DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

Analysis of genetic diversity and population structure of some Ethiopian barley (Hordeum vulgare L.) accessions using SSR markers

Understanding the genetic diversity of existing genetic resources at the DNA level is an effective approach for germplasm conservation and utilization in breeding programs. However, the patterns of genetic diversity and population structure remain poorly characterized, making germplasm conservation and breeding efforts difficult to succeed. Thus, this study is aimed to evaluate the genetic diversity and population structure of 49 barley accessions collected from different geographic origins in Ethiopia. Twelve SSR markers were used to analyze all accessions and a total of 61 alleles were found, with a mean of 5.08 alleles per locus. The analysis pointed out the existence of moderate to high values of polymorphic information content ranging from 0.39 to 0.91 and the mean Shannon diversity index(I) was 1.25, indicating that they were highly informative markers. The highest Euclidean distance (1.32) was computed between accession 9950 and two accessions (247011 and 9949), while the lowest Euclidean distance (0.00) was estimated between accessions 243191 and 243192. The result of molecular variance analysis revealed that the highest variation was found among accessions (47) relative to within accessions (44) and among geographic origins (9). Cluster analysis grouped the 49 barley accessions into three major clusters regardless of their geographic origin which could be due to the presence of considerable gene flow (2.72). The result of the STRUCTURE analysis was consistent with neighbor-joining clustering and principal coordinate analysis. Generally, this study concluded that the variation among accessions was more important than the difference in geographical regions to develop an appropriate conservation strategy and for parental selection to use in breeding programs. This information will be helpful for barley conservation and breeding, and it may speed up the development of new competing barley varieties.

Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm

Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (H_e = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (F_ST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (F_ST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.

Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation

A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of diversity and admixture, with significant SNP associations identified for environmental adaptation. Sorghum [Sorghum bicolor L. (Moench)] is a major staple food crop in Ethiopia, exhibiting extensive genetic diversity with adaptations to diverse agroecologies. The environmental and climatic drivers, as well as the genomic basis of adaptation, are poorly understood in Ethiopian sorghum and are critical elements for the development of climate-resilient crops. Exploration of the genome-environment association (GEA) is important for identifying adaptive loci and predicting phenotypic variation. The current study aimed to better understand the GEA of a large collection of Ethiopian sorghum landraces (n = 940), characterized with genome-wide SNP markers, to investigate key traits related to adaptation to temperature, precipitation and altitude. The Ethiopian sorghum landrace collection was found to consist of 12 subpopulations with high levels of admixture (47%), representing all the major racial groups of cultivated sorghum with the exception of kafir. Redundancy analysis indicated that agroecology explained up to 10% of the total SNP variation, and geographical location up to 6%. GEA identified 18 significant SNP markers for environmental variables. These SNPs were found to be significantly enriched (P < 0.05) for a priori QTL for drought and cold adaptation. The findings from this study improve our understanding of the genetic control of adaptive traits in Ethiopian sorghum. Further, the Ethiopian sorghum germplasm collection provides sources of adaptation to harsh environments (cold and/or drought) that could be deployed in breeding programs globally for abiotic stress adaptation.