Deployment of Intron Length Polymorphic (ILP) markers in dissipating diversity of Allium species

• Published in: South African journal of botany 2023-09, Vol.160, p.157-165
• Main Authors: Gowd, Talamarla Yeswanth Mahidar, Deo, Chandra, Manjunathagowda, Dalasanuru Chandregowda, Mahajan, Vijay, Dutta, Ram, Bhutia, Nangsol Dolma, Singh, Barun, Mounika, Vadde
• Format: Article
• Language: English
• Subjects: Allium; Diversity; ILPs; Molecular markers; Population structure
• ISSN: 0254-6299
• DOI: 10.1016/j.sajb.2023.06.053

•Diversity and phylogenetic relationship among the Allium species reveled by the ILP markers could be employed for genetic improvement Allium crops through inter-specific hybridization.•Intron-length polymorphic (ILP) markers were resulted their polymorphism and demonstrated co-dominance among alliums.•The population were grouped into three major clusters, by cultivated, semi-domesticated and wild species based on the ILP marker genotyping. Allium is one of the largest genera in monocots, it comprise of cultivated species like onion, garlic, leek, shallot, chive and bunching onion, and other semi-domesticated and wild species used as minor vegetables. Among species, the development and widespread of microsatellites have been reported, but there are least reports of systematic research and extensive use of intron-length polymorphic (ILP) markers among alliums. Introns endure less selection pressure, resulting in their polymorphism. Intron Length Polymorphic (ILP) markers derived from exon-flanking introns have been demonstrated to be accurate co-dominant markers in eukaryotes via the use of this polymorphism potential. In the present study, the genetic diversity aomong 95 accessions of alliums from the 13 species was revealed by ILP markers via UPGMA method, and population structure was also studied. Twenty-two ILP markers generated 75 loci with an average of 25.4 amplicons per loci. The Polymorphic Information content (PIC) ranges from 0.02 – 0.99, which is the lowest to highest polymorphic marker. The clustering pattern revealed the population, which were grouped into three major clusters, such as major cluster I grouped by semi-domesticated and wild species, major cluster II consist of cultivated Allium species (onion, garlic, and bunching onions) and major cluster III was out grouped which consisted of genotypes belong to Allium hookeri. The population structure studied also revealed the highest ΔK at 3, which inferred that the population was grouped into 3 genetic groups, which were correlated to the UPGMA clustering. From the finding of the diversity and phylogenetic relationship among the Allium species could be employed in further breeding programs for genetic improvement through inter-specific hybridization, to introgress the desirable traits from semi domesticated to the cultivated species.