Exploring the genetic basis of anthracnose resistance in Ethiopian sorghum through a genome-wide association study.

BACKGROUND: Sorghum anthracnose is a major disease that hampers the productivity of the crop globally. The disease is caused by the hemibiotrophic fungal pathogen Colletotrichum sublineola. The identification of anthracnose-resistant sorghum genotypes, defining resistance loci and the underlying genes, and their introgression into adapted cultivars are crucial for enhancing productivity. In this study, we conducted field experiments on 358 diverse accessions of Ethiopian sorghum. Quantitative resistance to anthracnose was evaluated at locations characterized by a heavy natural infestation that is suitable for disease resistance screening. RESULTS: The field-based screening identified 53 accessions that were resistant across locations, while 213 accessions exhibited variable resistance against local pathotypes. Genome-wide association analysis (GWAS) was performed using disease response scores on 329 accessions and 83,861 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS). We identified 38 loci significantly associated with anthracnose resistance. Interestingly, a subset of these loci harbor genes encoding receptor-like kinases (RLK), nucleotide-binding leucine-rich repeats (NLRs), stress-induced antifungal tyrosine kinase that have been previously implicated in disease resistance. A SNP on chromosome 4 (S04_66140995) and two SNPs on chromosome 2 (S02_75784037, S02_2031925), localized with-in the coding region of genes that encode a putative stress-induced antifungal kinase, an F-Box protein, and Xa21-binding RLK that were strongly associated with anthracnose resistance. We also identified highly significant associations between anthracnose resistance and three SNPs linked to genes (Sobic.002G058400, Sobic.008G156600, Sobic.005G033400) encoding an orthologue of the widely known NLR protein (RPM1), Leucine Rich Repeat family protein, and Heavy Metal Associated domain-containing protein, respectively. Other SNPs linked to predicted immune response genes were also significantly associated with anthracnose resistance. CONCLUSIONS: The sorghum germplasm collections used in the present study are genetically diverse. They harbor potentially useful, yet undiscovered, alleles for anthracnose resistance. This is supported by the identification of novel loci that are enriched for disease resistance regulators such as NLRs, LRKs, Xa21-binding LRK, and antifungal proteins. The genotypic data available for these accessions offer a valuable resource for sorghum breeders to effectively improve the crop. The genomic regions and candidate genes identified can be used to design markers for molecular breeding of sorghum diseases resistance.

Genetic variability among lowland sorghum accessions collected from southern Ethiopia for grain quality traits.

The study was carried out to assess the nature and magnitude of genetic variability for grain quality traits in lowland sorghum accessions. Understanding genetic diversity and trait association is crucial to designing an effective breeding plan to develop nutrient-rich varieties. Two hundred twenty-five accessions were evaluated using a simple lattice design with two replications at Weioto. Prepared samples per replication were scanned by mixing the grains and repacking the sample cup after each scan. Analysis of grain quality traits revealed significant (P ≥ 0.01) differences among the genotypes indicating a good chance for genetic improvement. Genotypic means of nutritional content showed that amylose (Am) content ranged from 19.11 to 20.80%, ash value ranged from 0.37 to 3.14%, starch content ranged from 42.29 to 72.77%, and protein (pr) in dry basis ranged from 2.62 to 10.45%. Similarly, iron (Fe) ranged from 1.38 to 73.21 ppm, zinc (Zn) ranged from 16.8 to 66.02 ppm, and tannin content ranged between -0.08 and 9105.21%. Broad-sense heritability (h2b) of all grain quality attributes such as amylose; ash; starch; moisture; iron; zinc; protein, and tannin was in the range of 13-92%. Principal component analysis showed the first three principal components with an eigenvalue equal to or greater than unity adequately explain the variation in the data. Significant positive genetic correlations (P < 0.001) with amylase, starch, iron, and zinc, while tannin had a weak association with grain yield. This result declares/signifies/a good prospect of southern Ethiopia lowland sorghum accessions for genetic improvement in grain yield and quality traits.

Farmers' perspectives on drivers of rice yield in the Fogera Plain of Ethiopia.

