Analysis of Bgenome derived simple sequence repeat (SSR) markers in Musa spp.

A study was conducted to investigate the genetic variability between 40 Musa genotypes maintained at the Musa germplasm collection of the International Institute for Tropical Agriculture, Ibadan using nine B-genome derived simple sequence repeat (SSR) markers. The nine primers produced reproducible and discrete fragments and generated a total of 23 alleles with an average of 2.1. The hierarchical cluster analysis showed clusters of diploid cultivars separate from triploid ones (with the exception of TMB149 (BB) and TMB131 (AB)). Average gene diversity was He = 0.412, and differentiation, given by the fixation index (FST) was low at 0.131

Validation of an apicoplast genome target for the detection of Plasmodium species using polymerase chain reaction and loop mediated isothermal amplification

AbstractThe genome of the Plasmodium apicoplast, which has a higher copy number compared with current targets for molecular diagnosis of malaria, appears to be a suitable target for detection of submicroscopic infections that are capable of sustaining transmission. Novel primers targeting a conserved segment of the apicoplast (PFC10_AP|0010:rRNA) were designed and used in a number of different high throughput platforms such as single-step PCR (ssPCR), nested PCR (nPCR) and loop-mediated isothermal amplification (LAMP) for parasite detection. Replicates of ten-fold serial dilutions of Plasmodium falciparum 3D7 DNA, with equivalent parasite density ranges of 200 000 to 0.2 parasites/μL, were used to determine the limit of detection and repeatability of each assay. A panel of 184 archived DNA samples extracted from either EDTA whole blood or dried blood spots, from across West Africa and South East Asia was used to determine the diagnostic performance of the assays. All assays amplified the 2 parasites/μL dilution except the ssPCR, which amplified two of the three replicates. Using an 18S rRNA PCR as reference, the sensitivity was 98% (95% CI 93–100%) for the LAMP assay, 87% (95% CI 79–93%) for ssPCR and 100% (95% CI 97–100%) for nPCR. Specificity was 91% (95% CI 83–96%) for LAMP, 82% (95% CI 72–90%) for ssPCR and 66% (95% CI 54–76%) for nPCR. The apicoplast genome-based nPCR detected more positive samples overall than the reference method. Discrepant samples were confirmed as true positives using a probe-based real-time quantitative PCR assay. The results show that the apicoplast genome is a suitable target for molecular diagnosis of malaria

Agronomical and molecular characterization of banana germplasm Caracterização agronômica e molecular de germoplasma de bananeira

The objective of the present work was to characterize banana accessions from the Germplasm Bank at Embrapa Mandioca e Fruticultura Tropical (Brazil), using agronomical, physical and physicochemical characteristics of fruit and simple sequence repeats (SSR) markers. Twenty-six accessions were analyzed, in which high genetic variability was found, especially for the agronomical characters number of fruit and weight of bunch. Accessions with high contents of carotenoids (diploid 'Jaran'), polyphenols (triploid 'Caipira' and tetraploid 'Teparod') and vitamin C (diploid 'Tuugia' and an unknown triploid AAA) in the fruit were identified. Thirteen microsatellite primers revealed an average of 7.23 alleles, which showed high variability. A dendrogram was prepared using the Gower algorithm for the distance matrices obtained from the agronomical, physical and physicolchemical analysis of fruit and SSR markers. Adopting the average genetic divergence as the cut-off point, three clusters were found: G1, formed by the diploids 'Jaran', 028003-01 and M-48; G2, by the diploids 'Malbut' and 'Ido 110'; and G3, by 21 tri-and tetraploid accessions, including one diploid, 'Tuugia'. The triploids with the B genome 'Thap Maeo', 'Walha', 'Pacha Nadan' and 'Champa Madras' were grouped in G2. Results from this work can be used for breeding hybrids with good agronomical traits and fruit quality.<br>O objetivo deste trabalho foi caracterizar acessos de bananeira do Banco de Germoplasma da Embrapa Mandioca e Fruticultura Tropical, por meio de características agronômicas, físicas e físico-químicas dos frutos e por marcadores "Simple sequence repeats" (SSR). Foram analisados 26 acessos, nos quais observou-se ampla variabilidade genética, em especial para número de frutos e peso de cacho. Foram identificados acessos com altos teores de carotenoides (diploide 'Jaran'), polifenóis (tetraploide 'Teparod') e vitamina C (diploide 'Tuugia' e um triploide AAA desconhecido). Os 13 iniciadores microssatélites testados apresentaram uma média de 7,23 alelos, que apresentaram alta variabilidade. Com uso do algoritmo de Gower, foi elaborado um dendrograma com as matrizes de distância obtidas por meio das análises agronômicas, físicas e físico-químicas dos frutos e análises moleculares. Com a divergência genética média usada como ponto de corte, foram identificados três agrupamentos: G1, formado pelos diploides 'Jaran', 028003-01 e M-48; G2, pelos diploides 'Malbut' e 'Ido 110'; e G3, pelos 21 acessos tri-e tetraploides, incluindo-se um diploide 'Tuugia'. Os triploides com genoma B 'Thap Maeo', 'Walha', 'Pacha Nadan' e 'Champa Madras' agruparam-se no G2. Os resultados obtidos podem ser utilizados no melhoramento genético, para o desenvolvimento de híbridos com boas características agronômicas e qualidade de frutos