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

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.

Nutraceutical profiling of elite onion germplasm and breeding hybrids with improved nutraceutical quality.

Onion (Allium cepa L) is a major reservoir of important nutraceutical ingredients. Herein, nutraceutical profiling of elite germplasm was assessed and hybrids with improved nutraceutical quality were selected. The nutraceutical components were screened through Fourier Transform Infrared Spectroscopy (FTIR) analysis (scan range 4000-400cm-1) followed by spectrophotometric/colorimetric quantification in oven dried bulb samples. Line × Tester (L×T) analysis was used to identify potential hybrids with better nutraceutical quality. Based on common functional groups obtained from FTIR analysis, as well as bulb color, the onion genotypes were categorized into six groups viz., white, yellowish brown, light brown, dark brown, brown and purplish brown. Results indicated that the purplish brown, yellowish brown and dark brown genotypes had maximum concentration of pyruvic acid, total flavonoids and total phenolic content, while vitamin C content showed weak association with color pigmentation. The onion variety 'Onion Swat' contained the highest level of pyruvic acid (17.18 µM) and 'MKS8823GO' had the highest vitamin C content (13.83mg/100mL). The L×T analysis revealed that out of 35 crosses, 'MKS-77127 × Onion Swat' and 'MKS-77127 × MKS777' were the best hybrids with improved nutraceutical quality. Further, observations for specific combining ability, general combining ability, genetic versus environmental variance, heritability and heterosis indicated that the studied parameters were genetically inherited and could be improved significantly by adopting an appropriate breeding strategy.