Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections.

Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei's genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.

Genetic Diversity and Population Structure in Ethiopian Mustard (Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers.

Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.

Genetic diversity and population structure of selected tef core germplasm lines based on microsatellite markers.

BACKGROUND: Tef is an indigenous and important food, feed, and cash crop for smallholder Ethiopian farmers. Knowledge of the natural genetic composition of the crop provides the option to further exploit its genetic potential through breeding. However, there are insufficient reports on the genetic variability of Ethiopian tef using a medium-throughput marker system. Hence, the current study was designed to evaluate the genetic variability of released and core germplasm that was collected earlier. METHODS AND RESULTS: Eighty-one tef genotypes collected from eight Ethiopian ecological zones and released varieties were targeted using 14 SSR markers. The study yielded a total of 122 alleles across the entire locus and population. The molecular variance analysis indicated the existence of large genetic differentiation (FIS and FIT = 0.87), with 86% and 13% of the total variation accounted for among genotypes within the population and across all genotypes used for this study, respectively. However, low genetic differentiation among the populations (FST = 0.014, which accounts for 1%) was observed. Multivariate analyses such as clustering and PCoA did not cluster genotypes into distinct groups according to their geographical areas of population. This is presumably due to gene flow among populations. CONCLUSION: In conclusion, our findings show that there is significant genetic diversity within populations, particularly in the Jimma, Tigray, and released varieties, as well as the presence of private alleles and heterozygosity. The study also indicates the existence of genotypic admixture in the studied materials. The identification of private alleles and their differentiation will be helpful in selecting breeding materials and creating breeding plans.

Corrigendum to "Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers" [Heliyon Volume 9, Issue 1, January 2023, Article e12830].

[This corrects the article DOI: 10.1016/j.heliyon.2023.e12830.].

Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm.

BACKGROUND: High-density single nucleotide polymorphisms (SNPs) are the most abundant and robust form of genetic variants and hence make highly favorable markers to determine the genetic diversity and relationship, enhancing the selection of breeding materials and the discovery of novel genes associated with economically important traits. In this study, a total of 105 barley genotypes were sampled from various agro-ecologies of Ethiopia and genotyped using 10 K single nucleotide polymorphism (SNP) markers. The refined dataset was used to assess genetic diversity and population structure. RESULTS: The average gene diversity was 0.253, polymorphism information content (PIC) of 0.216, and minor allelic frequency (MAF) of 0.118 this revealed a high genetic variation in barley genotypes. The genetic differentiation also showed the existence of variations, ranging from 0.019 to 0.117, indicating moderate genetic differentiation between barley populations. Analysis of molecular variance (AMOVA) revealed that 46.43% and 52.85% of the total genetic variation occurred within the accessions and populations, respectively. The heat map, principal components and population structure analysis further confirm the presence of four distinct clusters. CONCLUSIONS: This study confirmed that there is substantial genetic variation among the different barley genotypes. This information is useful in genomics, genetics and barley breeding.

On-farm diversity, use pattern, and conservation of enset (Ensete ventricosum) genetic resources in southern Ethiopia.

BACKGROUND: Enset is an important source of food and is consumed by about 25 million people as a staple or co-staple food crop mainly in southern parts of Ethiopia. Large numbers of enset landraces exist in different administrative zones of Ethiopia with a wide range of altitudes and agroclimatic zones. However, limited information is available on the diversity, distribution, and utilization pattern corresponding to the diverse ethnolinguistic as well as sociocultural communities of the country. Hence, this study was devised to explore and document the richness of farmers' tradition and practice on the diversity and distribution of enset landraces on the farm level and selection pattern for different purposes regarding the production, utilization, and conservation of enset genetic resources. METHODS: The study was conducted in four major enset-growing administrative zones of Ethiopia, namely Hadiya, Kembata-Tembaro, Gurage, and Silte. A total of 240 farm households were surveyed using individual interviews, 18 key informant interviews, 36 focus group discussions with 5 participants, and direct on-farm field observations for data collection. Considering that enset has a rich cultural background and indigenous knowledge, ethnobotanical research approach was applied to data collection and analysis. The Shannon-Weaver, Simpson, Pielou, and Jaccard's similarity indices were used to evaluate the diversity and similarity of the landraces as well as using descriptive statistics in SPSS Ver. 24. Preference in direct matrix ranking was also used to compute and rank the enset landraces most preferred by the people in the context of specific use value in the study area. RESULTS: A total of 282 farmer-named enset landraces have been identified, with a range from 2 to 32 on individual homegardens. The largest number of landraces was found in the Hadiya Zone (86), while the lowest was scored in the Silte Zone (57). The Shannon diversity index (H') ranged from 3.73 (Silte) to 3.96 (Hadiya). Similarly, landraces revealed a very narrow range of variances in Simpson's 1-D diversity index, and it ranged from 0.963 (Silte) to 0.978 (Hadiya). Likewise, the similarity index ranged from 0.24 to 0.73 sharing 16-47 landraces in common. Of the 282 landraces, 210 (74.5%) were recorded in more than one zones, whereas 72 (25.5%) had narrow distribution being restricted to a single zone. CONCLUSIONS: Farmers have established long-term practices and experiences in cultivation, utilization, and conservation of a diverse group of enset landraces to fill their domestic and market purposes in each zone. The variation is likely to be related to agroclimatic differences, ethnicity factors, food cultures, and historical backgrounds. Therefore, to facilitate on-farm conservation as well as sustainable utilization of the enset genetic resources, farmers need to be supported by different stakeholders for all their worth and also in crop improvement programs.

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers.

In the tropical and semi-arid regions of Africa, sorghum [Sorghum bicolor (L.) Moench] is mainly grown as a major food security crop. Understanding the extent and pattern of genetic variability is a prerequisite criterion for sorghum improvement and conservation. The genetic diversity and population structure of 100 genotypes of sorghum were profiled using 15 microsatellite loci. A total of 108 alleles, with an overall mean of 7.2 alleles per locus, were produced by all of the microsatellite loci used due to their high polymorphism. Polymorphic information content values ranging from 0.68 to 0.89 indicated that all of the loci are effective genetic tools for analysing the genetic structure of sorghum. Different diversity metrics were used to evaluate genetic diversity among populations, and Nei's gene diversity index ranged from 0.74 to 0.81 with an overall mean of 0.78. Poor genetic differentiation (FST: 0.02; p < 0.0001) was found, where 98% of entire variability was accounted by the within populations genetic variability, leaving only 2.32% among populations. The highest genetic differentiation and Nis's genetic distance were observed between the sorghum populations of the Southern Nation and Nationalities Peoples and Dire Dawa regions. Due to increased gene flow (Nm = 10.53), the clustering, principal coordinate analysis and STRUCTURE analysis failed to categorize the populations into genetically different groups corresponding to their geographic sampling areas. In general, it was found that the microsatellite loci were highly informative and therefore valuable genetic tools to unfold the genetic diversity and population structure of Ethiopian sorghum genotypes. Among the five populations studied, sorghum populations from Amhara and Oromia had the highest genetic variation, indicating that the regions could be perhaps hotspots for useful alleles for the development of better-performing genotypes, and also for designing appropriate germplasm management strategies.

Novel sources of drought tolerance in sorghum landraces revealed via the analyses of genotype-by-environment interactions.

Globally, sorghum is the fifth most important crop, which is used for food, feed and fuel. However, its production and productivity are severely limited by various stresses, including drought. Hence, this study aimed to determine the responses of different drought-tolerance related traits in the Ethiopian sorghum germplasm through multi-environment field trials, thereby identifying novel sources of germplasm that can be used for breeding the crop for drought-tolerance. Three hundred twenty sorghum landraces and four improved varieties were grown at three sites within drought-prone areas (Melkassa, Mieso and Mehoni) in Ethiopia. The targeted traits were chlorophyll content at flowering (CHLF), chlorophyll content at maturity (CHLM), green leaf number at flowering (GLNF), stay-green (SG), flag leaf area (FLA), peduncle length (PDL), and panicle exertion (PAE). Multi-variate analyses of the collected data revealed the presence of high phenotypic variation in all traits. The combined and AMMI Analysis of variance showed that phenotypic variation due to the genotypes was higher for SG, CHLM, CHLF and GLNF and lower for FLA, PE and PDL in comparison with variation due to the environments or genotype by environment interactions. High broad sense heritability was observed for CHLF, CHLM, SG, GLNF, FLA, and PDL, whereas PAE showed moderate heritability. Due to the high heritability of chlorophyll content and the relatively small effect of environmental factors on it, it could serve as a criterion for selecting desirable genotypes for drought-tolerant breeding in sorghum. It has been found that chlorophyll content has a significant positive correlation with stay-green and grain yield, indicating that high chlorophyll content contributes to increasing grain yield by delaying the process of leaf senescence. The analyses of AMMI, GGE biplot, and genotype selection index revealed that several sorghum landraces outperformed the improved varieties with respect to CHLF, CHLM, and SG. Such landraces could serve as novel sources of germplasm for improving drought tolerance through breeding.

Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor.

Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.

Morphological variations of qualitative traits of barley (Hordeum vulgare L.) accessions in Ethiopia.

Ethiopian barley germplasm is a potential source of useful traits to fight the production challenges of barley farming and to enhance yield productivity in favorable and marginal environments. A study was carried out to assess the distribution and patterns of 17 qualitative trait variations among 85 Ethiopian barley accessions using an alpha lattice design with two replications. The Shannon-Weaver diversity (H') index was used to estimate morphological diversity. Fifteen morphological traits of barley accessions originating from various regions of origins and altitude ranges were polymorphic. However, two traits including stem branching and lemma awn were monomorphic. The highest (0.94) overall mean of H' was obtained for glume colour, kernel row and kernel shape. The estimated H' ranged from 0.41 to 0.99 across regions, and 0.52 to 0.99 across altitude ranges with an overall mean of 0.76. The analysis of variance of H' showed significant variation for most studied traits. Principal components analysis revealed that eight traits were the major loading on the first two principal components that describe 38.3% of the total morphological variance. Heat map analysis based on morphological traits of barley accessions was also grouped into three distinct clusters. Thus, the present finding confirmed that the Ethiopian barley accessions showed vast morphological variations across the region of origins and altitude ranges. Based on the result, further evaluation is ongoing to exploit specific gene variations through phenotyping and genotyping trait association.

In Vitro Regeneration of Korarima (Aframomum corrorima (Braun) P. C. M. Jansen): A Threatened Spice and Medicinal Herb from Ethiopia.

Developing an in vitro regeneration system is very important to increase production and productivity of plants as well as for the conservation of rare and threatened medicinal plants like korarima (Aframomum corrorima (Braun) P. C. M. Jansen). To date, no study dealing with in vitro indirect regeneration system of korarima has been reported. Thus, in this study, we developed an efficient and reproducible protocol for in vitro regeneration of korarima via callus. The procedure involved soaking seeds in 50% H2SO4 for 16 h that resulted in 92.5% germination on plant growth regulators (PGRs)-free half-strength Murashige and Skoog (MS) basal medium after a month. Shoot and rhizome induction rate of 93.75% was obtained on the MS medium containing 1.5 mg/l BAP in combination with 0.1 mg/l IBA after five weeks. Whitish yellow friable callus was obtained from rhizome culture taken from in vitro grown plantlets. The MS medium containing 2.0 mg/l 2, 4D in combination with 0.5 mg/l kinetin, resulted in 77.5% callus induction. The shoot regeneration rate of 45% was obtained from callus on the MS medium containing 2.0 mg/l TDZ in combination with 0.5 mg/l IBA. The mean shoot number of 10.83 per explant was obtained upon multiplication on the MS medium containing 1.5 mg/l BAP with a mean shoot height of 5.37 cm. The best rooting responses were obtained on half MS medium supplemented with 0.5 mg/l IAA resulting in a mean number of root of 18.59, mean root length of 9.71 cm, and mean shoot height of 7.32 cm. The plantlets showed 75% survival efficiency after acclimatization. The present regeneration protocol offers a conceivable system towards effective conservation and genetic improvement of the crop by increasing the efficiency of genetic transformation.

Quantitative trait loci mapping of stem sugar content and stem diameter in sorghum recombinant inbred lines using genotyping-by-sequencing.

