Optimized semi-specific PCR amplification using arbitrarily degenerate primer for genome-wide genotyping and its application in peanut genetic diversity study DOI Open Access
Sheng Zhao, Yue Wang, Xuejiao Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 7, 2024

Abstract Cultivated peanut ( Arachis hypogaea L.) is an important legume crop with a large genome size but limited genetic diversity. Evaluating the variation among diverse germplasms using genome-wide molecular markers effective strategy to explore its diversity and thereby facilitate improvement. In this study, we introduced novel whole-genome genotyping (WGG) technique named dRAPD-seq (degenerate Random Amplification Polymorphic DNA sequencing), which relies on semi-specific PCR amplification by arbitrarily degenerate (AD) primer next-generation sequencing (NGS), demonstrated robust reproducibility high accuracy. Subsequently, applied investigate relatedness within population of 101 accessions identified low these accessions. Our phylogenetic tree, structure analyses, principal component analysis (PCA) indicated that could be clustered into three subpopulations, largely corresponding botanical types. conclusion, research not only cost-effective easy-to-conduct WGG method also provided valuable insights for utilizing in future breeding programs.

Language: Английский

Harnessing transposable elements for plant functional genomics and genome engineering DOI Creative Commons
Xiaoyuan Tao, Siyu Feng, Yuan Lü

et al.

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression driving genome evolution crop domestication. Despite advances understanding the functions mechanisms TEs, comprehensive review their integrated knowledge cutting-edge biotechnological applications TEs is still needed. We provide thorough overview that connects discoveries, mechanisms, technologies associated with TEs. discuss identification function driven by functional genomics, epigenetic regulation utilization active genomics engineering. In summary, expanding application will be beneficial to breeding synthetic biology future.

Language: Английский

Citations

0
Optimized semi-specific PCR amplification using arbitrarily degenerate primer for genome-wide genotyping and its application in peanut genetic diversity study DOI Open Access
Sheng Zhao, Yue Wang, Xuejiao Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 7, 2024

Abstract Cultivated peanut ( Arachis hypogaea L.) is an important legume crop with a large genome size but limited genetic diversity. Evaluating the variation among diverse germplasms using genome-wide molecular markers effective strategy to explore its diversity and thereby facilitate improvement. In this study, we introduced novel whole-genome genotyping (WGG) technique named dRAPD-seq (degenerate Random Amplification Polymorphic DNA sequencing), which relies on semi-specific PCR amplification by arbitrarily degenerate (AD) primer next-generation sequencing (NGS), demonstrated robust reproducibility high accuracy. Subsequently, applied investigate relatedness within population of 101 accessions identified low these accessions. Our phylogenetic tree, structure analyses, principal component analysis (PCA) indicated that could be clustered into three subpopulations, largely corresponding botanical types. conclusion, research not only cost-effective easy-to-conduct WGG method also provided valuable insights for utilizing in future breeding programs.

Language: Английский

Citations

0