Genetic Diversity Analysis of Onion (Allium cepa L.) from the Arid Region of Tunisia Using Phenotypic Traits and SSR Markers

Abstract

The present study was carried out to evaluate and characterize, for the first time, the genetic potential of a collection of onion (Allium cepa L.) local accessions from the arid region of southern Tunisia. The genetic diversity among 135 onion individuals, belonging to 23 accessions, was evaluated using microsatellite (SSR) markers and phenotypic information. A total of 35 alleles were generated with 11 SSRs. The polymorphic information content (PIC) value ranged from 0.08 to 0.95, with an average PIC of 0.43. The expected heterozygosity averaged 0.37, and the observed heterozygosity averaged 0.42. The analysis of molecular variance (AMOVA) revealed that 79% of genetic variation existed within individuals. Structure and cluster analysis grouped the accessions into two major clusters: landraces and pre-breeding lines. For the phenotypic traits evaluated, field trials were conducted in two different environments. Significant differences among accessions were shown, and for most traits, there was also a significant environmental effect and a significant interaction between environment and accession. Great variability was found for all the traits that could be exploited to create new varieties of onion adapted to local conditions by selecting appropriate parents in hybridization breeding.

Exploring Genetic Diversity and Phylogenetic Relationships in Camellia reticulata Cultivars Using Novel Low-Copy Nuclear Gene Markers

“…While AFLP (Amplified Fragment Length Polymorphism) markers have been employed to explore genetic diversity and structure [6], challenges arise from the hexaploid nature of C. reticulata, which also includes octaploid and decaploid cultivars [7,8]. Traditional molecular markers, such as AFLP, ITS (Internal Transcribed Spacer), and SSR (Simple Sequence Repeat), may present complications, such as double bands during amplification and multi-peaks during sequencing in polyploid groups [9][10][11]. It has been reported that the phylogenetic relationships of C. reticulata cultivars, based on ITS copies from clones, are confounded by the presence of numerous ITS pseudogenes [12].…”

Genetic Diversity and Population Structure Analysis of Excellent Sugar Beet (Beta vulgaris L.) Germplasm Resources

“…Integrating phenotypic identification and molecular markers can enhance the accuracy of genetic diversity studies. This is because molecular markers solely identify variations at the DNA level, which may not necessarily manifest in observable traits (phenotypes) [32][33][34]. To select excellent hybrid combinations and obtain high-quality innovative varieties, it is necessary to identify and analyze sugar beet germplasm resources.…”