BACKGROUND: Sweet sorghum is an important crop with sugary stem that can mainly be used for syrup, fodder and bio-fuel. Many sugar content QTLs have been discovered from different sources through breeding worldwide. Most of these QTLs are detected using exotic germplasm as a mapping population. This study aimed to detect and map QTLs for stem sugar content and stem diameter targeting Ethiopian recombinant inbred lines of sorghum using genotyping-by-sequencing. METHODS AND RESULT: Genotyping-by-sequencing and phenotyping using 139 recombinant inbred lines of sorghum as mapping populations were conducted. A total of 1082 polymorphic and high quality SNP markers that are evenly distributed across the ten linkage groups of sorghum were selected to detect and map the trait of interest. A genetic linkage map using 1082 SNP markers was constructed and several QTLs associated with stem sugar content and stem diameter were identified. Phenotypic variation explained by qBrix4-1 and qBrix2-1 ranged from 6.33 to 14%, respectively. Over two seasons, four QTLs for stem sugar content (qBrix1-1, qBrix2-1, qBrix4-1 and qBrix4-2) and three QTLs for stem diameter (qSD1-1, qSD8-1 and qSD9-1) were detected. CONCLUSION: QTLs that significantly associated with stem sugar content and stem diameter have been detected and mapped. This will help sorghum breeding program to develop superior sweet sorghum varieties through the use of appropriate crop improvement approaches like marker assisted breeding. This ultimately contributes to the current development plan to considerably improve food, feed and bio-fuel supply in developing countries like Ethiopia.

Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress.

MAIN CONCLUSION: Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.

Drought Tolerance and Application of Marker-Assisted Selection in Sorghum.

Sorghum is an important staple food crop in drought prone areas of Sub-Saharan Africa, which is characterized by erratic rainfall with poor distribution. Sorghum is a drought-tolerant crop by nature with reasonable yield compared to other cereal crops, but such abiotic stress adversely affects the productivity. Some sorghum varieties maintain green functional leaves under post-anthesis drought stress referred to as stay-green, which makes it an important crop for food and nutritional security. Notwithstanding, it is difficult to maintain consistency of tolerance over time due to climate change, which is caused by human activities. Drought in sorghum is addressed by several approaches, for instance, breeding drought-tolerant sorghum using conventional and molecular technologies. The challenge with conventional methods is that they depend on phenotyping stay-green, which is complex in sorghum, as it is constituted by multiple genes and environmental effects. Marker assisted selection, which involves the use of DNA molecular markers to map QTL associated with stay-green, has been useful to supplement stay-green improvement in sorghum. It involves QTL mapping associated with the stay-green trait for introgression into the senescent sorghum varieties through marker-assisted backcrossing by comparing with phenotypic field data. Therefore, this review discusses mechanisms of drought tolerance in sorghum focusing on physiological, morphological, and biochemical traits. In addition, the review discusses the application of marker-assisted selection techniques, including marker-assisted backcrossing, QTL mapping, and QTL pyramiding for addressing post-flowering drought in sorghum.

Genotype by environment interaction, correlation, AMMI, GGE biplot and cluster analysis for grain yield and other agronomic traits in sorghum (Sorghum bicolor L. Moench).

Genotype by environment (G×E) interaction is a major factor limiting the success of germplasm selection and identification of superior genotypes for use in plant breeding programs. Similar to the case in other crops, G×E complicates the improvement of sorghum, and hence it should be determined and used in decision-making programs. The present study aimed at assessing the G×E interaction, and the correlation between traits for superior sorghum genotypes. Three hundred twenty sorghum landraces and four improved varieties were used in alpha lattice experimental design-based field trial across three environments (Melkassa, Mieso and Mehoni) in Ethiopia. Phenotypic data were collected for days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT) and grain yield (GY). The results revealed that the variance due to genotype, environment and G×E interaction were highly significant (P < 0.001) for all traits. GY and PAWT were highly affected by environments and G×E whereas DTF, PALH, PAWD and PH were mainly affected by genotypic variation. Therefore, multi-environment testing is needed for taking care of G × E interaction to identify high yielding and stable sorghum landraces. GY and PAWT revealed highly significant positive correlations indicating the possibility of effective selection of the two traits simultaneously. Among the studied populations, South Wello, West Hararghe and Shewa zones had highly diverse genotypes that were distributed across all clusters. Hence, these areas can be considered as hotspots for identifying divergent sorghum landraces that could be used in breeding programs. Melkassa was the most representative environment whereas Mieso was the most discriminating. Five genotypes (G148, G123, G110, G203 and G73) were identified as superior across the test environments for grain yield with farmer-preferred trait, such as plant height. The identified stable and high yielding genotypes are valuable genetic resources that should be used in sorghum breeding programs.

