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

Marwa Ghonaim,Alan H Schulman,Ruslan Kalendar,Hoda Barakat,Naglaa Ashry,Nahla Elsherif

doi:10.1007/s11033-020-05246-4

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.

Highlights

The long terminal repeat (LTR) retrotransposons (RLX) [1, 2] are a large class of transposable elements that propagate in the genome by a “copy-and-paste” mechanism that is essentially identical to the intracellular phase of retrovirus replication [1,2,3,4,5], in contrast to the “cut-and-paste” mobility of DNA transposons
We performed in silico Inter-retrotransposon-amplified polymorphisms (IRAPs) analysis, using FastPCR software for the maize (B73 RefGen_v4) and sorghum (Sorghum bicolor (L.) Moench) (Sorghum_bicolor_NCBIv3) genomes, using a single LTR primer corresponding to a sequence highly conserved in the RLXs examined
The LTR primers that produced many in silico IRAP amplicons showed a strong background of multiple and overlapping IRAP amplicons in the experiments

Summary

Introduction

The long terminal repeat (LTR) retrotransposons (RLX) [1, 2] are a large class of transposable elements that propagate in the genome by a “copy-and-paste” mechanism that is essentially identical to the intracellular phase of retrovirus replication [1,2,3,4,5], in contrast to the “cut-and-paste” mobility of DNA transposons. The RLX lifecycle involves transcription of an integrated copy, reverse transcription of the transcript into cDNA, and integration of the new copy. Because the RLX mother copy remains part of the chromosome and the daughter copies integrate at new loci, the precise insertion points for the daughter are unlikely to be identical in lines diverging by descent. Complete understanding of the genome and the relationship between genotype and phenotype requires knowledge of both the role and function of the genes as well as of the repetitive component, regarding RLX dynamics [3]. In higher plants, RLXs compose more than half of the repetitive DNA; they facilitate homologous recombination, and can undergo intra- and inter-RLX recombination that is part of their dynamism [4, 8,9,10]. Retroelements have been suggested as an important creative force in genome evolution, driving processes such as mutation, recombination, genome expansion, and adaptation of an organism to changing environmental conditions [3, 14, 16]

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