Variation and association analysis in grass pea (Lathyrus sativus L.)

The study was conducted on 50 landrace populations of grass pea at Adet Research Center, Ethiopia, using randomised complete Block design in three replications to determine morphological variability and character associations. Evaluations were made on plant and yield characters from eight plants tagged randomly from each plot. The data were subjected to Analysis of Variance (anova), heritability, correlation and cluster analyses. Higher mean and cv values were recorded for most of the agronomic traits for populations collected from Gondar region and the higher altitude group (>2500 m) indicating the presence of high genetic diversity in this region and altitude group. Phenotypic coefficient of variation (pcv) was slightly higher than genotypic coefficient of variation (gcv) for all the characters studied signifying that genotypic factors exerted reasonable effect in estimating the variation. The wide difference between pcv (22.4%) and gcv (13.0%) for seed yield per plant indicated the complexity of this trait and the important role of other factors such as environment in influencing yield potential in addition to the genetic factors. The strong positive association of pods per plant, 100 seed weight and primary branches per plant with seed yield indicated the possibility of selecting lines for yield improvement based on these characters at the very early stage of the grass pea breeding program. Key words/phrases: Correlation grass pea, heritability, Lathyrus sativus, variation SINET: Ethiopian Journal of Science Vol.25(2) 2002: 191-20

Phenotypic Diversity in Tef [Eragrostis Tef (Zucc.) Trotter] Accessions from Different Regions of Ethiopia

Seventy nine tef landraces collected from ten administrative zones and seven altitude classes were planted with two improved varieties in simple lattice design at Gute and Bako in 2007 and 2008, respectively to assess the patterns of genetic variation for quantitative and qualitative traits. Loose and fairly loose panicle forms; gray lemma color and brown seed color were abundant across all regions and altitude classes while compact and semi-compact panicles, red and purple lemma color and white seed color were less frequent. Higher Shannon diversity indices were observed for East Gojam, East Wollega, Horro Guduru Wollega, Illubabor and Jimma collections. Mean squares due to genotypes were significantly different for all traits except number of culm internodes, number of spikelet per panicle and number of fertile floret/spikelet at top of the panicle. Genotypes and environments interacted highly significantly (P≤0.01) for number of panicle branches, lodging index, above ground biomass weight, grain yield per plant and harvest index. About 73% of the entire diversity among population was explained by the first six principal components (PCs), of which the first PC explained about 31% of the variation. This originated mainly due plant height, panicle length, culm length, first and second culm internode diameters, days to panicle emergency and days to maturity. Similarly, about 91% and 90% of the variations among regions of origin and altitude classes were explained by the first five and three PCs, respectively. At 50% similarity level, 11 clusters were formed, containing 2-33 landrace populations per cluster, while six tef landraces remain solitary. There is no cluster formed solely either from tef populations of a given region, tef populations collected from similar agro-ecological zones or populations collected from areas with similar soil type. Some neighboring regions were grouped together in one cluster, implying that there are extensive informal seed exchanges or inter-regional migration of farmers with their seed. Some other regions show strong similarity while they are geographically very far away from each other (for instance, South Wello and Horro Guduru Wollega). Six altitude classes were grouped in to two main clusters at about 50% similarity level. However, tef landraces collected from altitude class below 1576 m.a.s.l (class I) remain un-grouped

Isoenzyme analysis of five endemic and one widespread Kniphofia species (Asphodelaceae) of Ethiopia

There are seven species of genus Kniphofia in Ethiopian flora. K. foliosa, K. hildebrandtii, K. insignis, K. isoetifolia, and K. schimperiare endemic. Kniphofia pumila and K. thomsonii are widespread from West Africa to Eastern and Central Africa. In this study the genetic diversity and the relationships between five endemic and one widespread Kniphofia species in Ethiopia was conducted based on isoenzymes systems. The electrophoretic analyses of four enzymes systems in the species from ten experimental sites in ten locations revealed seven putative loci, of which PGM-1, PGM-2, AAT-2 and GPI-2 were polymorphic. The species have displayed higher genetic diversity parameters than other endemic plants. The over all mean inbreeding coefficient (F) was positive indicating slight deficiency in the number of heterozygotes. The total genetic diversity varies from 0.5 in K. schimperito 1.11 in K. isoetifolia indicating very low diversification between the populations with in a species. At the generic level HT ranges from 0.034 to 0.470 with a mean of 0.247. The genetic variation among the species (GST) is 6.6%. Over all mean of genetic distance (0.011) and genetic similarity (0.938) indicated high similarity among the populations. Despite morphological variation particularly in floral morphology and inflorescence architecture, the over all mean of unbiased genetic identity of the species (0.989) is much higher than described for congeneric species (I = 0.64). The results, therefore, indicate that the Ethiopian Kniphofia species share a fairly recent common ancestor, but have differentiated in floral and inflorescence character through rapid evolution. This hypothesis needs, however, further testing.Key words/phrases: Endemism, genetic diversity, isoenzyme, kniphofia, inbreeding coefficient SINET: Ethiopian Journal of Science Vol. 27 (2) 2004:143–15