Correction: Genetic diversity of Ethiopian cocoyam (Xanthosoma sagittifolium (L.) Schott) accessions as revealed by morphological traits and SSR markers.

[This corrects the article DOI: 10.1371/journal.pone.0245120.].

Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers.

BACKGROUND: Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. RESULTS: In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from - 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. CONCLUSIONS: Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

Genetic diversity of Ethiopian cocoyam (Xanthosoma sagittifolium (L.) Schott) accessions as revealed by morphological traits and SSR markers.

Cocoyam (Xanthosoma sagittifolium (L.) Schott) is an exotic species from tropical America that is widely cultivated in Ethiopia for its edible cormels and leaves. There is a dearth of information on the genetic diversity of Ethiopian cocoyam. In order to evaluate and select cocoyam germplasm for breeding and conservation, genetic diversity of 100 Ethiopian cocoyam accessions (65 green- and 35 purple- cocoyam) were analyzed using 29 morphological traits (16 qualitative and 13 quantitative) and 12 SSR loci. Two classes of qualitative traits were observed. ANOVA revealed significant variation in 11 (84.6%) of the 13 studied quantitative traits. The SSR marker analysis showed high genetic diversity. A total of 36 alleles were detected with a range of 2 to 5 (average of 3.273) alleles per locus. The average observed heterozygosity (Ho) and expected heterozygosity (He) values across populations were 0.503 and 0.443, respectively. The analysis of molecular variance showed that the variation among populations, among individuals within populations, and within individuals explained 14%, 18%, and 68% of the total variation, respectively. Cluster analysis grouped the accessions irrespective of the collection sites. A dendrogram based on Nei's standard genetic distance grouped the green cocoyam accessions together while the purple cocoyam accessions occupied a separate position within the dendrogram. Significant variation in quantitative traits and the high level of genetic diversity revealed by the SSR markers suggest that diverse cocoyam accessions, probably with multiple lineage, were introduced multiple times, through multiple routes and probably by multiple agents, an hypothesis that needs futher testing and analyis. The crop, therefore, needs more research efforts commensurate with its economic and social values than it has been accorded thus far. Further study is recommended to clarify the taxonomic status of Ethiopian cocoyam accesions and to trace their evolutionary relationships with Xanthosoma species elsewhere.

Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat.

BACKGROUND: Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. RESULTS: Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (- log10P ≥ 4) and 34 nominal (- log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). CONCLUSIONS: After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.

The Genetic Diversity of Enset (Ensete ventricosum) Landraces Used in Traditional Medicine Is Similar to the Diversity Found in Non-medicinal Landraces.

Enset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed, and fiber. It has immense contributions to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. These landraces are vulnerable to various human-related activities and environmental constraints. The genetic diversity among the landraces is not verified to plan conservation strategy. Moreover, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity. We evaluated the genetic diversity of 51 enset landraces, of which 38 have reported medicinal value. A total of 38 alleles across the 15 simple sequence repeat (SSR) loci and a moderate level of genetic diversity (He = 0.47) were detected. Analysis of molecular variation (AMOVA) revealed that only 2.4% of the total genetic variation was contributed by variation among the medicinal and non-medicinal groups of landraces, with an FST of 0.024. A neighbor-joining tree showed four separate clusters with no correlation to the use-values of the landraces. Except for two, all "medicinal" landraces with distinct vernacular names were found to be genetically different, showing that vernacular names are a good indicator of genetic distinctiveness in these specific groups of landraces. The discriminant analysis of the principal components also confirmed the absence of distinct clustering between the two groups. We found that enset landraces were clustered irrespective of their use-value, showing no evidence for genetic differentiation between the enset grown for 'medicinal' uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, might have resulted from the interaction of genotype with the environment or management practice, or partly misreported. The study provides baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces.