotas metabólicas, envolvidos nos mecanismos de tolerância aos estresses abióticos. Nesse estudo, a expressão de genes relacionados à resposta aos estresses abióticos em tecido foliar e radicular de dois genótipos de feijoeiro comum contrastantes quanto à tolerância ao estresse de seca foi avaliada pela análise de RNA-Seq. Um novo transcritoma de feijoeiro comum foi construído apresentando 1668 novos loci e 23 169 novas isoformas. Ao todo foram identificados 54 807 transcritos distribuídos em 28 640 genes. A análise de expressão diferencial em tecido foliar e radicular foi realizada através do pacote edgeR, Bioconductor, possibilitando identificar 1242 genes diferencialmente expressos (GDE). Destes, 458 genes tiveram expressão diferenciada no genótipo tolerante (191 induzidos e 267 reprimidos) quando comparado ao genótipo sensível. A anotação funcional revelou no genótipo tolerante um predomínio de genes nas categorias enriquecidas oxidoreductase activity, oxidation-reduction process, regulation of gene expression, regulation of macromolecule metabolic process e dioxygenase activity. Por meio da técnica de qPCR, dos 15 GDEs selecionados para caracterização, 74,42% foram validados quanto à expressão diferencial. Adicionalmente, um total de 151 283 variantes foram identificadas, sendo 135 167 SNPs e 16 115 Indels. A anotação e predição de efeitos das variantes foi realizada com SnpEff v.4.2, onde foram identificados 330 378 efeitos putativos para as variantes encontradas. Os dados utilizados nesse estudo serão disponibilizados no Sequence Read Archive (NCBI). Os resultados deste estudo contribuem para a ampliação do conhecimento sobre os mecanismos gênicos, bem como das variantes funcionais, relacionados com a tolerância à estresses abióticos em feijoeiro comum

USO DE GOMA DE CAJUEIRO EM SUBSTITUIÇÃO AO ÁGAR EM MEIO DE CULTURA

O cajueiro da espécie Anacardium occidentale produz exsudato (goma) com grande quantidade de polissacarídeos e podem ser encontradas em várias regiões do Brasil. A estrutura e composição da goma do cajueiro apresenta grande potencial para aplicações biotecnológicas como fonte de polissacarídeos, devido a sua grande quantidade de carboidratos. Nesse trabalho avaliou-se a viabilidade da utilização do polissacarídeo de goma de cajueiro (PEJU) como substituto para o ágar em meios de cultura sólidos, utilizados em microbiologia. Definiu-se a proporção mais adequada entre o PEJU e o ágar, e os parâmetros avaliados para a produção dos meios foram: perda de umidade, alteração da textura durante armazenamento e a capacidade de promover o crescimento de microrganismos. A substituição do ágar pelo PEJU nos meios de cultura apresentou boa eficiência, promovendo condições de crescimento microbiano similares aos meios controle

USO DE GOMA DE ANGICO EM SUBSTITUIÇÃO AO ÁGAR EM MEIO DE CULTURA

O angico da espécie Anadenanthera macrocarpa, encontrado em várias regiões do país e principalmente no cerrado produz exsudato gomoso cuja composição apresenta grande quantidade de polissacarídeos. Os polissacarídeos da goma do angico apresentam grande potencial para aplicações biotecnológicas, seja por ser fonte de carboidratos complexos, seja por suas propriedades funcionais como, por exemplo, sua capacidade de formar filmes e géis. Nesse trabalho avaliou-se a viabilidade da utilização da goma do angico (pegico) como substituto para o ágar em meios de cultura sólidos, utilizados comumente em microbiologia. Definiu-se a proporção mais adequada entre o pegico e o ágar, e os parâmetros avaliados para comparação foram: perda de umidade, alteração da textura durante armazenamento e a capacidade de promover o crescimento de microrganismos. A substituição do ágar pelo pegico nos meios de cultura foi de boa eficiência, promovendo condições de crescimento microbiano similares aos meios de cultura controle.&nbsp

A drought transcriptional map reveals new genes for the Mesoamerican common bean germplasm. [Complementary files].

This repository contains annotation files for <i>Phaseolus vulgaris</i> L. (Common bean) transcriptome assembly under drought conditions, including gene and exon annotations, non-coding RNAs prediction, ORFs prediction and variants annotations. The files are originated in analyse of RNA-Seq data. <br