High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

Abstract

Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

Genetic diversity of Alternaria species associated with black point in wheat grains

“…However, DNA profiling applications based on retrotransposons are limited by a paucity of knowledge about nucleotide sequences of LTR retrotransposons in species without a sequenced genome. In particular, phytopathogenic fungi have a small genome, so the development of genetic markers based on retrotransposons is difficult relative to species with a large genome (e.g., green plants and animals; Mandoulakani et al, 2015;Doungous et al, 2015;Ghonaim et al, 2020;Leigh et al, 2003;Li et al, 2020;Teo et al, 2005;Vukich et al, 2009;Vuorinen et al, 2018). However, the Inter-primer Binding Site (iPBS) amplification technique has proved to be a powerful DNA fingerprinting method that does not require information about retrotransposon sequences (Kalendar et al, 2010).…”

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

“…Polymorphism in RBIP is usually detected by gel electrophoresis or hybridization, using agarose or dot assays respectively. In high-throughput RBIP analysis, data is obtained usually by fluorescent scoring from generated tagged microarray marker profiles ( Ghonaim et al., 2020 ). A major challenge with RBIP characterization is the need for information on sequence of sections adjoining the retrotransposon insertion sites.…”

Genotypic variability and relationships of Sorghum bicolor accessions from Java Island, Indonesia based on IRAP markers

“…Similarly, molecular genotyping of sweet sorghum using SSR markers analyzed using NJ clustering method by Disasa et al (2014) showed the grouping of accessions based on geographical origin. Recently, Ghonaim et al (2020) in genetic diversity study of maize reported the clustering pattern resulted from retrotransposon data resulted in the grouping of samples based on ecogeographical origin. The structure of the dendrogram figuring out the clustering of 23 accessions into three groups with varying degree taxonomic distance showed high genotypic variability.…”