Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation

Menamo, Temesgen; Kassahun, Beemnet Mengesha; Borrell, Andrew; Jordan, David R.; Tao, Yongfu; Hunt, Colleen H.; Mace, Emma

doi:10.1007/s00122-020-03727-5

Cited by 36 publications

(28 citation statements)

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“…The Ethiopian sorghum gene pool has been used as a novel source of biotic and abiotic stress tolerance, greatly contributing to the improvement of sorghum, globally ( Adugna, 2014 ). The gene pool has been utilized in various studies that aimed at the identification of novel QTLs and genes governing complex traits ( Cuevas and Prom, 2013 , 2020 ; Cuevas et al, 2017 ; Menamo et al, 2021 ). Since polymorphism within genes or their close vicinity is expected to be the main basis of phenotypic variation, priority was given to SNPs located in genes in the SNP selection process in this study.…”

Section: Discussionmentioning

confidence: 99%

“…The Ethiopian sorghum gene pool has been used as a novel source of biotic and abiotic stress tolerance, greatly contributing to the improvement of sorghum, globally (Adugna, 2014). The gene pool has been utilized in various studies that aimed at the identification of novel QTLs and genes governing complex traits Prom, 2013, 2020;Cuevas et al, 2017;Menamo et al, 2021). Since polymorphism within FIGURE 6 | Average number of pairwise differences within and between sorghum accessions: average number of pairwise differences among the accessions (π xy ) (above diagonal, in green), average number of pairwise differences within accessions (π) (diagonal, in orange), and pairwise net number of allele differences among the accessions (d) (below diagonal, in blue).…”

Section: Snp Markers and Their Use In Genetic Diversity Analysis Of Sorghum Gene Poolmentioning

confidence: 99%

“…Previous studies on the genetic diversity of sorghum have been carried out by using random amplified polymorphism DNA (RAPD) analysis ( Ayana et al, 2000 ; Ruiz-Chután et al, 2019 ), simple sequence repeat (SSR) markers ( Djè et al, 2000 ; Ghebru et al, 2002 ; Manzelli et al, 2007 ; Ali et al, 2008 ; Wang et al, 2009 ; Ng’uni et al, 2011 , 2012 ; Burow et al, 2012 ; Adugna et al, 2013 ; Adugna, 2014 ; Mofokeng et al, 2014 ; Motlhaodi et al, 2014 , 2017 ), and express sequence tags (EST) SSR markers ( Ramu et al, 2013 ), SNP markers ( Cuevas et al, 2017 ; Afolayan et al, 2019 ; Cuevas and Prom, 2020 ). More recently, a few studies have been performed on the genetic diversity of Ethiopian sorghum accessions using SNP markers ( Girma et al, 2019 ; Menamo et al, 2021 ; Wondimu et al, 2021 ). These studies brought out the contribution of geographic regions and agro-ecological zones for the genetic variation and population structure of sorghum grown in Ethiopia.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

et al. 2022

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Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy–Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.

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Section: Discussionmentioning

confidence: 99%

“…The Ethiopian sorghum gene pool has been used as a novel source of biotic and abiotic stress tolerance, greatly contributing to the improvement of sorghum, globally (Adugna, 2014). The gene pool has been utilized in various studies that aimed at the identification of novel QTLs and genes governing complex traits Prom, 2013, 2020;Cuevas et al, 2017;Menamo et al, 2021). Since polymorphism within FIGURE 6 | Average number of pairwise differences within and between sorghum accessions: average number of pairwise differences among the accessions (π xy ) (above diagonal, in green), average number of pairwise differences within accessions (π) (diagonal, in orange), and pairwise net number of allele differences among the accessions (d) (below diagonal, in blue).…”

Section: Snp Markers and Their Use In Genetic Diversity Analysis Of Sorghum Gene Poolmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

et al. 2022

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“…According to Amede et al (2015) eight agro-ecological zones (cool/humid, cool/subhumid, cool/semiarid, cool/arid, warm/humid, warm/subhumid, warm/semiarid, and warm/arid) have been identified in Ethiopia based on the Global 16 Class Classification System. Given the fact that sorghum is grown in all these agroecologies except warm/humid and cool/arid ( Menamo et al 2021 ), we hypothesized that genetic groups could reflect to population structure across the agro-ecological zones of Ethiopia. Consistent with this hypothesis, we observed strong geographic clustering when the accessions were mapped by group ( Figure 3B ), suggesting significant contribution of agro-ecological variation to ancestry, with individuals in specific subgroup found to co-locate in geographic regions.…”

Section: Resultsmentioning

confidence: 99%

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

Wondimu

Dong

Paterson

et al. 2021

G3 Genes|Genomes|Genetics

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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.

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“…In addition, a total of 318 Sudanese sorghum core collections were evaluated with 183,144 SNP markers using the model-based clustering method that portrayed five subpopulations [ 11 ]. Furthermore, 940 diverse sorghum landraces of Ethiopia were assessed using 54,080 SNP markers that identified 12 subpopulations [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

Mengistu

Shimelis

Assefa³

et al. 2021

PLoS ONE

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In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

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Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation

Cited by 36 publications

References 48 publications

Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

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

Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

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