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

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Ghonaim , M , Kalendar , R , Barakat , H , Elsherif , N , Ashry , N & Schulman , A 2020 , ' High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis ' , Molecular Biology Reports , vol. 47 , no. 3 , pp. 1589-1603 . https://doi.org/10.1007/s11033-020-05246-4

Title: High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis
Author: Ghonaim, Marwa; Kalendar, Ruslan; Barakat, Hoda; Elsherif, Nahla; Ashry, Naglaa; Schulman, Alan
Contributor: University of Helsinki, Department of Agricultural Sciences
University of Helsinki, University Management
Date: 2020-03
Language: eng
Number of pages: 15
Belongs to series: Molecular Biology Reports
ISSN: 0301-4851
URI: http://hdl.handle.net/10138/317283
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.
Subject: ACCUMULATION
BARLEY
Biodiversity
FAST PRIMER
FASTPCR
IRAP
MARKERS
POPULATIONS
REMAP
Retrotransposons
SOFTWARE
TRANSPOSABLE ELEMENTS
Transposable elements
Zea mays
1182 Biochemistry, cell and molecular biology
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