Dominant allele phylogeny and constitutive subgenome haplotype inference in bananas using mitochondrial and nuclear markers

Article purchased; Published online: 27 Aug 2017Cultivated bananas (Musa spp.) have undergone domestication patterns involving crosses of wild progenitors followed by long periods of clonal propagation. Majority of cultivated bananas are polyploids with different constitutive subgenomes and knowledge on phylogenies to their progenitors at the species and subspecies levels is essential. Here, the mitochondrial (NAD1) and nuclear (CENH3) markers were used to phylogenetically position cultivated banana genotypes to diploid progenitors. The CENH3 nuclear marker was used to identify a minimum representative haplotype number in polyploids and diploid bananas based on single nucleotide polymorphisms. The mitochondrial marker NAD1 was observed to be ideal in differentiating bananas of different genomic constitutions based on size of amplicons as well as sequence. The genotypes phylogenetically segregated based on the dominant genome; AAB genotypes grouped with AA and AAA, and the ABB together with BB. Both markers differentiated banana sections, but could not differentiate subspecies within the A genomic group. On the basis of CENH3 marker, a total of 13 haplotypes (five in both diploid and triploid, three in diploids, and rest unique to triploids) were identified from the genotypes tested. The presence of haplotypes, which were common in diploids and triploids, stipulate possibility of a shared ancestry in the genotypes involved in this study. Furthermore, the presence of multiple haplotypes in some diploid bananas indicates their being heterozygous. The haplotypes identified in this study are of importance because they can be used to check the level of homozygozity in breeding lines as well as to track segregation in progenies

Leaf Disc Regeneration of Passion Fruit

A leaf disc regeneration system was developed for passion fruit, Passiflora edulis Sims. Leaf discs were cultured on a modified MS medium containing 8.90 \ub5M BAP or on 8.90 \ub5M BAP and 2.32 \ub5M KIN. Shoots appeared within four weeks. These could be rooted when transferred to the same medium containing 0.54, 2.69 and 5.37 \ub5M NAA. Leaf discs cultured on medium supplemented with 11.42 \ub5M IAA, 10.74 \ub5M NAA and 1.86 \ub5M KIN formed callus only. Those cultured on medium supplemented with 10.74 \ub5M NAA and 2.32 \ub5M KIN formed callus and root

Molecular characterization and identification of biocontrol isolates of Trichoderma harzianum from Embu District, Kenya

Species in the genus Trichoderma are important as commercial source of several enzymes, biofungicides, and growth promoters. The most common biological control agents of the genus are strains of T. harzianum, T .viride and T. viriens. In this study, sixteen selected isolates of T. harzianum from different land use types in Embu, Kenya were tested for anatogonistic action against five soil borne phytopathogenic fungi (Rhizoctonia solani, Pythium sp, Fusarium graminearum, F. oxysporum f. sp phaseoli and F. oxysporum f. sp Lycopersici) using dual culture assay and through production of non-volatile inhibitors. Seven isolates were further characterized using RAPD-PCR procedure to determine genetic variability. All T. harzianum isolates had considerable antagonistic effect on mycelial growth of the pathogens in dual cultures compared to the controls. Maximum inhibition occurred in Pythium sp-055E interaction (73%).The culture filtrates obtained from Czapek’s liquid medium reduced the dry weight (mg) of the mycelia significantly while those from the potato dextrose broth showed minimum inhibition growth. Pythium sp was inhibited the most compared to other pathogens. Genetic similarities generated using Jaccard’s coefficient of similarity ranged from 0.231 between isolates 055E and 011E to 0.857 between isolates 010E and 015E. The technique of RAPD was efficient in demonstrating the DNA polymorphism in the isolates of T. harzianum tested showing intraspecific genetic variability. Since all T. harzianum isolates evaluated were effective in controlling colony growth of the soil borne pathogens both in dual cultures and in culture filtrates they should be tried as a broad spectrum biological control agent in the greenhouse and under field conditions

Microsatellite analysis of the correlation between molecular and morphological traits in assorted maize inbred lines

The success in identifying heterosis in hybrid maize ( Zea mays L.) breeding depends on the availability of reliable genetic diversity among maize inbred lines. Conventional methods of breeding have been boosted by the availability and efficiency of molecular markers. Coupling simple sequence repeat (SSR) markers with morphological markers provides thorough starting information for new inbred lines, especially from different genetic backgrounds. Furthermore, recent evidences that the environment can influence the epigenetic structure of the genome have necessitated morphological screening of crops during breeding programmes. This study used 28 agronomic traits and 14 SSR markers which are distributed uniformly in ten (1-10) inbred lines, namely EM11-133, EM12-210, OSU23i, CML395, CML202, CML442, CML444, CML208, CML312 and CML204 from Kenya, International Centre for the Improvement of Maize and Wheat (CIMMYT), and another (OSU 23i) from USA. The aim was to investigate their morphological and genetic diversity, categorise the inbred lines into useful groups based on the molecular profiles and morphological traits, and lastly determine the level of phenotype-genotype correlation. The dissimilarity calculated using SSR markers had a mean morphological dissimilarity of 0.895403, an r value of -0.1421 and a p -0.9840. The dissimilarity between the molecular and morphological traits was 0.860465. Comparison between the molecular and morphological data had a dissimilarity matrix with an r -0.2323 and a p value of 0.0120. This was probably due to intrinsic synteny in maize genome. The dendrograms generated with hierarchical Unweighted Pair Group Method with Arithmetic mean (UPGMA) cluster analysis of the Jaccard's similarity coefficient matrices revealed four major clusters. The Co-ancestry distance showed six tied groups with the Kenya cluster showing some differentiation with Exact Tests for population differentiation with a p = 0.0513. The American inbred line (OSU 23i) segregated alone, while the Kenya lines (EM11-133 and EM12-210) had close homology with the CIMMYT inbred lines (CMLs). A total of 2.0 alleles were detected among the inbred lines using bulk DNA samples and 14 SSR loci. Clustering analysis based on the genetic similarity coefficients separated the inbred lines into 4 groups with the American inbred line seeming to be genotypically more diverse from the others.Le succès dans l'identification des hétérosis de maïs hybrides ( Zea mays L.) dépend de la disponibilité d'une diversité génétique fiable dans les lignées endogames du maïs. Les méthodes conventionnelles de l'hybridation avaient été améliorées par la disponibilité et l'efficacité des marqueurs moléculaires. Le couplage des marqueurs simples de sequence répétée (SSR) avec les marqueurs morphologiques fournit des informations fondamentales précises pour les nouvelles lignées endogames, principalement de différente constitution génétique. En outre, les recentes évidences selon lesquelles l'environnement peut influencer la structure épigénétique du génome ont nécessité une selection morphologique des cultures au cours des programmes d'hybridation. Cette étude avait utilisé 28 caractéristiques agronomiques et 14 marqueurs SSR distribués uniformément en dix (1-10) lignées endogames à savoir EM11-133, EM12-210, OSU23i, CML395, CML202, CML442, CML444, CML208, CML312, CML204 qui avaient été respectivement obtenus à partir du Kenya, Centre International pour l'amélioration du maïs et du blé (CIMMYT) et l'autre des États-Unis. L'objectif de cette étude était de déterminer la diversité morphologique et génétique, catégoriser les lignées endogames en groupes importants sur base des profils moléculaires ainsi que les caractéristiques morphologiques et enfin déterminer le niveau de la corrélation phénotype-génotype. La dissimilarité calculée à l'aide de marqueurs SSR avait une difference morphologique moyenne de 0,895403, valeur de r de -0,1421 et un p de -0,9840. La différence entre les caractéristiques moléculaires et morphologiques était de 0,860465. Une comparaison entre les données moléculaires et morphologiques avait révelé une matrice non simulaire avec r= -0.2323 et une valeur de p de 0,0120. Ceci était probablement dû à la composition intrinsèque dans le génome du maïs. Le dendrogramme généré par la méthode de groupes paires hiérarchiques non pondérés avec le cluster de l'analyse de la moyenne arithmétique (UPGMA) des matrices de coefficient de similarité de Jaccard avait révélé la présence de quatre regroupements majeurs, tandis que la distance de Co-ascendance a montré six groupes liés avec le regroupement Kenya montrant une certaine différence avec les Tests Précis de différenciation de la population avec un p = 0,0513. La lignée américaine non hybride (OSU 23i) se divisait individuellement, tandis que les lignées Kenya (EM11-133 et EM12-210) avaient une homologie étroite avec les lignées non hybrides CIMMYT (CMLs). Un total de 2,0 allèles avaient été détectés parmi les lignées non hybrides à l'aide des échantillons d'ADN et 14 loci SSR. L'analyse par regroupement fondée sur les coefficients de similarité génétique avait permi la séparation des lignées non hybrides en 4 groupes ainsi que la lignée américaine non hybride semblant être genotypiquement plus diversifiée des autres

Detection of species substitution in the meat value chain by high-resolution melting analysis of mitochondrial PCR products

Substituting high commercial-value meats with similar cheaper or undesirable species is a common form of food fraud that raises ethical, religious, and dietary concerns. Measures to monitor meat substitution are being put in place in many developed countries. However, information about similar efforts in sub-Saharan Africa is sparse. We used PCR coupled with high-resolution melting (PCR-HRM) analysis targeting three mitochondrial genes—cytochrome oxidase 1 (CO1), cytochrome b (cyt b), and 16S rRNA—to detect species substitution in meat sold to consumers in Nairobi, Kenya. Out of 107 meat samples representing seven livestock animals, 11 (10.3%) had been substituted, with the highest rate being observed in samples sold as goat. Our results indicate that PCR-HRM analysis is a cost- and time-effective technique that can be employed to detect species substitution. The combined use of the three mitochondrial markers produced PCR-HRM profiles that successfully allowed for the consistent distinction of species in the analysis of raw, cooked, dried, and rotten meat samples, as well as of meat admixtures. We propose that this approach has broad applications in the protection of consumers against food fraud in the meat industry in low- and middle-income countries such as Kenya, as well as in developed countries