Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

Abstract

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses

“…Analysis of molecular variance (AMOVA) revealed highly significant genetic differentiations among groups of accessions classified based on the geographic region of origin, country of origin, flowering time, panicle shape, and Al tolerance ( p < 0.01). The significant differentiation among groups of finger millet accessions was in agreement with the previously published research using EST and genomic SSR markers ( Babu et al, 2014 ; Pandian et al, 2018 ; Brhane et al, 2021 ). In the present study, the highest level of differentiation was observed between Ethiopian and Zimbabwean accessions accounting for 43% of the total genetic variation ( Table 2 ).…”

“…This study revealed that the 288 genotypes from diverse sources originate from three genetic populations (K = 3). Similar to the present study, population structure analyses in previous research on finger millet using SSR and SNP markers revealed three genetic groups with different levels of admixture ( Dida et al, 2008 ; Kumar A. et al, 2016 ; Ramakrishnan et al, 2016 ; Lule et al, 2018 ; Pandian et al, 2018 ; Brhane et al, 2021 ). In the present study, the Zimbabwean accessions and Ethiopian accessions appeared to have originated from different genetic populations with few exceptions, which is expected due to the clear geographic separation between the two countries.…”

“…The fact that accessions representing all populations were found within Cluster-II of PCoA strongly suggests a countrywide gene flow, albeit to a different degree. Overall, the clustering pattern of accessions generally agrees with a recent study on Ethiopian finger millet accessions based on genomic and EST-derived SSR markers ( Brhane et al, 2021 ).…”

“…Eleven of the 14 released cultivars were clustered together in Cluster-VII, with nine of them showing tight clustering. A recent study based on SSR markers reported similar close clustering of finger millet cultivars ( Brhane et al, 2021 ). The clustering of cultivars close together indicates that they were developed based on genetically similar germplasm and/or selected for similar traits during breeding.…”

“…The slightly higher mean PIC value in Gimode et al (2016) could most likely be due to the use of more diverse accessions (wild and cultivated) and much fewer SNP loci (80) with more frequent alleles when compared to the present study (MAF > 0.05). Similarly, it is also lower than the average PIC of earlier studies using expressed sequence tags and genomic microsatellites (SSR) markers ( Gimode et al, 2016 ; Krishna et al, 2018 ; Lule et al, 2018 ; Pandian et al, 2018 ; Brhane et al, 2021 ). The PIC values of SNP markers are generally lower than those of SSR markers, as the average number of alleles per locus is higher in SSRs than in bi-allelic SNPs ( Chao et al, 2009 ).…”