Identification and characterization of Allium cepa potential intron polymorphism markers

Abstract Allium cepa is a widely grown crop for its spice and culinary properties. For molecular breeding of Allium cepa and its improvement, mining and utilization of various sequence-based markers have been widely reported.Unfortunately, none has reported its molecular breeding using potential intron polymorphism (PIP) markers. Due to advantage of intron positioning prediction and practical utility, the PIP markers could be superior over the other molecular markers. These essential attributes, necessitated to establish an experiment for screening the possible PIP for polymorphism and cross-transferability in the Alliums. The screening results showed that among 500 Allium cepa potential intron polymorphism (AcPIP) markers, 275 are cross-transferable and polymorphic. Among the 275 AcPIPs, 111 polymorphic markers were physically mapped on to1st to 8th chromosomes of the Allium cepa. Out of the 275 AcPIP containing functionally significant markers, 118 were mapped in onion with arabidopsis proteome. BLAST analysis of 275 AcPIP containing expressed sequence tags (ESTs) showed their tolerance function to the large number of biotic and abiotic stresses. A set of 10 Alliums including cultivated Allium cepa (5), Allium sativum (3), and wild Alliums (2) were utilized to interpret the polymorphic possibilities of the 500 AcPIP markers. In totality, 55 percent AcPIP markers were polymorphic and cross-transferable among the Alliums. Across the 275 screened AcPIP markers, the highest percentage (92.7%) cross-transferability was found in Allium sativum var. Bhima Purple while it was lowest (82.1%) in the Allium fistulosum with 86.2% average cross transferability. The polymorphic information content (PIC) of AcPIP markers ranged from 0.03 to 0.47. Heterozygosity index (H) varied between 0.16 and 0.80. The constructed phylogenetic tree based on the AcPIP markers of 10 Alliums revealed different clusters due to differences in their taxonomic positions. Out of 275AcPIP markers, 10 AcPIP markers were selected for genotyping of 96 individuals of Allium cepa. Bayesian model-based structure and Jaccard dissimilarity-based NJ tree used for grouping of 96 individuals of Allium cepa showed two distinct groups (high total soluble solid; HTSS and low total soluble solid; LTSS), hence confirmed the reliabilities of these AcPIP markers. DNA fingerprint of Alliums with 20AcPIP markers suggested geographical reach of the released onion varieties and further validated the relevance of these 275 AcPIP markers. The results suggest that the 275 AcPIP validated functional molecular markers may be useful for the understanding of population structure, genomic association and comparative genomics of the Alliums for accelerating the breeding programme of the Alliums and other species.