Analysis of the molecular diversity of Kenyan sorghum germplasm using microsatellites

In Vitro Screening of Molecular Diversity Among Sorghums (Sorghum bicolor (L.) Landraces in Marathwada Region by Molecular Markers

Allelic variation is a valuable tool for displaying high levels of polymorphism within species and is closely correlated with crop productivity. In Marathawada, there is a significant amount of phenotypic heterogeneity among sorghum landraces. However, molecular variability needs to be reevaluated in order to identify any potential barriers that can interfere with current improvement initiatives. In the current work, we used 5 SSR markers to categorize 20 genotypes of elite (Sorghum bicolor L. Moench) accession from the Marathwada region, including one standard cultivar from various agro-economic zones. According to the results of this study, 14 alleles were found among the 20 genotypes, with a PIC value that ranged from 0.37 to 0.70 and a mean of 0.44 per locus. Each locus had anything from 1 (gpsb089) and 5 (mSbCIR223), with an average of 2.80 alleles per locus. A neighbor-joining tree was constructed and showed clustering of genotypes into two groups; this indicates that there is considerable diversity in genotypes compared with advanced cultivar for desired genotype (IS1042) by using SSR markers. Results show that most diverse cultivars were IS-4564, IS18357, and IS-18381, and significant variation was also reported in IS4566 and IS18379.

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.

Analysis of in situ diversity and population structure in Ethiopian cultivated Sorghum bicolor (L.) landraces using phenotypic traits and SSR markers

Genetic diversity is a fundamental input for every plant breeding program, genetic resources conservation, and evolutionary studies. In situ diversity and population genetic structure of eight cultivated sorghum landrace populations were investigated in the center of origin, Ethiopia using seven phenotypic traits and 12 highly polymorphic sorghum SSR markers. In farmers' fields, DNA samples were collected using Whatman® plant saver card and quantitative phenotypic traits were measured from 160 individual plant samples belonging to the eight populations representing three diverse geographical regions. High diversity was observed among the various populations for the measured phenotypic traits. The 12 SSR loci produced a total of 123 alleles of which 78 (63.41%) were rare (frequency ≤0.05) with an average of 10.25 alleles per polymorphic locus. The polymorphism information content (PIC) was in the range 0.39-0.85 showing the good discriminatory power of the SSR loci used. Average observed heterozygosity and gene diversity across all populations and loci ranged 0.04-0.33 and 0.41-0.87, respectively. Neighbor-joining and STRUCTURE analyses grouped the 160 samples from the eight populations differently. AMOVA showed 54.44% of the variation to be within populations, 32.76% among populations within regions, and 12.8% among the regions of origin. There was high divergence in the total populations (FST = 0.40) indicating low level of gene flow (Nm = 0.38), but high gene flow was also observed in some adjacent populations. The populations from Wello displayed close relationship with remote Gibe and Metekel populations indicating that the variation followed human migration patterns. Implications of the results for sorghum improvement and germplasm conservation are discussed.

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.