Clonación, secuenciación y caracterización bioinformática de candidatos A microRNAs de yuca (Manihot esculenta Crantz Var. Tai 16)

Los microRNAs (miRNAs) son smallRNAs endógenos que regulan la expresión de genes en plantas y animales. Estos RNAs de ~21 nucleótidos son sintetizados a partir de secuencias intrónicas o a partir de genes de microRNAs por la RNA pol II, cuyo precursor forma una estructura tallo y asa, el cual es a su vez procesado por la enzima Dicer 1 hasta secuencias más cortas que son reclutadas por el complejo RISC, el cual dirige la degradación de mRNAs blanco. Estos pequeños transcritos han sido descubiertos mediante predicciones bioinformáticas o mediante su clonación y secuenciación, y se ha visto que los miRNAs en plantas están involucrados en múltiples procesos biológicos, incluyendo diferenciación celular, desarrollo de órganos, cambios de fases, señalización, respuesta a estrés biótico y abiótico, entre otros. Por otro lado, la yuca (Manihot esculenta Crantz) es considerada como uno de los cultivos más importantes en las regiones tropicales del mundo. En este sentido, este estudio representa el primer esfuerzo por identificar miRNAs en yuca a través de una aproximación experimental (clonación y secuenciación) y posterior análisis bioinformático, en el cual se obtuvieron secuencias en 6 familias diferentes, una de las cuales, fue validada como candidato a microRNA basada en el genoma de Ricinus communis. Esta secuencia puede ser un transcrito cuyo origen es a partir de transposones, por lo que se explicaría el porqué está presente en la mayoría de los clones secuenciados y podría estar involucrada con procesos asociados a la fotosíntesis.MicroRNAs (miRNAs) are endogenous smallRNAs that regulate gene expression in plants and animals. These RNAs of ~21 nucleotides are synthesized from intron sequences or microRNA s genes for the RNA pol II, which form a precursor stemloop structure, which is in turn processed by the enzyme Dicer 1 to shorter sequences who are loaded into silencing complex RISC, where directs the degradation of target mRNAs. MiRNAs have been discovered using two basic approaches: bioinformatic prediction and direct cloning and sequencing, and lots of investigations indicate that are involved in multiple biological processes, including stem cell differentiation, organ development, phase change, signalling and response to biotic and abiotic environmental stresses. In other hand, cassava (Manihot esculenta Crantz) is considered one of the most important crops in tropical regions of the world. Thus, this study represents the first effort to identify miRNAs in cassava through an experimental approach (cloning and sequencing) and bioinformatic analysis, in which were obtained sequences in 6 different families, but only one, was validated as a candidate microRNA based on Ricinus communis genome. This sequence could be transcribed from transposons, which explain why it is present in the majority of clones sequenced and this sequence might be involved in processes associated with photosynthesis.Biólogo (a)Pregrad

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding

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

Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars with genetics from this wild accession provided improved food security and reduced use of fungicide sprays. However, this study also highlights the perilous consequences of changes in legal frameworks and attitudes concerning biodiversity. These changes have greatly reduced the botanical collections, seed exchanges, and international collaborations which are essential for the continued diversification of crop genetics and, consequently, the long-term resilience of crops against evolving pests and pathogens and changing climate.The narrow genetics of most crops is a fundamental vulnerability to food security. This makes wild crop relatives a strategic resource of genetic diversity that can be used for crop improvement and adaptation to new agricultural challenges. Here, we uncover the contribution of one wild species accession, Arachis cardenasii GKP 10017, to the peanut crop (Arachis hypogaea) that was initiated by complex hybridizations in the 1960s and propagated by international seed exchange. However, until this study, the global scale of the dispersal of genetic contributions from this wild accession had been obscured by the multiple germplasm transfers, breeding cycles, and unrecorded genetic mixing between lineages that had occurred over the years. By genetic analysis and pedigree research, we identified A. cardenasii–enhanced, disease-resistant cultivars in Africa, Asia, Oceania, and the Americas. These cultivars provide widespread improved food security and environmental and economic benefits. This study emphasizes the importance of wild species and collaborative networks of international expertise for crop improvement. However, it also highlights the consequences of the implementation of a patchwork of restrictive national laws and sea changes in attitudes regarding germplasm that followed in the wake of the Convention on Biological Diversity. Today, the botanical collections and multiple seed exchanges which enable benefits such as those revealed by this study are drastically reduced. The research reported here underscores the vital importance of ready access to germplasm in ensuring long-term world food security.Genome sequence, genotyping, pedigree information, and yield trial data have been deposited in National Center for Biotechnology Information (NCBI), PeanutBase, and USDA Data Repository (NCBI: JADQCP000000000) (14). Datasets S1–S6 are available at USDA Ag Data Commons: https://data.nal.usda.gov/dataset/data-legacy-genetics-arachis-cardenasii-peanut-crop-v2 (17). All other study data are included in the article and/or supporting information

Quantitative Trait Analysis Shows the Potential for Alleles from the Wild Species Arachis batizocoi and A. duranensis to Improve Groundnut Disease Resistance and Yield in East Africa

International audienceDiseases are the most important factors reducing groundnut yields worldwide. In East Africa, late leaf spot (LLS) and groundnut rosette disease (GRD) are the most destructive diseases of groundnut. Limited resistance is available in pure pedigree cultivated groundnut lines and novel sources of resistance are required to produce resistant new varieties. In this work, 376 interspecific lines from 3 different populations derived from crosses with the wild species A. duranensis, A. ipaënsis, A. batizocoi and A. valida were phenotyped for 2 seasons and across 2 locations, Serere and Nakabango, in Uganda. Several genotypes showed a higher yield, a larger seed, an earlier flowering, and similar resistance to the local cultivar checks. Genotypic data was used to construct a linkage map for the AB-QTL population involving the cross between Fleur11 and [A. batizocoi x A. duranensis]4x. This linkage map, together with the phenotypic data was used to identify quantitative trait loci controlling disease resistance. These lines will be useful in combining good agronomic traits and stacking disease resistance to improve the groundnut crop in sub-Saharan Africa

Genetic Mapping of Resistance to Meloidogyne arenaria in Arachis stenosperma: A New Source of Nematode Resistance for Peanut.

Root-knot nematodes (RKN; Meloidogyne sp.) are a major threat to crops in tropical and subtropical regions worldwide. The use of resistant crop varieties is the preferred method of control because nematicides are expensive, and hazardous to humans and the environment. Peanut (Arachis hypogaea) is infected by four species of RKN, the most damaging being M. arenaria, and commercial cultivars rely on a single source of resistance. In this study, we genetically characterize RKN resistance of the wild Arachis species A. stenosperma using a population of 93 recombinant inbred lines developed from a cross between A. duranensis and A. stenosperma. Four quantitative trait loci (QTL) located on linkage groups 02, 04, and 09 strongly influenced nematode root galling and egg production. Drought-related, domestication and agronomically relevant traits were also evaluated, revealing several QTL. Using the newly available Arachis genome sequence, easy-to-use KASP (kompetitive allele specific PCR) markers linked to the newly identified RKN resistance loci were developed and validated in a tetraploid context. Therefore, we consider that A. stenosperma has high potential as a new source of RKN resistance in peanut breeding programs

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