Agro-Morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian Potato [Plectranthus Edulis (Vatke) Agnew] From Ethiopia
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Date
2018-06-03
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Addis Ababa University
Abstract
Agro-morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian
Potato [Plectranthus edulis (Vatke) Agnew] from Ethiopia
Fekadu Gadissa
Addis Ababa University, 2018
Ethiopian potato syno. Ethiopian dinich [Plectranthus edulis (Vatke) Agnew] (Lamiaceae) is one of the
ancient annual edible tuber crops, originating in Ethiopia. The crop is commonly cultivated by
smallholder farmers around homesteads in the highland and semi-highland areas, usually for household
consumption and rarely for marketing. In spite of its’ wide economic importances, the crop is neglected
by research and development community and currently it is at risk of total extinction.
Hence, this study was conducted with the main aims of assessing agro-morphological and molecular
(EST-SSRs) markers-based extents of genetic diversity analysis as well as chromosome number and
ploidy level determination using 174 accessions from diverse agro-ecologies in Ethiopia.
For agro-morphological diversity analysis, the experimental samples were tested at Ambo and Holeta
agricultural research centres, using an alpha lattice design at the locations and three blocks/replication
followed by appropriate management practices. Agronomic and morphological traits-based data were
collected on twenty-eight (12 qualitative and 16 quantitative) traits at the right growth stage and
analysed using SAS v9.0, MINITAB® v14.13 and FigTree v1.4.3. Cytogenetic characterization was
also carried out using very young root tips generated from soil covered stem rings, followed by
appropriate pre-treatment, fixation and maceration. For molecular genetic diversity analysis, genomic
DNA was extracted form silcagel dried young leaves collected from 287 plants (1-3 plants per
accessions) following CTAB protocol. EST-SSRs marker were designed from Plectranthus barbatus
cDNA sequences deposited in the GenBank, followed by PCR amplification, capillary electrophoresis,
peak identification, and scoring. The scored allele size data were analysed for polymorphism, diversity
indices and genetic relationship and structure using windows compatible applications.
The agro-morphological traits considered showed varied morphotypes in all of the leaf (four in leaf
color, three in leaf arrangement, three in leaf shape), stem (three in stem color, two in each of stem spot
and stem spot colors) and tuber (four in tuber skin color, three in each of tuber texture, tuber shape and
tuber hair) characterstics. Similarly, the traits revealed a wide range of variability in mean performance
(minimum range of 1.39 – 2.13 cm observed in tuber diameter and maximum range of 112.90 – 165.10
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days observed in days to 50% flower initiation) and variance components among and within the
accessions. Similarly, the mean square of all the traits showed a highly significant (P< 0.001) variation
among the tested accessions. Such wide variation suggests the presence of variability which can be
exploited through selection. Several of the traits showed a slightly greater or nearly equal phenotypic
coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV), suggesting larger
contribution of the genotypic effect for phenotypic expression of such characters and hence, phenotypic
values-based selection for the traits may be effective. High estimates of GCV (>23%) coupled with high
estimate of heritability (Hb%) (>94%) and high genetic advance as a percent of mean (GAM) (>46)
were revealed in tuber weight per hill, number of primary branches per plant, number of tubers per hill,
and number of plants per hill indicating the importance of such traits for selection in Ethiopian potato
improvement programs. The significantly positive phenotypic, and genotypic correlation in tuber
weight per hill and number of tubers per hill with each other and several other traits as well as their
negative phenotypic correlation with some other traits indicates the direction of selection. Moreover,
the significantly higher absolute magnitudes in genotypic correlation compared to their corresponding
phenotypic correlation suggest the genetic base of those traits.
Cytogenetic characterization revealed a very smaller sized metaphase chromosome with a count of 2n
= c.56 and hepta- or octa-ploidy was speculated on the bases of basic chromosome number reports (x =
8 or 7) for the species of genus Plectranthus and other members of the Lamiaceae family. Such
chromosome count and ploidy level report could serve as a baseline information in selection and crosshybridization
of Ethiopian potato with other closely related species.
In total, twenty new polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs)
markers have successfully been developed and used in genetic diversity analyses. The marker detected
a total of 128 alleles (6.4 alleles per locus) over the entire loci and populations with effective number
of alleles ranging from 1.06 - 3.17 (an average of 1.67). The marker showed an overall highest (94.17%)
percent polymorphism, and extents of PIC in the range of slightly informative to highly informative
suggesting the potential of those developed markers as a valuable genetic tool and resource to evaluate
the extent of genetic diversity and population structure of not only Ethiopian potato but also various
other species within the Lamiaceae family.
The ranges and levels of mean observed heterozygosity (0.33 – 0.429), Shanon’s information index
(0.523 – 0.663), and Nei’s gene diversity (0.307 – 0.384) across loci showed a medium degree of
variation among the populations which is a direct reflection of sharing of most of the alleles among the
populations that partly resulted from high overall gene flow (Nm=18.29). Comparatively, Wenbera
(Wen), Wolaita Sodo (WSo), Hadiya and Kambata-Tembaro (HKT) and Southwest Shewa (SwSh)
populations could be considered as Ethiopian potato diversification and in-situ conservation sites.
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Hierarchical analysis of molecular variance (AMOVA) showed significant but low population
differentiation with at most 3% of the total variation in each of the groupings, such as among the
populations, among geographic regions, and among regions of accessions. Likewise, cluster analysis in
all the cases and STRUCTURE analyses did not group the populations into sharply distinct clusters,
which could be attributed to historical and contemporary gene flow and/or the reproductive biology of
the crop.
In conclusion, this study has wider implications in bringing such a ‘super-neglected’ crop to the
scientific agenda and thus, opens up the door to its improvement and conservation. However, it is
important to exhaust all areas and regions in the country and more number of SSRs or other up-to-date
molecular marker systems to come up with more accurate level of genetic diversity estimates.
Description
Keywords
Cytogenetics, Expressed Sequence Based Simple Sequence Repeats, Ethiopian, Potato, Genetic Diversity, Morphological Trait, Plectranthus Edulis, Population Structure