Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

GWAS analysis revealed variations at loci harboring seed storage, late embryogenesis abundant protein, and a tannin biosynthesis gene associated with sorghum grain mold resistance. Grain mold is the most important disease of sorghum [Sorghum bicolor (L.) Moench]. It starts at the early stages of grain development due to concurrent infection by multiple fungal species. The genetic architecture of resistance to grain mold is poorly understood. Using a diverse set of 635 Ethiopian sorghum accessions, we conducted a multi-stage disease rating for resistance to grain mold under natural infestation in the field. Through genome-wide association analyses with 173,666 SNPs and multiple models, two novel loci were identified that were consistently associated with grain mold resistance across environments. Sequence variation at new loci containing sorghum KAFIRIN gene encoding a seed storage protein affecting seed texture and LATE EMBRYOGENESIS ABUNDANT 3 (LEA3) gene encoding a protein that accumulates in seeds, previously implicated in stress tolerance, were significantly associated with grain mold resistance. The KAFIRIN and LEA3 loci were also significant factors in grain mold resistance in accessions with non-pigmented grains. Moreover, we consistently detected the known SNP (S4_62316425) in TAN1 gene, a regulator of tannin accumulation in sorghum grain to be significantly associated with grain mold resistance. Identification of loci associated with new mechanisms of resistance provides fresh insight into genetic control of the trait, while the highly resistant accessions can serve as sources of resistance genes for breeding. Overall, our association data suggest the critical role of loci harboring seed protein genes and implicate grain chemical and physical properties in sorghum grain mold resistance.

A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits

Understanding population genetic structure and diversity of a crop is essential in designing selection strategies in plant breeding. About 2010 Ethiopian sorghum accessions were phenotyped for different traits at multiple locations. A subset of the collection, 1628 accessions, predominantly landraces, some improved varieties, and inbred lines were genotyped by sequencing. Phenotypic data revealed association of important traits with different sorghum growing agro-climatic regions, high genetic diversity and the presence of rare natural variation in the Ethiopian sorghum germplasm. Subsequent genotypic analysis determined optimum number of sub-populations, distinct cluster groups and ancestries of each sorghum accessions. To improve utilization of germplasm, a core subset of 387 lines were selected following posteriori grouping of genotypes based on cluster groups obtained through GBS analysis followed by stratified random sampling using quantitative traits. In order to evaluate how well this new sorghum and millet innovation lab (SMIL) collection from Ethiopia is represented within the largest world sorghum collection at United States Department of Agriculture - National Plant Germplasm System (USDA-NPGS) and the sorghum association panel (SAP), comparisons were conducted based on SNP data. The SMIL collection displayed high genetic diversity with some redundancy with the USDA-NPGS germplasm but SAP showed clear distinction. Furthermore, genome-environment association analysis identified candidate genes associated with adaptation to abiotic factors, that will be important for exploitation of adaptive potential to different environments. In summary, our results described the diversity and relationship of sorghum collections, representativeness of developed core and provide novel insights into candidate genes associated to abiotic stress tolerance.

A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits

The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.

Bacterial Wilt caused by Ralstonia solanacearum in Ethiopia: StatusaAnd Management Approaches: A Review

Bacterial wilt caused by Ralstonia solanacearum is one of the most devastating plant diseases of economically important crops mainly Solanaceous family such as tomato, potato, pepper and eggplant. These crops play a significant role primarily as sources of income and food security for the small scale farming community in Ethiopia. The occurrence of bacterial wilt disease in Ethiopia was reported in 1956 and is known to cause significant yield loss on different Solanaceous crops in different parts of the country. On the basis of conventional characterization and classification, the strains of R. solanacearum found in Ethiopia have been identified as biovar 1 and 2. Recent characterization of R. solanacearum strains based on phylotype grouping using multiplex PCR and partial endoglucanase gene sequencing identified the occurrences of phylotype II and III. The association of biovar and phylotyping schemes indicated that phylotype II comprises only biovar 2, and phylotype III comprises strains of biovar 1 and biovar 2. The importance of the disease on Solanaceous crop is increasing from time to time specially in potato producing areas of the country. Apart from Solanaceous crops, the disease has also been posing a catastrophic damage to ginger production. Latently infected ginger rhizomes and potato seed tuber and decreasing of land holdings that limit crop rotation have contributed to the wider spread of the disease. In this review attempt has been made to summarize relevant scientific studies on this economically important disease in Ethiopia as well as its different disease management options, challenges and future considerations. Because, there is no single effective control measure against the target pathogen so far, a well-coordinated effort is required to develop an integrated disease management program that will help to minimize the damage and yield loss caused by the disease.

