Kifle Dagne

Genetic Diversity and Population Structure of Ethiopian Chickpea (Cicer arietinum L.) Germplasm Accessions from Different Geographical Origins as Revealed by Microsatellite Markers

Genetic diversity and population structure were studied in 155 chickpea (Cicer arietinum L.) entries using 33 polymorphic microsatellite (SSR) markers. Molecular analysis of variance showed variations of 73% within and 27% among populations. Introduced genotypes exhibited highest polymorphism (70.27%) than the landraces (36–57%). Collections from Shewa, Harerge, W. Gojam and S. Gonder regions also showed higher polymorphism (50–57%) than the rest of the local accessions (36–45%). Analyses of pairwise population Nei genetic distance and PhiPT coefficients, expected heterozygosity (He) and unbiased expected heterozygosity (UHe), Shannon’s information index (I) and percent polymorphism (% P) showed existence of high genetic variation between geographical regions. Accessions from adjoining geographical regions mostly showed more genetic similarities than those from origins far isolated apart. This could be associated with the ease and likelihood of inter-regional gene flow and seed movement particularly during times of drought. The 155 entries were grouped into five clusters following analysis of population structure. The first cluster (C1) constituted accessions from Arsi; the second (C2) from Gojam and Gonder; the third (C3) from Harerge and E. and N. Shewa; and the fourth (C4) from W. Shewa, Tigray, and Wello regions. The fifth cluster (C5) was entirely consisted of improved genotypes. Improved genotypes of both Kabuli and Desi types distinctly fell into cluster five (C5) regardless of their difference in seed types. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. Further implications of the findings as regards to chickpea germplasm management and its utilization in breeding program are also discussed.

Molecular phylogeny of genus Guizotia (Asteraceae) using DNA sequences derived from ITS

Complete sequences for the internal transcribed spacers of the 18s–26s nuclear ribosomal DNA were generated to establish phylogenetic relationships among five species of the genus Guizotia. Parsimony analysis and pairwise distance data produced a single tree with four clearly distinguished clades that accord with previously reported chromosomal data. The clades produced here have been discussed with reference to existing taxonomic treatments. It appears that Guizotia scabra ssp. scabra, G. scabra ssp. schimperi and Guizotia villosa have contributed to the origin of Guizotia abyssinica, the cultivated species of the genus. The present composition of the species of genus Guizotia and the subtribe the genus presently placed in are suggested to be redefined.

Genetic diversity of Guizotia abyssinica (L. f.) Cass. (Asteraceae) from Ethiopia as revealed by random amplified polymorphic DNA (RAPD)

Genetic diversity of 70 populations of niger (Guizotia abyssinica) representing all its growing regions in Ethiopia was investigated using random amplified polymorphic DNA (RAPD) to reveal the extent of its populations genetic diversity. Ninety-seven percent of the loci studied was revealed to be polymorphic for the whole data set. The within population diversity estimated by Shannon diversity index and Nei gene diversity estimates was revealed to be 0.395 and 0.158, respectively. The extent of genetic variation of populations from major niger producing regions was significantly lower than that of populations from other regions; however, it is distributed regardless of altitude of growth. Genetic differentiation between populations was estimated with Shannon index as G′ST (0.432), Nei’s GST (0.242) and AMOVA based FST (0.350) and appears to be equivalent to the average values calculated from various RAPD based studies on outcrossing species. Higher proportion of the variation detected by AMOVA resided within populations (64.58%) relative to the amount of variation among populations (35.42%). UPGMA cluster analysis showed that most of the populations were clustered according to their region of origin. However, some populations were genetically distant from the majority and seem to have unique genetic properties. It is concluded that the crop has a wide genetic basis that may be used for the improvement of the species through conventional breeding and/or marker assisted selection. Collection of germplasm from areas not yet covered and/or underrepresented is the opportunity to broaden the genetic basis of genebank collection.

Phylogenetics and taxonomic delimitation of the genus Guizotia (Asteraceae) based on sequences derived from various chloroplast DNA regions

Parsimony-based phylogenetic analyses of the genus Guizotia were undertaken based on DNA sequence data from the following chloroplast DNA (cpDNA) regions: trnT-trnL, trnL-trnF, trnY-rpoB, trnC-petN, psbM-trnD and rps16-trnQ intergenic spacers, trnL, rps16 and matK-5′trnK introns and matK gene. Out of the 26 primers used in this study, 14 were newly designed. The study was conducted to determine (1) the closest relative of Guizotia abyssinica, (2) the taxonomic status of some Guizotia taxa and (3) the subtribal placement of Guizotia in the tribe Heliantheae. The analyses of the sequence data showed that G. abyssinica, G. scabra ssp. scabra, G. scabra ssp. schimperi and G. villosa are phylogenetically closely related. However, G. scabra ssp. schimperi appeared as the most closely related taxon to G. abyssinica. Based on this phylogenetic analysis, we suggest that the two subspecies of G. scabra are better treated as separate species. The analysis also clearly demonstrated that “Chelelu” and “Ketcha” are distinct Guizotia species. The trnT-trnL and trnL-trnF intergenic spacer-based phylogenetic analysis of various subtribes of the tribe Heliantheae strongly supports the placement of the genus Guizotia within the subtribe Milleriinae.

