Retrotransposon insertional polymorphism in sunflower (Helianthus annuus L.) lines revealed by IRAP and REMAP markers

Retrotransposons are ubiquitous components of plants genomes, making them useful molecular markers for genetic diversity studies. We used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers to assess genetic diversity and survey activity of LTR retrotransposon elements in 106 sunflower (Helianthus annuus L.) genotypes from different research centers. We found 118 (out of 128) and 113 (out of 120) polymorphic loci using 14 IRAP and 14 REMAP primers, respectively. The Mantel test between IRAP and REMAP cophenetic matrices revealed low correlation (r = 0.55) between them. Dice similarities based on combined (IRAP + REMAP) data ranged from 0.34 to 0.93 among (“11 × 12” and “F1250/03”) and (“HA335B” and “TMB51”) genotypes, respectively. Classification of genotypes using the Dice similarity matrix derived from IRAP+REMAP data based on the un-weighted pair-group method using the arithmetic average algorithm resulted in nine distinct groups. The studied genotypes were divided into seven groups considering their origins (research centers). Classification of genotypes can be useful to assess the genetic variation and gene flow between and within research centers. Analysis of molecular variance based on IRAP+REMAP data revealed a higher level of genetic variation within (94%) than between (6%) research centers. A high amount of gene flow was detected among USDA, ASGROW, and ENSAT groups. Because environmental factors have no influence on molecular markers, the construction of heterotic groups based on retrotransposon markers will be useful for the selecting of parents with a high probability of producing superior hybrids.