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The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). Th...


Worthington, MargaretEbina, MasumiYamanaka, NaokiHeffelfinger, ChristopherQuintero, ConstanzaZapata, Yeny PatriciaPérez, Juan GuillermoSelvaraj, MichaelIshitani, ManabuDuitama, JorgeHoz, Juan Fernando de laRao, Idupulapati M.Dellaporta, Stephen L.Tohme, Joseph M.Arango, Jacobo[Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola]Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola

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
Rao, Idupulapati M.Ishitani, ManabuMiles, John W.Peters, MichaelTohme, Joseph M.Arango, JacoboMoreta, Danilo ELópez, HernánCastro, AracelyHoek, Rein van derMartens, Siriwan D.Hyman, GlennTapasco, JeimarDuitama, JorgeSuárez Baron, HaroldBorrero, GonzaloNúñez, JonathanHartmann, KatharinaDomínguez, MoralbaSotelo Cabrera, Mauricio EfrenVergara, DanielLavelle, PatrickSubbaraoa, Guntur V.Rincón, ÁlvaroPlazas, CamiloMendoza, ReynaldoRathjen, LenaKarwat, HannesCadisch, Georg[Climate-smart crop-livestock systems for smallholders in the tropics: integration of new forage hybrids to intensify agriculture and to mitigate climate change through regulation of nitrification in soil]Climate-smart crop-livestock systems for smallholders in the tropics: integration of new forage hybrids to intensify agriculture and to mitigate climate change through regulation of nitrification in soil
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

Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic region...


Pulido Tamayo, SergioDuitama, JorgeMarchal, Kathleen[EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis]EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties wit...


Lobaton, Juan DavidMiller, TamaraGil, JuanitaAriza, DanielHoz, Juan Fernando de laSoler Garzón, AlvaroBeebe, Stephen E.Duitama, JorgeGepts, PaulRaatz, Bodo[Resequencing of common bean identifies regions of inter- gene pool introgression and provides comprehensive resources for molecular breeding]Resequencing of common bean identifies regions of inter- gene pool introgression and provides comprehensive resources for molecular breeding

Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 mi...


Fuentes, Roven RommelChebotarov, DmytroDuitama, JorgeSmith, SeanHoz, Juan Fernando de laMohiyuddin, MarghoobWing, Rod A.McNally, Kenneth L.Tatarinova, TatianaGrigoriev, AndreyMauleon, RamilAlexandrov, Nickolai[Structural variants in 3000 rice genomes]Structural variants in 3000 rice genomes

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

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