Ricardo Abdelnoor - Academia.edu (original) (raw)

Papers by Ricardo Abdelnoor

Soybean is the legume of most economic importance in the international market, with world product... more Soybean is the legume of most economic importance in the international market, with world production of almost two hundred and thirty million tons in the 2007/2008 harvest. The Brazil appears as the largest exporter of the product in the world, with about twenty-five percent of the world production. In 2007 the brazilian government started the GENOSOJA project with the main objective of discover new treats to improve the plant production process, emphasizing in stresses that affect the national production like the occurrence of droughts, pests attacks and the Asian rust disease. This work is inserted in the GENOSOJA scope and aims to generate bioinformatics tools to integrate the public soybean data like ESTS and genomic sequences, with all data generated during the project like SuperSAGE tags, MicroRNAs and subtractive libraries sequences analysis. These sequences were generated using high throughput sequencing technologies and for each analysis a specific pipeline have to be imple...

Meloidogyne javanica causing root-knot nematode in soybean is an important problem in soybean are... more Meloidogyne javanica causing root-knot nematode in soybean is an important problem in soybean areas, leading to several yield losses. Some accessions have been identified carrying resistance loci to this nematode specie. In this study, a set of 317 soybean accessions were characterized for resistance to M. javanica. Genome-wide association study (GWAS) was performed using SNPs from genotyping-by-sequencing (GBS), and a region of 29.2 Kbp on chromosome 13 was identified. The haplotype analysis showed that SNPs were able to discriminate susceptible and resistant accessions, leading to 25 accessions sharing the resistance locus. Furthermore, 5 accessions may be new M. javanica resistance sources. The screening of the SNPs in the USDA soybean germplasm showed that several accessions previous reported as resistance to other nematodes also showed the resistance haplotype on chromosome 13. High levels of concordance among the phenotypes of Brazilian cultivars and the SNPs in chromosome 13 ...

Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous) ... more Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous) is an important soybean disease, which has been responsible for severe losses in the past. The main strategy to control this fungus is through the introgression of resistance genes. So far, five main loci have been associated with resistance to Southern stem canker. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers useful in breeding programs. Results We characterized the response to Southern stem canker infection in a panel of 295 accessions from different regions of the world including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped and we identified marker loci associated with Diaporthe aspalathi resistance using GWAS analysis. We id...

Molecular Breeding

Soybean [Glycine max (L.) Merrill] is one of the most important traded commodities for the world’... more Soybean [Glycine max (L.) Merrill] is one of the most important traded commodities for the world’s economy. However, soybean cultivation is often affected by biotic and abiotic factors that prevent the crop from attaining its full yield potential. With the advent of new tools for next-generation sequencing, the genomic knowledge gained from the study of this major oilseed crop has increased considerably in recent years. In this study, we performed a genotypic characterization of 188 plant introductions (PIs) and five cultivars using a genotyping-by-sequencing (GBS) approach and a phenotypic characterization for resistance/tolerance to the southern root-knot nematode, Meloidogyne incognita. We then performed a genome-wide association study (GWAS) for this important trait. From 46,196 SNP markers identified and validated on this set of genotypes, three were significantly associated with nematode resistance. Remarkably, all of these were in a single, very small (3.4 kb) region of chromosome 10. Most lines (48 out of 57) with the highest level of resistance shared the haplotype composed of the alleles associated with resistance at these three SNP loci. Interestingly, nine of the lines exhibiting a high level of resistance did not exhibit the “resistant haplotype” on Gm10. This suggests either that recombination has broken the association between the SNPs and the resistance locus or that resistance is conferred by a different locus altogether. In the latter case, these lines represent a putative alternative source of resistance, an important information for breeding programs.