In Ethiopia, rice productivity varies over locations. However, there is limited understanding about rice yield drivers for design appropriate policies and strategies to enhance rice productivity. This study focuses on assessing the patterns of rice yield and its drivers. Data were collected from 220 households and field measurements were made accordingly. Descriptive statistics, the Kruskal-Wallis test, and biplot were to assess yield groups, drivers ranking, and driver yield group association, respectively. Four yield groups were identified 2.1 (Y1) t ha-1, 3.0 (Y2) t ha-1, 4.1(Y3) t ha-1, and 5.2 (Y4) t ha-1. Water stress, low soil fertility, lack of draft animals, shortage of credit, pests, weak extension, and weeds were yield affecting drivers in Y1. Similarly, labor shortage, increase input price, credit, and weed was yield-limiting drivers in Y2 while flooding, poor marketing, and the lack of storage were the drivers in Y3. Poor seed system, post-harvest losses, lack of farm tools, price fluctuation, lack of storage, and poor marketing were drivers in Y4. This study showed that the major drivers that significantly affect yield varied among the yield groups. Perceived drivers of the different yield groups have a better understanding and prospect for strategic target policy and intervention support to minimize yield losses thereby increasing productivity.

Genotype-by-environment interaction on canning and cooking quality of advanced large-seeded common bean genotypes.

Developing beans for high canning and cooking quality has been a major concern of plant breeders as the demand of consumers for beans in terms of quality is increasing. This study determined the effect of genotype-by-environment (GEI) on canning and cooking quality of common beans. Twenty three newly developed large-seeded bean genotypes and two standard checks collected from five growing sites of Ethiopia were tested using randomized completed block design with three replicates. Additive main effect and multiplicative Interaction (AMMI) and genotype plus genotype-by-environment interaction (GGE) biplot models were used in the data analysis. Genotypes were genetically different (P ≤ 0.01) for all of the quality traits varied from 42.3 to 57.4 minutes for cooking time and 260.4-278.6g for washed drained weight. Percent washed drained weight of all the tested genotypes was >60%, as required by processors. However, hydration coefficient (HC) was below the desired optimum level of 1.8, which could be improved through prolonged soaking period. From moderate to no clumping, and from moderately clear to clear brine were observed for canned beans. Generally, the newly developed genotypes had better canning and cooking quality except for HC. However, GEI exerted considerable effect on the quality traits especially cooking time. The interaction effect (34.25%) shared nearly three times greater effect than genotype (13.31%) and environment (11.44%); hence highly determined the cooking time. Both AMMI2 and GGE polygon view biplots captured 69.05 and 74.10% of the GEI variation, respectively, using the first and the second principal component axes (PCAs). In conclusion, plant breeders should think of GEI when testing beans for canning and cooking quality at substantial environments.

Supplementary irrigation for managing the impact of terminal dry spells on the productivity of rainfed rice (Oryza sativa L.) in Fogera Plain, Ethiopia.

A terminal dry spell is one of the main limiting factors for rice productions. Therefore, this study was conducted to assess the effect of supplemental irrigation for managing the impact of terminal dry spells on the productivity of different rice varieties grown under rainfed conditions in the Fogera Plain. The experiment was designed in a split-plot design with water regimes as main plot factors and rice varieties as a subplot factor with three replications. The water regimes were: dry planted rainfed rice (farmers practice) (FP), transplanted but not irrigated (IWOI), transplanted and irrigated to saturation (SAT), transplanted and ponding to 1 cm water (PD1), and transplanted and ponding to 3 cm water (PD2). The rice varieties were: X-Jigna (V1), Edget (V2), Hiber (V3), Fogera-1 (V4), and Nerica-4 (V5). The combined effect of PD2 with V1 had the highest grain yield (t/ha) (4.35 t/ha) while FP with V3 had the lowest grain yield (2.12 t/ha). The highest (205%) relative grain yield was obtained when V1 was grown under PD2 followed by V4 under PD2 (199%) and V5 under PD2 (192%) compared to FP with V3. Irrigation water productivity (WPIR) varied between water regimes x varieties from as low as 1.84kg grain mm-1ha-1 for V3 in FP to as high as the yield of 3.07kg grain mm-1ha-1 for V1 in PD2. The highest and lowest net benefits were recorded for V1 grown under PD2 (65, 550 ETB) and for V3 grown under TWOI (33, 500 ETB ha-1), respectively. Hence, the combined application of 3 cm ponding depth (PD2) with X-Jigna (V1) and 1cm ponding depth with Fogera-1 (V4) rice varieties could be suggested as effective terminal stress management to increase the yield and profitability of rainfed rice in the Fogera Plain and similar agro-ecologies.

