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Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give n...


Duitama, JorgeSilva, AlexanderSanabria, YamidCruz, Daniel FelipeQuintero, ConstanzaBallen, CarolinaLorieux, MathiasScheffler, BrianFarmer, AndrewTorres Castro, Edgar AlonsoOard, JamesTohme, Joseph M.[Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection]Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several ge...


Rebolledo, María CamilaPeña, Alexandra L.Duitama, JorgeCruz, Daniel FelipeGrenier, CécileTohme, Joseph M.[Combining image analysis,genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice]Combining image analysis,genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice
Duitama, JorgeSilva, AlexanderSanabria, YamidCruz, Daniel FelipeQuintero, ConstanzaBallen, CarolinaLorieux, MathiasScheffler, BrianFarmer, AndrewTorres Castro, Edgar AlonsoOard, JamesTohme, Joseph M.[Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection]Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

With the aim to find new sources of resistance to rice hoja blanca (white leaf) disease, transmitted by the insect Tagosodes orizicolus, 660 genotypes were evaluated under greenhouse and field conditions. Seven resistant genotypes were identified, and genomic studies were performed to demonstrate...


Cruz Gallego, MaribelRebolledo, María CamilaCuasquer, Juan B.Cruz, Daniel FelipePeña-Fernández, Alexandra LorenaQuintero, ConstanzaSilva-Córdoba, AlexanderÁlvarez, María FernandaJojoa-Cruz, SebastiánLorieux, MathiasStuart, Jeffrey J.Correa, Fernando[Identification of new sources of resistance to RHBV- rice hoja blanca virus = Identificación de nuevas fuentes de resistencia al virus hoja blanca en arroz-RHBV]Identification of new sources of resistance to RHBV- rice hoja blanca virus = Identificación de nuevas fuentes de resistencia al virus hoja blanca en arroz-RHBV

Background Therecent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective approach to perform high-resolution genomic analysis of entire populations in different species. The central component of all these protocols is the digestion of the ini...


Perea, ClaudiaHoz, Juan Fernando de laCruz, Daniel FelipeLobaton, Juan DavidIzquierdo, PauloQuintero, Juan CamiloRaatz, BodoDuitama, Jorge[Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP]Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP
Rebolledo, María CamilaDingkuhn, MichaelCourtois, BrigitteGibon, YClément-Vidal, ACruz, Daniel FelipeDuitama, JorgeLorieux, MathiasLuquet, D[Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping]Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping

Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis st...


Duitama, JorgeQuintero, Juan CamiloCruz, Daniel FelipeQuintero, ConstanzaHubmann, GeorgFoulquié Moreno, Maria R.Verstrepen, Kevin J.Trevelein, Johan MTohme, Joseph M.[An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments]An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments

NGSEP (Next Generation Sequencing Eclipse Plugin), an integrated framework for analysis of high throughput sequencing reads. The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, indels, and CNVs. NGSEP also provides a user interface for bo...


Cruz, Daniel FelipeHoz, Juan Fernando de laPerea, Claudia SamanthaQuintero, Juan CamiloDuitama, Jorge[NGSEP (Next Generation Sequencing Eclipse Plugin)]NGSEP (Next Generation Sequencing Eclipse Plugin)

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