6 research outputs found
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 Ă©tĂ© respectivement obtenus Ă
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
Ă 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 Ă©tait 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 Ă©tait probablement dĂ» Ă 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
Ă l'aide des Ă©chantillons 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
Hybridizarion potential between cultivated rice <em>Oryza sativa</em> and African wild rice <em>Oryza longistaminata</em>
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