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.

Folksong based appraisal of bioecocultural heritage of sorghum (Sorghum bicolor (L.) Moench): a new approach in ethnobiology.

BACKGROUND: Sorghum is one of the main staple crops for the world's poorest and most food insecure people. As Ethiopia is the centre of origin and diversity for sorghum, the crop has been cultivated for thousands of years and hence the heritage of the crop is expected to be rich. Folksong based appraisal of bioecocultural heritage has not been done before. METHODS: In order to assess the bioecocultural heritage of sorghum by folksongs various research methods were employed. These included focus group discussions with 360 farmers, direct on-farm participatory monitoring and observation with 120 farmers, and key informant interviews with 60 farmers and development agents. Relevant secondary data was also collected from the museum curators and historians. RESULTS: The crop is intimately associated with the life of the farmers. The association of sorghum with the farmers from seed selection to utilization is presented using folksongs. These include both tune and textual (ballad stories or poems) types. Folksongs described how farmers maintain a number of varieties on-farm for many biological, socio-economic, ecological, ethnological and cultural reasons. Farmers describe sorghum as follows: Leaf number is less than twenty; Panicle hold a thousand seeds; a clever farmer takes hold of it. In addition, they described the various farmers' varieties ethnobotanically by songs. The relative importance of sorghum vis-à-vis others crops is similarly explained in folksong terms. CONCLUSION: The qualitative description of farmers' characterisation of the crop systems based on folksongs is a new system of appraising farmers' bioecocultural heritage. Hence, researchers, in addition to formal and quantitative descriptions, should use the folksong system for enhanced characterisation and utilization of bioecocultural heritages. In general, the salient characteristics of the folksongs used in describing the bioecocultural heritages are their oral traditions, varied function, communal or individual recreation and message transmissions.

Infra-specific folk taxonomy in sorghum (Sorghum bicolor (L.) Moench) in Ethiopia: folk nomenclature, classification, and criteria.

BACKGROUND: Sorghum is one of the main staple food crops for the poorest and most food insecure people of the world. As Ethiopia is the centre of origin and diversity for sorghum, the crop has been cultivated for many thousands of years. Hence, indigenous knowledge based sorghum classification and naming has a long tradition. METHODS: In order to assess folk taxonomy, various research methods were employed, including, focus group interviews with 360 farmers, direct on-farm participatory monitoring with 120 farmers, key informant interviews with 60 farmers and development agents and semi-structured interviews with 250 farmers. In addition, diversity fairs were conducted with over 1200 farmers. Assessment of folk taxonomy consistency was assessed by 30 farmers' evaluation of 44 folk species. RESULTS: Farmers have been growing sorghum for at least 500 years (20 generations). Sorghum is named as Mishinga in the region. Farmers used twenty five morphological, sixty biotic and abiotic and twelve use-related traits in folk taxonomy of sorghum. Farmers classified their gene-pool by hierarchical classifications into parts that represented distinguishable groups of accessions. Folk taxonomy trees were generated in the highland, intermediate and lowland sorghum ecologies. Over 78 folk species have been identified. The folk species were named after morphological, use-related and breeding methodology used. Relative distribution of folk species over the region, folk taxonomy consistency, and comparison of folk and formal taxonomy are described. CONCLUSION: New folk taxonomy descriptors have been identified and suggested to be used as formal taxonomy descriptors. It is concluded that integrated folk-formal taxonomy has to be used for enhanced collection, characterisation and utilization of on farm genetic resources.