Comparative analysis of genetic relationship and diagnostic markers of several taxa of Guizotia Cass. (Asteraceae) as revealed by AFLPs and RAPDs

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) were employed to examine the genetic relationship between Guizotia taxa, to suggest the taxonomic status of some of these taxa, and to identify their diagnostic markers. Results from AFLPs and RAPDs share some features in common, both revealing G. scabra ssp. schimperi as the most closely related taxon to G. abyssinica, and indicating that G. arborescens and G. zavattarii are the most divergent taxa. Most of the diagnostic markers revealed in this study were specific to G. arborescens and G. zavattarii. Our analysis suggests that G. scabra ssp. scabra, G. scabra ssp. schimperi, Chelelu and Ketcha are separate species. In this study, AFLP was found to be superior to RAPD in detecting genetic variation, in internal consistency of the data and in the fitness of its clusters to genetic similarity data. AFLPs revealed genetic relationship between Guizotia taxa that is more inline with the cytogenetic and hybridization studies than that revealed by RAPDs.

Assessment of genetic diversity in Ethiopian cowpea [Vigna unguiculata (L.) Walp.] germplasm using simple sequence repeat markers

The genetic diversity of cowpea (Vigna unguiculata L. Walp.) in Ethiopia was analyzed using 19 uniform accessions, 62 variable accessions (yielding 185 sub-types), and two mungbean (Vigna radiata) accessions (four subtypes) as outgroup. A set of 23 polymorphic simple sequence repeat (SSR) markers was identified, and polymorphism in the various accessions was scored by determining amplicon variability. Allele frequency, genetic diversity, and polymorphism information content (PIC) were determined for each SSR marker, and a neighbor joining dendrogram was generated to show the genetic relationship among the individual accessions. A total of 75 allelic variants was defined, with the average number of alleles per locus calculated to be three. The average genetic diversity (D) was 0.47, and PIC was 0.4. Three main clusters were identified by phylogenetic analysis, and the clusters and sub-grouping were supported by STRUCTURE and principal component analysis. This grouping had a moderate fixation index value of 0.075 and gene flow (Nm) of 3.176, indicating that the accessions possess wide diversity within individuals and populations. The accessions showed no clustering by geographical origins. Three well-characterized molecular markers (SSR1, C42-2B, and 61RM2) for race specific resistance to Striga gesnerioides in the cowpea cultivar B301 were used to evaluate the accessions for their potential for use in genetic improvement against this pest. Based on this analysis, only two accessions, 222890–2 from Gambela and 286–2 from the Southern Nations, Nationalities, and Peoples (SNNP) region, were found to cluster with B301 and contain the SSR1 resistance allele. These findings will assist in germplasm conservation efforts by the Institute of Biodiversity and Conservation of Ethiopia, and contribute to future studies aimed at the genetic improvement of local germplasm for improved overall agronomic performance as well as Striga resistance in particular.

A 24-well plate assay for simultaneous testing of first and second line drugs against Mycobacterium tuberculosis in a high endemic setting

BackgroundEarly detection of drug resistance is one of the priorities of tuberculosis (TB) control programs as drug resistance is increasing. New molecular assays are only accessible for a minority of the second line drugs and their availability in high endemic settings is also hampered by high cost and logistic challenges. Therefore, we evaluated a previously developed method for drug susceptibility testing (DST) including both first- and second line anti-TB drugs for use in high endemic areas.ResultsBaseline mycobacterial isolates from 78 consecutive pulmonary TB patients from Addis Ababa, Ethiopia who were culture positive for Mycobacterium tuberculosis at the end of a two-month directly observed treatment short course (DOTS) were included. The isolates were simultaneously tested for isoniazid, rifampicin, ethambutol, streptomycin, amikacin, kanamycin, capreomycin, ofloxacin, moxifloxacin, ethionamide and para-aminosalicylic acid susceptibility using the indirect proportion method adopted for 24-well agar plates containing Middlebrook 7H10 medium. Applying the 24-well plate assay, 43 (55.1%) isolates were resistant to one or more of the first line drugs tested (isoniazid, rifampicin and ethambutol). MDR-TB was identified in 20.5% of this selected group and there was a perfect correlation for rifampicin resistance with the results from the genotype MTBDRplus assay. All isolates were susceptible to aminoglycosides and fluoroquinolones in agreement with the genotype MTBDRsl assay. The only tested second line drug associated to resistance was ethionamide (14.1% resistant). The method was reproducible with stable results for internal controls (one multi-drug resistant (MDR) and one pan-susceptible strain (H37Rv) and DST results could be reported at two weeks.ConclusionsThe 24-well plate method for simultaneous DST for first- and second line drugs was found to be reproducible and correlated well to molecular drug susceptibility tests. It is likely to be useful in high-endemic areas for surveillance as well as for the detection of second line drug resistance in targeted groups such as in those who fail empirical MDR treatment.

