Origin, evolution and genome differentiation in Guizotia abyssinica and its wild species

Analysis of genetic diversity and population structure of oilseed crop noug (Guizotia abyssinica) accessions collected from Ethiopia

BACKGROUND

Noug is an Ethiopian indigenous oilseed crop cultivated primarily for its oil and various economic importance. Evaluating the extent of genetic diversity within and among populations is one of the most important steps in breeding and conservation measures. Thus, this study aimed to uncover the extent of genetic diversity and population structure of noug accessions collected from different regions of Ethiopia using microsatellite markers.

METHODS AND RESULTS

A total of 161 accessions from fourteen regions of Ethiopia, including some from Eritrea using 13 microsatellite markers were analyzed. All the 13 microsatellite markers were polymorphic and highly informative with a mean PIC value of 0.82. The analysis generated a total of 158 alleles with a mean of 12.15 per locus. The overall mean of Shannon information index and heterozygosity/gene diversity were 1.57 and 0.74, respectively suggesting the presence of higher genetic diversity across the collection regions. AMOVA revealed that 96.06% of the total genetic variation was attributed to within populations while only 3.94% was attributed to among populations. Likewise, the dendrogram clustering, PCoA, and the model-based population structure analysis didn't exactly corresponded the grouping of the genotypes according to their regions of origin.

CONCLUSION

The microsatellites used in the present study are highly informative and could be targeted for developing markers for future marker-assisted breeding. Genotypes collected from Shewa, Wollo, Gojjam, Tigray, and B/G showed a higher genetic diversity and private alleles as compared to other populations. Hence, these areas can be considered as hotspots which could help for the identification of genotypes that can be used in breeding programs as well as for the implementation of further conservation programs.

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.

AFLP and RAPD analyses of genetic diversity of wild and/or weedy Guizotia (Asteraceae) from Ethiopia

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were used to provide estimates of the comparative genetic variation within and among populations of various Guizotia taxa with the goal of conserving and utilizing their genetic diversity. The percentage of polymorphic loci (P(S)) ranged from 28.5%-90% (AFLP) and 85.6%-99.6% (RAPD). The overall gene diversity estimate () has shown slight variation among taxa ranging from 0.32-0.37 (AFLP) and from 0.22 to 0.28 (RAPD). The within population diversity of "Chelelu" and "Ketcha" was found to be unexpectedly high. Both parameters used to estimate population differentiation (G(ST) and F(ST)) revealed the highest population differentiation G. zavattarii in followed by G. arborescens. Genetic variation among populations within a taxon was highly significant for all the five taxa as revealed by AMOVA (P<0.0001). The need for immediate conservation activities for G. arborescens and G. zavattarii, and factors that contribute to the existing genetic variability and population genetic structures are discussed.