BMC genomics, Jan 13, 2016

Soybean [Glycine max (L.) Merrill] is one of the most important legumes cultivated worldwide, and... more Soybean [Glycine max (L.) Merrill] is one of the most important legumes cultivated worldwide, and Brazil is one of the main producers of this crop. Since the sequencing of its reference genome, interest in structural and allelic variations of cultivated and wild soybean germplasm has grown. To investigate the genetics of the Brazilian soybean germplasm, we selected soybean cultivars based on the year of commercialization, geographical region and maturity group and resequenced their genomes. We resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, p...

Crop Breeding and Applied Biotechnology, 2013

In this study, the influence of genetic background on the resistance level of a soybean line carr... more In this study, the influence of genetic background on the resistance level of a soybean line carrying Rpp2, Rpp4, and Rpp5 was evaluated by backcrossing it with a susceptible variety. It was also evaluated eight lines which carry these Rpp genes against five Asian soybean rust (ASR) isolates, in order to determine the likely range of resistance against ASR isolates differing in pathogenicity. The results indicated that a high level of resistance against various ASR isolates could be retained in lines carrying the three Rpp genes in susceptible genetic backgrounds, although minor influences of plant genetic background and ASR pathogenicity to the ASR resistance could occur. Thus, lines with the pyramided three Rpp genes should be effective against a complex pathogen population consisting of diverse Phakopsora pachyrhizi isolates.

BMC Plant Biology, 2014

Background: Many previous studies have shown that soybean WRKY transcription factors are involved... more Background: Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of WRKY genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to P. pachyrhizi were identified. Results: As a result of a soybean genomic databases search, 182 WRKY-encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to P. pachyrhizi infection were identified using superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight WRKY genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and/or stronger compared with a susceptible genotype in response to P. pachyrhizi infection. Soybean somatic embryos were transformed in order to overexpress or silence WRKY genes. Embryos overexpressing a WRKY gene were obtained, but they were unable to convert into plants. When infected with P. pachyrhizi, the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants. Conclusions: The present study reports a genome-wide annotation of soybean WRKY family. The participation of some members in response to P. pachyrhizi infection was demonstrated. The results contribute to the elucidation of gene function and suggest the manipulation of WRKYs as a strategy to increase fungal resistance in soybean plants.

Pesquisa Agropecuária Brasileira, 2012

O objetivo deste trabalho foi avaliar, por meio de enzimas marcadoras, a indução de resistência à... more O objetivo deste trabalho foi avaliar, por meio de enzimas marcadoras, a indução de resistência à ferrugem-asiática-da-soja em genótipos de soja contrastantes quanto à suscetibilidade a Phakopsora pachyrhizi. Aproteína total e as atividades de cinco enzimas marcadoras da indução de resistência (lipoxigenases, peroxidases, fenilalanina amônia-liase, quitinases e β-1, 3-glucanases) foram avaliadas em extratos de folhas de plantas de soja dos genótipos Embrapa 48 (suscetível) e PI 561356 (resistente), submetidas à inoculação ou não com o patógeno. Foram observadas respostas de defesa discrepantes entre os dois genótipos e entre os tempos de coleta (12, 72 e 168 horas após inoculação). A resposta de indução dessas enzimas assemelha-se à defesa bifásica, para Embrapa 48, e é consistente com o observado para outros patossistemas. No entanto, o genótipo PI 561356 respondeu com diminuição da concentração de proteína total e das atividades enzimáticas, o que indica redução do metabolismo ger...

Fitopatologia Brasileira, 2003

Macrophomina phaseolina has been considered one of the most prevalent soybean (Glycine max) patho... more Macrophomina phaseolina has been considered one of the most prevalent soybean (Glycine max) pathogens in Brazil. No genetic resistance has been determined in soybean and very little is known about the genetic diversity of this pathogen in tropical and sub-tropical regions. Fifty-five isolates from soybean roots were collected in different regions and analyzed through RAPD for genetic diversity. The UPGMA cluster analysis for 74 loci scored permitted identification of three divergent groups with an average similarity of 99%, 92% and 88%, respectively. The three groups corresponded to 5.45%, 59.95% and 34.6%, respectively of all isolates used. A single plant had three different haplotypes, while 10.9% of the analyzed plants had two different haplotypes. In another study the genetic similarity was evaluated among isolates from different hosts [soybean, sorghum (Sorghum bicolor), sunflower (Helianthus annuus), cowpea (Vigna unguiculata), corn (Zea mays) and wheat (Triticum aestivum)] as...

TAG Theoretical and Applied Genetics, 2001

Resistance of soybean [Glycine max (L.) Merr.] to cyst nematode (SCN) (Heterodera glycines Ichino... more Resistance of soybean [Glycine max (L.) Merr.] to cyst nematode (SCN) (Heterodera glycines Ichinohe), one of the most destructive pathogens affecting soybean, involves a complex genetic system. The identification of QTLs associated with SCN resistance may contribute to the understanding of such system. The objective of this work was to identify and map QTLs for resistance to SCN Race 14 with the aid of molecular markers. BC 3 F 2:3 and F 2:3 populations, both derived from an original cross between resistant cv. Hartwig and the susceptible line BR-92-31983 were screened for resistance to SCN Race 14. Four microsatellite (Satt082, Sat_001, Satt574 and Satt301) and four RAPD markers (OPAA-11 795 , OPAE-08 837 , OPR-07 548 and OPY-07 2030) were identified in the BC 3 F 2:3 population using the bulked segregant analysis (BSA) technique. These markers were amplified in 183 F 2:3 families and mapped to a locus that accounts for more than 40% of the resistance to SCN Race 14. Selection efficiency based on these markers was similar to that obtained with the conventional method. In the case of the microsalellite markers, which identify homozygous resistant genotypes, the efficiency was even higher. This new QTL has been mapped to the soybean linkage group D2 and, in conjunction with other QTLs already identified for SCN resistance, will certainly contribute to our understanding of the genetic basis of resistance of this important disease in soybean.

Theoretical and Applied Genetics, 2008

Asian soybean rust (ASR) is caused by the fungal pathogen Phakopsora pachyrhizi Sydow & Sydow. It... more Asian soybean rust (ASR) is caused by the fungal pathogen Phakopsora pachyrhizi Sydow & Sydow. It was Wrst identiWed in Brazil in 2001 and quickly infected soybean areas in several countries in South America. Primary eVorts to combat this disease must involve the development of resistant cultivars. Four distinct genes that confer resistance against ASR have been reported: Rpp1, Rpp2, Rpp3, and Rpp4. However, no cultivar carrying any of those resistance loci has been released. The main objective of this study was to genetically map Rpp2 and Rpp4 resistance genes. Two F 2:3 populations, derived from the crosses between the resistant lines PI 230970 (Rpp2), PI 459025 (Rpp4) and the susceptible cultivar BRS 184, were used in this study. The mapping populations and parental lines were inoculated with a Weld isolate of P. pachyrhizi and evaluated for lesion type as resistant (RB lesions) or susceptible (TAN lesions). The mapping populations were screened with SSR markers, using the bulk segregant analysis (BSA) to expedite the identiWcation of linked markers. Both resistance genes showed an expected segregation ratio for a dominant trait. This study allowed mapping Rpp2 and Rpp4 loci on the linkage groups J and G, respectively. The associated markers will be of great value on marker assisted selection for this trait. Communicated by D. A. Lightfoot.

Proceedings of the National Academy of Sciences, 2003

Plant physiology, 2009

Asian soybean rust is a formidable threat to soybean (Glycine max) production in many areas of th... more Asian soybean rust is a formidable threat to soybean (Glycine max) production in many areas of the world, including the United States. Only five sources of resistance have been identified (Resistance to Phakopsora pachyrhizi1 [Rpp1], Rpp2, Rpp3, Rpp4, and Rpp5). Rpp4 was previously identified in the resistant genotype PI459025B and mapped within 2 centimorgans of Satt288 on soybean chromosome 18 (linkage group G). Using simple sequence repeat markers, we developed a bacterial artificial chromosome contig for the Rpp4 locus in the susceptible cv Williams82 (Wm82). Sequencing within this region identified three Rpp4 candidate disease resistance genes (Rpp4C1-Rpp4C3 [Wm82]) with greatest similarity to the lettuce (Lactuca sativa) RGC2 family of coiled coil-nucleotide binding site-leucine rich repeat disease resistance genes. Constructs containing regions of the Wm82 Rpp4 candidate genes were used for virus-induced gene silencing experiments to silence resistance in PI459025B, confirmin...

Molecular Plant-Microbe Interactions, 2007

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is now established in all major soybea... more Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is now established in all major soybean-producing countries. Currently, there is little information about the molecular basis of ASR–soybean interactions, which will be needed to assist future efforts to develop effective resistance. Toward this end, abundance changes of soybean mRNAs were measured over a 7-day ASR infection time course in mock-inoculated and infected leaves of a soybean accession (PI230970) carrying the Rpp2 resistance gene and a susceptible genotype (Embrapa-48). The expression profiles of differentially expressed genes (ASR-infected compared with the mock-inoculated control) revealed a biphasic response to ASR in each genotype. Within the first 12 h after inoculation (hai), which corresponds to fungal germination and penetration of the epidermal cells, differential gene expression changes were evident in both genotypes. mRNA expression of these genes mostly returned to levels found in mock-inoculated plan...

Journal of Phytopathology, 2001

Journal of Molecular Evolution, 2006

Mitochondrial processes influence a broad spectrum of physiological and developmental events in h... more Mitochondrial processes influence a broad spectrum of physiological and developmental events in higher eukaryotes, and their aberrant function can lead to several familiar disease phenotypes in mammals. In plants, mitochondrial genes directly influence pollen development and the occurrence of male sterility in natural plant populations. Likewise, in animal systems evidence accumulates to suggest important mitochondrial functions in spermatogenesis and reproduction. Here we present evidence for a convergent gene fusion involving a MutS-homologous gene functioning within the mitochondrion and designated Msh1. In only plants and soft corals, the MutS homologue has fused with a homing endonuclease sequence at the carboxy terminus of the protein. However, the endonuclease domains in the plants and the soft corals are members of different groups. In plants, Msh1 can influence mitochondrial genome organization and male sterility expression. Based on parallels in Msh1 gene structure shared by plants and corals, and their similarities in reproductive behavior, we postulate that this convergent gene fusion might have occurred in response to coincident adaptive pressures on reproduction.

Journal of Biomedicine and Biotechnology, 2010

During earlier experiments, an SSR molecular marker (176 Soy HSP) showing high correlation (70%) ... more During earlier experiments, an SSR molecular marker (176 Soy HSP) showing high correlation (70%) with resistance/susceptibility to javanese root-knot nematodeMeloidogyne javanicawas identified in soybean. After being sequenced, results indicated that the SSR 176 Soy HSP marker was inserted in the promoter region ofGmhsp17.6-Lgene. It was also detected in this region that resistant genotypes presented insertions betweenAT(31)andAT(33)in size and susceptible genotypes,AT(9).Gmhsp17.6-Lgene coding region presented a perfect match in amino acid sequence in all soybean genotypes. A ribonuclease protection assay showed thatGmhsp17.6-Lgene mRNA transcripts were present in all genotypes. A real-time relative quantification (qPCR) indicated in the resistant individuals higher mRNA transcripts levels, which presented in the sequencing moreAT(n)insertions. These results suggest that the number ofAT(n)insertions inside this promoter region could modulate up or down gene levels. Those findings c...

Japan Agricultural Research Quarterly: JARQ, 2011

Genetics and Molecular Biology, 2007