Breeding chickpea ( Cicer arietinum [Fabaceae]) for better seed quality inadvertently increased susceptibility to adzuki bean beetle ( Callosobruchus chinensis [Coleoptera: Bruchidae])

Continuous breeding efforts in Ethiopia resulted in the release of 15 improved chickpea (Cicer arietinum L.) varieties with improved yield, seed quality, disease resistance and better adaptation to different production zones within Ethiopia. This study was conducted to examine whether breeding for increased yield and other important agronomic traits without direct selection for resistance to the adzuki bean beetle (Callosobruchus chinensis L.) has inadvertently resulted in a significant level of susceptibility to this seed pest within the new cultivars. Field and laboratory studies were conducted to see whether breeding for better seed quality has increased susceptibility to infestation by the adzuki bean beetle. Seeds of 130 accessions/genotypes were infested with the beetle in 2009 under ambient temperature and relative humidity at Holetta, Ambo and Debre Zeit, Ethiopia. Data were recorded on attributes of infestation level and seed damage. Data on seed size, proportion of seed coat and grain yield were collected from a replicated field trial conducted with the same accessions/genotypes grown under the same conditions in 2009/10 at Ginchi and Ambo, Ethiopia. Differences among the genotypes were significant for most traits with the exception of the number of uninfested seeds. Accessions with partial resistance include 41320, 41289, 41291, 41134, 41315, 207658, 41103, 41168, 41142, 41174, 41029, 41207, 209087, 231327, 41161 and 41008. The improved varieties were more susceptible than germplasm accessions. The results indicate that genetic progress was achieved both in grain yield and seed size, but breeding efforts for these traits had also inadvertently increased seed susceptibility to C. chinensis. Improvements in seed size resulted in higher infestation levels and seed damage. Future breeding to improve seed quality should simultaneously consider corrective measures to incorporate resistance to the adzuki bean beetle.

The importance of legumes in the Ethiopian farming system and overall economy: an overview.

Crops, livestock and trees are major components of farming systems in Ethiopia. Crop production is dominant in Ethiopian agriculture as well as in the farming system. Legumes are among the various crops produced in all regions of the country in different volumes after cereals. More than twelve legume species are grown in the country. Pulses production by volume has been increased by 71.92% for the duration of nearly 20 years and with a growth rate of 3.78% per annum. Area coverage by pulse crops for the same period grown by 53% with a growth rate of 3% per year. Total pulses grain yield, which is volume of production per unit area, showed good increment from 8.79 quintal s per hectare in the cropping year 1994/1995 to 14.76 quintals per hectare in

Phenotypic diversity for symbio-agronomic characters in Ethiopian chickpea (Cicer arietinum L.) germplasm accessions

Breeding chickpea ( Cicer arietinum L.) cultivars combining desirable symbiotic and agronomic characters has both economic and ecological significance. An experiment was conducted at Ambo and Ginchi, Ethiopia, in 2009/10 to characterize and evaluate 155 genotypes of chickpea for symbiotic and agronomic performance. A randomized complete block design with four replications and the difference technique, with a genetically non-nodulating chickpea genotype as a reference crop were employed to estimate the amount of symbiotic nitrogen fixation. Data analysis of 32 agronomic and symbiotic characters showed significant differences among the genotypes for all traits under study. Trait-based cluster analysis grouped the genotypes into six different classes. Standardized Mahalanobis D 2 statistics showed significant genetic distances between all clusters constituted local landraces and introduced genotypes. This indicated that there were distinct multivariate differences between landraces and introduced genotypes. No clear interrelationship was observed between the geographic origins of the landraces and the pattern of genetic diversity, as there were accessions from the same source of origin that fell into different clusters and vice versa. Different symbiotic and agronomic characters had different contribution to the total differences among the populations. Those characters that contributed more to the total differentiation of the populations and genotypes into the different clusters should be exploited in future breeding. Keywords: Chickpea ( Cicer arietinum ), cluster analysis, genetic diversity, germplasm, symbiotic nitrogen fixation