Single nucleotide polymorphism based assessment of genetic diversity in local and exotic onion genotypes

• Published in: Molecular biology reports 2022-06, Vol.49 (6), p.5511-5520
• Main Authors: Tabussam, Najma, Rana, Rashid Mehmood, Wattoo, Fahad Masoud, Khan, Azeem Iqbal, Amir, Rai Muhammad, Javed, Talha, Ahmar, Sunny, Dessoky, Eldessoky S., Abdelsalam, Nader R.
• Format: Article
• Language: English
• Subjects: Animal Anatomy; Animal Biochemistry; Ascorbic acid; Biomedical and Life Sciences; Eigenvalues; Gene polymorphism; Genetic diversity; Genetic variability; Genotyping; Germplasm; Heterozygosity; Histology; Life Sciences; Morphology; Original Article; Polymorphism; Population structure; Principal components analysis; Progress in genomics; Single-nucleotide polymorphism; transcriptomics and breeding of crops; Variance analysis
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-022-07431-z

Background Onion is an economically important vegetable cultivated worldwide on a large scale. Liberal exchange of germplasm and frequent selection caused narrow genetic diversity in most crops, including onion. Thus, it is essential to estimate and understand genetic diversity before launching of any breeding program. The current study was conducted to explore genetic diversity among 39 short-day onion genotypes (indigenous and exotic). Methods and Results All the genotypes were evaluated for various phenotypic traits by using single nucleotide polymorphism (SNP) genotyping based on KASPar assays. Principal component analysis (PCA) was performed to determine the variability among genotypes. The four principal components with eigenvalue greater than 1 accounted for 67.5656% variability for quantitative traits, whereas first five principal components with eigenvalue greater than 0.7 accounted for 86.24% variation among the genotypes for qualitative traits. The principal component analysis identified diverse traits including bulb weight, bulb diameter, plant height, number of survived plants and vitamin C. These traits were further analyzed through ANOVA (Analysis of Variance) following augmented block design to describe genotypic variability for selected traits. Onion genotypes showed significant variation for bulb weight, bulb diameter and Vitamin C. Genotypic clustering based on PCA showed that 15 indigenous genotypes were clustered with exotic genotypes (14) while remaining indigenous genotypes (10) were distant. A total of 30 SNPs were used for assessment of genetic diversity out of these, 24 SNPs were detected with polymorphic loci (0.8%, heterozygosity), while only six markers were with monomorphic sites (0.2% heterozygosity). Subsequently, population structure analysis revealed three different populations indicating significant variability. Conclusion Conclusively, a significant similarity between exotic and a group of indigenous genotypes indicates direct adoption of exotic genotypes or their sister lines. A further broadening of the genetic base is required and could be done by crossing distant genotypes.