Genetic characterization and genome-wide association mapping for stem rust resistance in spring bread wheat

BACKGROUND: Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI). RESULTS: Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log(10) (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B. CONCLUSIONS: This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-022-01030-4

Challenges Associated with Crop Breeding for Adaptation to Drought-Prone Environments

Crop production is the main source of food, and drought is among the most important crop production constraints in the world, particularly in sub-Saharan Africa. The use of improved cultivars can at least partly ameliorate the calamities of drought stress, and considerable investments and efforts have been made worldwide to develop drought tolerant crop cultivars. A number of improved cultivars of different crops have also been released for production in different countries. As related to the situation under normal environments, it is yet hardly possible to say that these investments and efforts have modernized the production under drought-prone environments as a whole and boosted the actual productivity as desired. Therefore, the limitations and strategic implications of past experiences made to develop drought tolerant crop cultivars needs to be synthesized in order to formulate better strategies and approaches. In this review article, the scope and impacts of drought, approaches to breeding for drought tolerance and the associated challenges and ways out of the challenges have been discussed. We believe that this review will enhance the efforts underway to meaningfully adopt plant breeding for improving crop production in the face of the changing climate.Keywords፡ Adaptation to drought, drought-prone environments, drought toleranc

Phenotypic Diversity in Ethiopian Chickpea (Cicer arietinum L.) Germplasm Accessions for Phosphorus Uptake and Use Efficiency

Ethiopia is known as the secondary center of diversity for chickpea (Cicer arietinum L.). Plant breeders primarily interested in utilizing the available  germplasm for improving phosphorus uptake and use efficiency have no background information on the genetic diversity for this attribute. A field study  involving 155 chickpea genotypes was undertaken at Ambo and Ginchi, Ethiopia, in 2009/2010 to characterize the genotypes for nutrient uptake and use  efficiencies. Cluster analysis grouped the genotypes into five clusters in the absence and six clusters in the presence of phosphorus. The higher number  of clusters when the crop was grown with phosphorus may be a manifestation of more genetic diversity due to the application of phosphorus. The  Mahalanobis’s D2 statistics mostly showed significant genetic distances between clusters constituted local landraces on the one hand and introduced  genotypes on the other. This indicated that there were distinct multivariate differences between landraces and introduced genotypes. No clear  interrelationship was observed between the origins of the landraces within Ethiopia and the pattern of genetic diversity. Different characters had  different contribution to the total differentiation of the populations in all the cases. The result of this study suggests existence of adequate genetic  diversity for attributes of phosphorus uptake and use efficiency in these chickpea genotypes, which should be exploited in future breeding.&nbsp

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 D2 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 fixatio

New transcriptome-based SNP markers for noug (Guizotia abyssinica) and their conversion to KASP markers for population genetics analyses

The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics

gga-mir-133a-3p Regulates Myoblasts Proliferation and Differentiation by Targeting PRRX1

Non-coding RNAs play a regulatory role in the growth and development of skeletal muscle. Our previous study suggested that gga-mir-133a-3p was a potential candidate for regulating myoblast proliferation and differentiation in skeletal muscle. The purpose of our study was to reveal the regulatory mechanism of gga-mir-133a-3p in the proliferation and differentiation of chicken myoblasts. Through the detection of cell proliferation activity, cell cycle progression and EdU, we found that gga-mir-133a-3p can significantly inhibit the proliferation of myoblasts. In the process of myogenic differentiation, gga-mir-133a-3p is up-regulated, while gga-mir-133a-3p can significantly promote the up-regulation of differentiation-related muscle-derived factors, indicating that gga-mir-133a-3p can promote the differentiation of myoblasts. Validation at the transcriptional level and protein level proved that gga-mir-133a-3p can inhibit the expression of PRRX1, and the dual-luciferase assay also showed their direct targeting relationship. Correspondingly, PRRX1 can significantly promote myoblast proliferation and inhibit myoblast differentiation. In our study, we confirmed that gga-mir-133a-3p participates in the regulation of proliferation and differentiation of myoblasts by targeting PRRX1

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt