Plant Retrotransposons: Genomic, Evolutionary and Biotechnological Perspectives

Retrotransposons are mobile genetic elements within the Class 1 transposon family that replicate through a “copy and paste” mechanism involving reverse transcription. This process creates multiple copies of DNA sequences within the plant genome. Retrotransposons are categorized into two main types based on their structure and transposition method: Long Terminal Repeat (LTR) Retrotransposons: LTR retrotransposons have LTR sequences at both 5′ and 3′ ends and are further divided into Ty1-copia and Ty3-gypsy classes. LTR retrotransposons are the most abundant and widespread retrotransposons. Non-LTR Retrotransposons: Non-LTR retrotransposons lack LTR sequences and include Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs). Functions and Impact: Retrotransposons can insert near or within genes, affecting their expression, causing genetic variations, and influencing evolution. They play a crucial role in genome size alteration, genome structure remodeling, and gene function displacement. During plant evolution, retrotransposons often remain inactive but can be activated under stress, suggesting their role in stress tolerance and phenotypic plasticity. Significance in Plants: This volume explores the role of retrotransposons which constitute a significant portion of plant genome. Retrotransposons make up a significant portion of the genome in plants like barley (Hordeum vulgare) (76%), maize (Zea mays) (75%), wheat (Triticum aestivum), soybean (Glycine max), Brassica, and Nicotiana species. These serve as molecular markers in crop cultivars and impact gene structure and function, contributing to plant development and stress responses. Biotechnological Applications: Retrotransposons are now recognized as key components in genomic organization, mutation, regulation, plant genetics, epigenomics, and evolution. These are used as genetic tools for creating climate-smart crops for sustainable agriculture. Retrotransposon insertion polymorphisms serve as molecular markers in crop cultivars. Transposition can impact gene structure and function, playing a crucial role in plant development and stress responses. The book gives an up-to-date outlook on the origin, evolution, structure, and genomic organization, expression, retrotransposon regulation and transposition mechanism of retrotransposons in the plant genome and computational tools and algorithms to analyze retrotransposons across different species, and use as genetic tools in crop breeding and improvement. The book also highlights the biotechnological applications of retrotransposon transposable elements. Previously dismissed as parasites or selfish or JUNK DNA, but today’s “Just Unexplored Novel Know-how” are recognized as key components in genomic organization, mutation, regulation, plant genetics, epigenomics, evolution, and finds use as genetic tool for the creation of climate-smart crops for sustainable agriculture.