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

Abstract

Ethiopia, the probable center of origin and diversity for sorghum (Sorghum bicolor L. [Moench]) and with unique eco-geographic 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 (GBS). 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 (He = 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 (GWAS). While we found no evidence of genetic differentiation among administrative regions (FST = 0.02, p = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 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 and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers

“…Different molecular markers such as Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), Diversity Arrays Technology, (DArT), Microsatellites or Simple Sequence Repeats (SSR), and Single Nucleotide Polymorphism (SNP) came to be utilized in different sorghum researches including its genetic structure analysis [ 13 – 15 ]. Microsatellite markers have shown great potential to detect the genetic diversity and relationships of organisms due to their allele-specific and co-dominant nature [ [16] , [17] , [18] ]. Their higher polymorphism, informativeness, and ease of identification from genomic sequences have made microsatellites a marker of choice in molecular studies.…”

Cultural Effects on Sorghum Varieties Grown, Traits Preferred, and Seed Management Practices in Northern Ethiopia

“…In terms of area of cultivation, it is the fifth most important cereal crop worldwide and the third most important crop in Ethiopia (FAOSTAT 2019). Ethiopia is located in a center of diversity for sorghum and all of the five botanical races of sorghum are found cultivated by farmers in the country (Wondimu et al 2021). The diversity of sorghum in Ethiopia is due to the historic movement of people and plants and the diversity of agroecological conditions in the country (Stemler et al 1977).…”

“…In recent years, several studies have focused on evaluating sorghum diversity in Ethiopia, including genetic variability of sorghum (Gebregergs and Mekbib 2020;Mola and Ejeta 2021;Wondimu et al 2021), on-farm sorghum landrace diversity and farmers' selection criteria (Mekbib et al 2009;Teshome et al 2016), the role of traditional farmers in the maintenance of sorghum landrace diversity in the north Shewa and south Welo regions of Ethiopia (Teshome et al 1999a), a botanical classification of sorghum landraces of the north Shewa and south Welo regions of Ethiopia (Teshome et al 1997), how agronomic traits have shaped sorghum diversity (Wubeneh and Sanders 2006), or how socioeconomic factors drive variety use, e.g., gender (Abebe et al 2021). However, these studies focused more on the genetic diversity and botanical classification of sorghum and only to a limited extent on the sociocultural factors influencing sorghum diversity.…”

Exploiting genetic variation from unadapted germplasm—An example from improvement of sorghum in Ethiopia

“…Numerous traits have been characterized in a wide range of sorghum germplasm (Cuevas & Prom, 2020; Upadhyaya et al, 2009; Vadez et al, 2011). Genomic diversity of sorghum has also been well characterized on a global scale (Hu et al, 2019; Lasky et al, 2015; Morris et al, 2013) and regional scale such as Ethiopian sorghum landraces (Girma et al, 2019; Menamo et al, 2021; Wondimu et al, 2021) and West African sorghum panel (Faye et al, 2021). Interspecific cross and backcross are common practices in introgressing desirable traits from exotic germplasm into adapted cultivars (Cox & Frey, 1984; Kong et al, 2020; Menkir et al, 1994; Piper & Kulakow, 1994).…”