TY - JOUR
T1 - High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis
AU - Ghonaim, Marwa
AU - Kalendar, Ruslan
AU - Barakat, Hoda
AU - Elsherif, Nahla
AU - Ashry, Naglaa
AU - Schulman, Alan H.
N1 - Funding Information:
Open access funding provided by University of Helsinki including Helsinki University Central Hospital. This work was supported under "Enhancing Development of Water Use Efficient Crops & Production Methods to Dry and Saline Conditions" (Grant No. EGY/IKY MTT/FCRI 14208006) funded by the Ministry of Foreign Affairs of Finland, and partially by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan in the framework of program funding for research (Grant Nos. BR05236334, BR06349586). The authors wish to thank Dr. James Thompson (University of Helsinki) for outstanding editing and proofreading of the manuscript.
Publisher Copyright:
© 2020, The Author(s).
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020/3/1
Y1 - 2020/3/1
N2 - 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.
AB - 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.
KW - Biodiversity
KW - Retrotransposons
KW - Transposable elements
KW - Zea mays
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U2 - 10.1007/s11033-020-05246-4
DO - 10.1007/s11033-020-05246-4
M3 - Article
C2 - 31919750
AN - SCOPUS:85077702277
SN - 0301-4851
VL - 47
SP - 1589
EP - 1603
JO - Molecular Biology Reports
JF - Molecular Biology Reports
IS - 3
ER -