RESUMO
BACKGROUND: Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. METHODS: We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. RESULTS: In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. CONCLUSIONS: We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.
Assuntos
Musa , Filogenia , Musa/genética , Genoma de Planta/genética , Diploide , Recombinação Genética/genéticaRESUMO
Bananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection (CMC) conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7X per accession, resulting in 187,133 SNPs against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker-trait associations (MTAs). The mixed linear model (MLM) revealed four MTAs, while the BLINK and FarmCPU models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A-genome and B-genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement.
RESUMO
La calidad del aire de los ambientes internos puede estar influenciada por distintas partículas suspendidas en la atmósfera (polvo, polen, bacterias, hongos, virus) que pueden causar daños a documentos y presentar reacciones alérgicas en personas que trabajan con éstos. Con este trabajo, se identificaron hasta género los microorganismos presentes en el ambiente del archivo central, Universidad Pedagógica y Tecnológica de Colombia, que podrían causar alergias respiratorias en los trabajadores de esta área. Para las muestras de ambiente se empleó el método de sedimentación en placa utilizando agar papa dextrosa y se midieron temperatura y humedad relativa durante cada muestreo. Asimismo, se aplicó una encuesta a los trabajadores con el fin de conocer sintomatología respiratoria sugestiva que pudieran presentar por el manejo de documentos y se tomaron muestras de fosas nasales a algunos de ellos. Se aislaron del ambiente 14 géneros entre hongos, levaduras y bacterias, y dos categorías de microorganismos no identificadas. Los géneros fúngicos predominantes fueron Mucor spp., y Penicillium spp., con un 36,6% y 27,5%, respectivamente, del total de colonias aisladas. Las formas levaduriformes principalmente del género Rhodotorula, y bacterianas con predominio de formas cocoides fueron aisladas en menor proporción. No se encontró correlación estadísticamente significativa entre el promedio de unidades formadoras de colonia con temperatura y humedad relativa del ambiente. Además, en las muestras de fosas nasales sólo se encontró microbiota normal de nariz, lo cual indica que los síntomas respiratorios sugestivos que presentan los trabajadores no estuvieron influenciados directamente por la presencia de esporas de hongos en el ambiente del archivo central.
Air quality of indoor environments can be influenced by different particles suspended in the atmosphere (dust, pollen, bacteria, fungi, and virus) that could cause damage to documents and induce allergic reactions in people working with these documents. In this work, we identified until genera the microorganisms present in the environment of the central archive of Universidad Pedagógica y Tecnológica de Colombia; specifically those that could cause respiratory allergies to personnel of this area. For the environment samples, we used the open Petri dish sedimentation method using potato dextrose agar, and measured temperature and relative humidity during each sampling. Also, a survey was taken of the workers to record respiratory symptoms that could arise from handling documents. Samples were taken from the nostrils of some of these workers. Fourteen genera among fungi, yeasts, and bacteria, and two non identified categories were isolated from the environment. The predominant fungal genera were Mucor spp. and Penicillium spp. with 36.6% and 27.5% of the total of isolated colonies, respectively. Yeast, mainly Rhodotorula genera, and bacteria with prevalence coccus forms were isolated in smaller proportions. There was not statistically significant correlation among the average of colony forming units and the temperature and relative humidity in the environment. In addition, nostril samples yielded only normal microbiota of the nose, indicating that suggestive respiratory symptoms workers presented are not directly influenced by the presence of fungal spores in the environment at the central archive.