Use of a proximal humeral plate for a paediatric peri-prosthetic femoral fracture

In this case an 18-year-old female with cerebral palsy sustained a peri-prosthetic femoral fracture adjacent to a blade plate previously inserted for a femoral varus osteotomy. The injury was treated using a long proximal humeral locking plate. The existing blade plate was removed. The fracture was reduced and held, and a 10-hole PHILOS™ plate applied with near anatomical reduction. There were no post-operative complications. Radiographic union was confirmed at 11 months. To our knowledge, this is the first reported use of a PHILOS™ plate in the management of a femoral peri-prosthetic fracture and successfully demonstrated a straightforward method for revision fixation.

Malnutrition and iron deficiency in lactating women in urban slum communities from Addis Ababa, Ethiopia

OBJECTIVE

To determine the status of iron deficiency anaemia (IDA) and malnutrition in lactating women.

DESIGN

A cross-sectional study.

SETTING

Six urban slum communities in Teklehaimanot district, Addis Ababa.

SUBJECTS

One thousand and seventeen lactating women were enrolled and assessed for their haemoglobin (Hgb), serum ferritin level and body mass index (BMI) during the month of March 2001. Iron deficiency anaemia was considered when Hgb and serum ferritin concentrations were less than 12gm/dl and 12 microg/l respectively, whereas, a BMI less than 18.5% kg/m2 was considered malnourished.

MAIN OUTCOME MEASURES

Determinations of haemoglobin, serum ferritin and BMI measurements.

RESULTS

The overall prevalence of iron deficiency anaemia (IDA) and protein energy malnutrition in the slum communities was 22.3% and 27.1% respectively. The mean age of mothers (28.4 +/- 6.12 years) indicates that prevalence of malnutrition and iron deficiency anaemia was higher among younger mothers than among older mothers. The prevalence of malnutrition was positively correlated with the serum ferritin concentration status, of the mothers (r=0.12, p=0.2, RR=1.03).

CONCLUSION

It is observed that malnutrition and IDA are major health problems and therefore, an appropriate nutrition intervention package to improve the nutrition situation of the communities is recommended.

Daily versus weekly iron supplementation and prevention of iron deficiency anaemia in lactating women

OBJECTIVE

To demonstrate the effectiveness and social feasibility of weekly versus daily iron supplementation in preventing and treating iron deficiency anaemia among anaemic mothers.

DESIGN

A longitudinal in nature.

SETTING

Seven urban slum communities in Teklehaimanot Wereda, Addis Ababa, Ethiopia.

SUBJECTS

Two hundred seven eligible mothers were assigned to the daily supplementation, weekly supplementation or control groups following randomisation between March and May 2001. The daily supplemented groups (n=71) received 60 mg of elemental iron containing 300 mg ferrous sulphate and 400 microg folic acid from Monday to Friday. The weekly group (n=68) received one tablet once a week every Monday supervised while the control group (n=68) was advised to take no medications without the knowledge of the investigators until the completion of the study. To eliminate a major source of variation, subjects participating in the study were de-wormed at the beginning of the study.

MAIN OUTCOME MEASURES

Haemoglobin and serum ferritin concentrations were compared before and after the intervention among the groups.

RESULTS

The mean haemoglobin (Hgb), and serum ferritin concentration (SFC) at baseline were practically similar among the groups. Haemoglobin levels significantly increased at the end of the study in all the groups and the proportion of anaemia decreased from 6.9% to 1.6% in the daily, 6.7% to 1.7% in the weekly supplemented and 6.7% to 6.1% in the control groups. The difference noted between the daily and weekly supplemented groups was not significant. The improvement of SFC concentration was better in the daily than the weekly group but not statistically significant. Daily supplementation schedule caused more side effects and lower compliance level than the weekly supplementation schedule.

CONCLUSION

Weekly supplementation is simple, comparable to daily supplementation and economically advantageous. Thus, it is recommended to adopt the strategy for controlling anaemia. Further because of higher compliance rate and lower side effects, it is deemed to be socially feasible.

