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Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

McBenedict B, Chimwamurombe P, Kwembeya E, Maggs-Kölling G - ScientificWorldJournal (2016)

Bottom Line: Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions.Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets.It is recommended that efforts should be made to widen the current gene pool in Namibia.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Namibia, 340 Mandume Ndemufayo Avenue, Windhoek, Namibia.

ABSTRACT
Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

No MeSH data available.


Related in: MedlinePlus

Principal Coordinate Analysis of the 96 P. glaucum genotypes based on SSRs marker data.
© Copyright Policy - open-access
Related In: Results  -  Collection


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fig2: Principal Coordinate Analysis of the 96 P. glaucum genotypes based on SSRs marker data.

Mentions: PCoA was employed on the six alleles (see Figure 2) that were identified by SSRs from the 96 P. glaucum accessions. In comparison to SSRs results that produced 12 clusters from the 96 accessions analyzed based on UPGMA, 12 groupings were produced when the same 96 accessions were analyzed using PCoA. This suggests that the clusters initially generated using UPGMA were reliable and furthermore supports the argument that the use of the SSRs technique in such a study is reliable. However, previous studies have used Principal Component Analysis (PCA) to assess genetic diversity mostly between wild and cultivated accessions [27, 28]. It was revealed [28] that wild and cultivated accessions demonstrated a comparable distribution in the PCA while another study [27] found a noticeable variation between accessions of wild P. glaucum which displayed unique allele combinations and cultivated P. glaucum which revealed homogeneity. Similarly, a clear variation between accession groupings was achieved by PCoA in the present study. However the study revealed a low level of genetic diversity based on SSRs compared to that obtained previously using isozymes [29, 30]. This discrepancy could be due to the different evolutionary properties of SSRs and isozyme loci.


Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

McBenedict B, Chimwamurombe P, Kwembeya E, Maggs-Kölling G - ScientificWorldJournal (2016)

Principal Coordinate Analysis of the 96 P. glaucum genotypes based on SSRs marker data.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4940581&req=5

fig2: Principal Coordinate Analysis of the 96 P. glaucum genotypes based on SSRs marker data.
Mentions: PCoA was employed on the six alleles (see Figure 2) that were identified by SSRs from the 96 P. glaucum accessions. In comparison to SSRs results that produced 12 clusters from the 96 accessions analyzed based on UPGMA, 12 groupings were produced when the same 96 accessions were analyzed using PCoA. This suggests that the clusters initially generated using UPGMA were reliable and furthermore supports the argument that the use of the SSRs technique in such a study is reliable. However, previous studies have used Principal Component Analysis (PCA) to assess genetic diversity mostly between wild and cultivated accessions [27, 28]. It was revealed [28] that wild and cultivated accessions demonstrated a comparable distribution in the PCA while another study [27] found a noticeable variation between accessions of wild P. glaucum which displayed unique allele combinations and cultivated P. glaucum which revealed homogeneity. Similarly, a clear variation between accession groupings was achieved by PCoA in the present study. However the study revealed a low level of genetic diversity based on SSRs compared to that obtained previously using isozymes [29, 30]. This discrepancy could be due to the different evolutionary properties of SSRs and isozyme loci.

Bottom Line: Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions.Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets.It is recommended that efforts should be made to widen the current gene pool in Namibia.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Namibia, 340 Mandume Ndemufayo Avenue, Windhoek, Namibia.

ABSTRACT
Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

No MeSH data available.


Related in: MedlinePlus