Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation
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ORIGINAL ARTICLE
Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation T. Menamo1 · B. Kassahun1 · A. K. Borrell2 · D. R. Jordan2 · Y. Tao2 · C. Hunt3 · E. Mace2,3 Received: 18 May 2020 / Accepted: 6 November 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message 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. Abstract 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 25% missing values, a subset of 50,367 SNPs was identified and missing values inferred using the Beagle 5.0 software
Theoretical and Applied Genetics
package (Browning et al. 2018). The data set was further filtered to exclude SNPs with MAF 0.60, using the R packages factoextra and hierfstat. The genetic variation revealed by the neighbor-joining tree analysis (Fig. 3d) was in-line with the previous analyses and in particular highlighted the divergence of subpopulations G2 (durra types), G6 (durra types) and G8 (bicolor types) from the other subpopulations (Online Resource 3).
Sorghum genetic and agroecology diversity
Fig.2 LD (r2) Decay per Kb between pairs of loci across all chromosomes for the Ethiopian landraces (blue) and the sorghum diversity panel (red) described in Tao et al (2020) (color figure online)
Genome-wide nucleotide variation was quantified across landraces and subpopulations to investigate the genetic diversification in Ethiopian sorghum. The overall SNP genetic variation (π) per nucleotide was 0.12582 across all 940 Ethiopian sorghum germplasm. A total of 487 genotypes were selected based on group membership coefficient matrix > = 0.60 (60%) and geographical information used to calculate the genetic diversity among
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