Retinopathy in patients of Tikur Anbessa Hospital diabetic clinic

A total of 302 diabetic patients were selected from regular attendants of the Tikur Anbessa Hospital (TAH) diabetic clinic to determine the prevalence of retinopathy from December 1994 to March 1995. The mean age was 41.4 +/- 14.4 years (range 14-85). There were 160 males (53%) and 142 females (47%). One hundred forty (46%) were type 1 and 162 (53.6%) were type 2. The mean duration of diabetes was 9.4 +/- 5.4 years and the mean Hemoglobin Alc (HbAlc) was 10.4 + 2.2%. On the day of the examination the mean fasting blood glucose (FBG) and random blood glucose (RBG) were 195.5 +/- 79.9 mg/dl and 273.1 +/- 114.5 mg/dl respectively. The mean serum total cholesterol, triglycerides, LDL, VLDL and GDL were 166.5 +/- 45.5 mg/dl, 129.9 +/- 92.4 mg/dl, 94.5 +/- 36.4 mg/dl, 24.4 +/- 15.1 mg/dl and 44.3 +/- 11.5 mg/dl respectively. The overall prevalence of retinopathy was 37.8% out of which 108 patients (36.1%) had background retinopathy and 5 patients (1.7%) had proliferative retinopathy. The retina could not be visualized in three patients because of dense cataract. Retinopathy correlated positively with age, duration of diabetes and blood pressure respectively, however no significant correlation was seen with mean total HgAlc and serum lipids. Prevalence of retinopathy was comparable in type 1 and type 2 (p > 0.05). The prevalence of retinopathy in our patients relative to the duration of diabetes mellitus is high. Therefore, improving facilities for the diagnosis and treatment of retinopathy is recommended.

Profile of coronary artery risk factors in Ethiopian diabetic patients

OBJECTIVES

To assess the coronary artery risk factors in Ethiopian diabetic patients.

DESIGN

A cross sectional study done on a representative sample of diabetic patients to evaluate the coronary risk factors.

SETTING

Hospital-based study.

SUBJECTS

A total of 302 diabetic patients randomly selected from the 3000 regularly attending diabetic patients in the Tikur Anbessa Hospital Diabetes Centre of whom 161(53.3%) were males, 141(46.7%) were females, 140(46.4%) were Type 1 and 162(53.6%) were Type 2.

OUTCOME MEASURES

Assessment of the coronary risk factors in diabetic patients.

RESULTS

There were 20(6.6%) smokers and no ex-smokers. All smokers were males of whom five (25%) were Type 1 and 15(75%) were Type 2. Hypertension and obesity were found in 64(21.2%) and 69(22.8%) patients respectively. Sixty one (20.2%) patients and 43(14.2%) patients had hypercholesterolaemia and hypertriglyceridaemia respectively.

CONCLUSION

Our diabetic patients share the risk factors for developing coronary artery disease like any other diabetic patient in the developed countries but at a lower level.

Interrelationship between vitamin A, iodine and iron status in schoolchildren in Shoa Region, central Ethiopia

A total of 14,740 schoolchildren in seven provinces of Shoa Administrative Region in Central Ethiopia were surveyed for the prevalence of goitre, xerophthalmia and anaemia. Haemoglobin and packed cell volume were assessed in 966 children in one province while an in-depth study was conducted on 344 children in the same province and two others. Goitre, xerophthalmia (Bitot's spots) and clinical anaemia were observed in 34.2, 0.91 and 18.6% respectively of the children. Most biochemical variables were within the normal range while those of haemoglobin (Hb), mean corpuscular Hb concentration (MCHC) and urinary I excretion were lower, and mean corpuscular volume, mean corpuscular Hb (MCH), and immunoglobulins G and M were higher. Hb was strongly correlated with retinol, ferritin, MCHC, MCH, packed cell volume and erythrocyte count while retinol formed a triad with transthyretin (TTR) and retinol-binding protein (RBP) which were all correlated with one another. Total and free thyroxin and total and free triiodothyronine were positively correlated as were the concentrations of the total and free hormones. Thyrotropin (TSH) was negatively correlated with total and free thyroxin and positively correlated with free triiodothyronine. Thyroxin and triiodothyronine in both free and combined forms were all correlated with thyroxin-binding globulin which in turn was negatively correlated with the triad retinol, RBP and TTR. The triad was also negatively correlated with C-reactive protein. Urinary I excretion was positively associated with total thyroxin and negatively associated with TSH. The anaemia found was not nutritional in origin but due to the effect of infestation with intestinal parasites and malaria.