Two QTLs govern the resistance to Sclerotinia minor in an interspecific peanut RIL population

Sclerotinia blight is a soilborne disease caused by Sclerotinia minor Jagger and can produce severe decrease in yield. Cultural management strategies and chemical treatment are not completely effective; therefore, growing peanut-resistant varieties is likely to be the most effective control method for this disease. Sclerotinia blight resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring Sclerotinia blight resistance within a tetraploid genetic background, this study evaluated a population of recombinant inbred lines (RIL) with introgressed genes from three wild diploid species: A. cardenasii, A. correntina, and A. batizocoi. Two consistent quantitative trait loci (QTLs), qSbIA04 and qSbIB04 located on chromosomes A04 and B04, respectively, were identified. The QTL qSbIA04 was mapped at 56.39 cM explaining 29% of the phenotypic variance and qSbIB04 was mapped at 13.38 cM explaining 22% of the overall phenotypic variance

Mitogenome and Nuclear-encoded Fungicide-target Genes of Thecaphora frezii - Causal Agent of Peanut Smut

Background: Thecaphora frezii Carranza and Lindquist causes smut disease in peanut (Arachis hypogaea L.) resulting in up to 35% yield losses. Fungicides have shown ineffective in controlling the disease; whereas research on the molecular basis of that fungicide resistance has been hindered because of the lack of genetic information about T. frezii. The goal of this work was to provide molecular information about fungicide-target loci in T. frezii, including its mitochondrial genome (mitogenome) and critical nuclear-encoded genes. Results: Here we report the complete annotated mitogenome of T. frezii, a 123,773 bp molecule containing the standard 14 genes that form part of mitochondrial complexes I, III, IV and V, 22 transfer RNAs, small and large subunits of ribosomal RNA, DNA polymerase, ribonuclease P, GII-reverse transcriptase/maturase, nine hypothetical open-reading frames and homing endonucleases (LAGLIDADG, GIY-YIG, HEG). In addition, we report the full-length cDNA sequence of T. frezii cytochrome b (cob) and cytochrome oxidase 1 (cox1) genes; as well as partial sequences of T. frezii succinate dehydrogenase (sdhb), ergosterol biosynthesis (Erg4), cytochrome P450 (cyp51), and beta tubulin (β-tubulin) genes, which are respective targets of strobilurins, quinone oxidation inhibitors, triazoles and beta-tubulin inhibitor fungicides commonly used in the peanut crop. Translation of cob and sdhb genes in this particular T. frezii isolate suggests potential resistance to strobilurin and carboxamide fungicides. Conclusion: The mitogenome and nuclear-encoded gene sequences presented here provide the molecular tools to research T. frezii fungicide-target loci

Introgression of peanut smut resistance from landraces to elite peanut cultivars (\u3ci\u3eArachis hypogaea\u3c/i\u3e L.)

Smut disease caused by the fungal pathogen Thecaphora frezii Carranza & Lindquist is threatening the peanut production in Argentina. Fungicides commonly used in the peanut crop have shown little or no effect controlling the disease, making it a priority to obtain peanut varieties resistant to smut. In this study, recombinant inbred lines (RILs) were developed from three crosses between three susceptible peanut elite cultivars (Arachis hypogaea L. subsp. hypogaea) and two resistant landraces (Arachis hypogaea L. subsp. fastigiata Waldron). Parents and RILs were evaluated under high inoculum pressure (12000 teliospores g-1 of soil) over three years. Disease resistance parameters showed a broad range of variation with incidence mean values ranging from 1.0 to 35.0% and disease severity index ranging from 0.01 to 0.30. Average heritability (h2) estimates of 0.61 to 0.73 indicated that resistance in the RILs was heritable, with several lines (4 to 7 from each cross) showing a high degree of resistance and stability over three years. Evidence of genetic transfer between genetically distinguishable germplasm (introgression in a broad sense) was further supported by simple-sequence repeats (SSRs) and Insertion/Deletion (InDel) marker genotyping. This is the first report of smut genetic resistance identified in peanut landraces and its introgression into elite peanut cultivars

Genetic mapping and QTL analysis for peanut smut resistance

Background: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. Results: A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. Conclusions: A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.Fil: de Blas, Francisco Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Bruno, Cecilia Ines. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Arias, Renee S.. National Peanut Research Laboratory; Estados UnidosFil: Ballén Taborda, Carolina. University of Georgia; Estados UnidosFil: Mamaní, Eva Maria Celia. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Oddino, Claudio Marcelo. Universidad Nacional de Río Cuarto; ArgentinaFil: Rosso, Melina. No especifíca;Fil: Costero, Beatriz. Universidad Nacional de Córdoba; ArgentinaFil: Bressano, Marina. Universidad Nacional de Córdoba; ArgentinaFil: Soave, Juan H.. No especifíca;Fil: Soave, Sara Josefina. No especifíca;Fil: Buteler, Mario I.. No especifíca;Fil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Massa, Alicia N.. National Peanut Research Laboratory; Estados Unido

First draft genome of \u3ci\u3eThecaphora frezii\u3c/i\u3e, causal agent of peanut smut disease

Objectives: The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the pathogen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics of the pathogen. Knowing the genome of T. frezii will help analyze potential variants of this pathogen and contribute to develop enhanced peanut germplasm with broader and long-lasting resistance. Data description: Thecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7) was obtained from a single hyphal-tip culture, its DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq6000 (Nova). Data from both sequencing platforms were combined and the de novo assembling estimated a 29.3 Mb genome size. Completeness of the genome examined using Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the assembly had 84.6% of the 758 genes in fungi_odb10

First draft genome of Thecaphora frezii, causal agent of peanut smut disease

Objectives: The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the pathogen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics of the pathogen. Knowing the genome of T. frezii will help analyze potential variants of this pathogen and contribute to develop enhanced peanut germplasm with broader and long-lasting resistance. Data description: Thecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7) was obtained from a single hyphal-tip culture, its DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq6000 (Nova). Data from both sequencing platforms were combined and the de novo assembling estimated a 29.3 Mb genome size. Completeness of the genome examined using Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the assembly had 84.6% of the 758 genes in fungi_odb10.Instituto de Patología VegetalFil: Arias, Renee S. USDA-ARS National Peanut Research Laboratory (NPRL); Estados UnidosFil: Conforto, Erica Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Conforto, Erica Cinthia. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Orner, Valerie A. USDA-ARS National Peanut Research Laboratory (NPRL); Estados UnidosFil: Carloni, Edgardo José. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales; ArgentinaFil: Soave, Juan H. El Carmen S.A.; ArgentinaFil: Massa, Alicia N. USDA-ARS National Peanut Research Laboratory (NPRL); Estados UnidosFil: Lamb, Marshall C. USDA-ARS National Peanut Research Laboratory (NPRL); Estados UnidosFil: Bernanrdi Lima, Nelson. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Bernanrdi Lima, Nelson. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Rago, Alejandro Mario. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones Agropecuarias (CIAP); ArgentinaFil: Rago, Alejandro Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin

Two QTLs govern the resistance to Sclerotinia minor in an interspecific peanut RIL population

Sclerotinia blight is a soilborne disease caused by Sclerotinia minor Jagger and can produce severe decrease in yield. Cultural management strategies and chemical treatment are not completely effective; therefore, growing peanut-resistant varieties is likely to be the most effective control method for this disease. Sclerotinia blight resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring Sclerotinia blight resistance within a tetraploid genetic background, this study evaluated a population of recombinant inbred lines (RIL) with introgressed genes from three wild diploid species: A. cardenasii, A. correntina, and A. batizocoi. Two consistent quantitative trait loci (QTLs), qSbIA04 and qSbIB04 located on chromosomes A04 and B04, respectively, were identified. The QTL qSbIA04 was mapped at 56.39 cM explaining 29% of the phenotypic variance and qSbIB04 was mapped at 13.38 cM explaining 22% of the overall phenotypic variance.Fil: Rosso, Melina H.. No especifíca;Fil: de Blas, Francisco Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Massa, Alicia N.. No especifíca;Fil: Oddino, Claudio Marcelo. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; ArgentinaFil: Giordano, Damian Francisco. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Arias, Renee S.. No especifíca;Fil: Soave, Juan H.. No especifíca;Fil: Soave, Sara J.. No especifíca;Fil: Buteler, Mario I.. No especifíca;Fil: Bressano, Marina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentin

Archivo adicional 8 de Mapeo genético y análisis QTL para la resistencia al tizón del cacahuete

Additional file 8: Custom UNIX script for filtering the genotyping data generated in this study.Archivo adicional 8: Script UNIX personalizado para filtrar los datos de genotipado generados en este estudioFil: De Blas, Francisco Javier. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: De Blas, Francisco Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil: Bruno, Cecilia I. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Bruno, Cecilia I. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Arias, René S. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: Ballén-Taborda, Carolina. Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia; Estados Unidos.Fil: Mamani, Eva. Instituto Nacional Tecnología Agropecuaria; Argentina.Fil: Odinno, Claudio. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Odinno, Claudio. Criadero El Carmen; Argentina.Fil: Rosso, Melina. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Rosso, Melina. Criadero El Carmen; Argentina.Fil: Costero, Beatriz P. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Bressano, Marina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Soave, Juan H. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Soave, Juan H. Criadero El Carmen; Argentina.Fil: Soave, Sara J. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Soave, Sara J. Criadero El Carmen; Argentina.Fil: Buteler, Mario I. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Buteler, Mario I. Criadero El Carmen; Argentina.Fil: Seijo, J. Guillermo. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentina.Fil: Seijo, J. Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica del Nordeste; Argentina.Fil: Massa, Alicia N. USDA-ARS-National Peanut Research Laboratory; Estados Unidos

Genotyping tools and resources to assess peanut germplasm: Smut-resistant landraces as a case study

Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.Fil: Massa, Alicia N.. National Peanut Research Laboratory; Estados UnidosFil: Bressano, Marina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Fitopatología y Fisiología Vegetal; ArgentinaFil: Soave, Juan H.. Criadero El Carmen; ArgentinaFil: Buteler, Mario I.. Criadero El Carmen; ArgentinaFil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Sobolev, Victor S.. National Peanut Research Laboratory; Estados UnidosFil: Orner, Valerie A.. National Peanut Research Laboratory; Estados UnidosFil: Oddino, Claudio Marcelo. Criadero El Carmen; ArgentinaFil: Soave, Sara J.. Criadero El Carmen; ArgentinaFil: Faustinelli, Paola Carmen. National Peanut Research Laboratory; Estados UnidosFil: de Blas, Francisco Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Lamb, Marshall C.. National Peanut Research Laboratory; Estados UnidosFil: Arias, Renee S.. National Peanut Research Laboratory; Estados Unido

Smut disease incidence and disease index mean, standard error (SE), and range for the parental lines (P1, P2) and generations of RILs from the three peanut corsses: JS31411 (I), JS34212 (II), and JS35112 (III).

Smut disease incidence and disease index mean, standard error (SE), and range for the parental lines (P1, P2) and generations of RILs from the three peanut corsses: JS31411 (I), JS34212 (II), and JS35112 (III).Fil: Bressano, Marina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Massa, Alicia N. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: Arias, René S. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: De Blas, Francisco Javier. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: De Blas, Francisco Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil: Odinno, Claudio. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Odinno, Claudio. Criadero El Carmen; Argentina.Fil: Faustinelli, Paola C. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: Soave, Sara J. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Soave, Sara J. Criadero El Carmen; Argentina.Fil: Soave, Juan H. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Soave, Juan H. Criadero El Carmen; Argentina.Fil: Pérez Flores, María Antonieta. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Sobolev, Víctor S. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: Lamb, Marshall C. USDA-ARS-National Peanut Research Laboratory; Estados Unidos.Fil: Balzarini, Mónica. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina.Fil: Buteler, Mario I. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; Argentina.Fil: Buteler, Mario I. Criadero El Carmen; Argentina.Fil: Seijo, J. Guillermo. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentina.Fil: Seijo, J. Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica del Nordeste; Argentina