Protocol for the identification of selected genes and haplotype analysis in soybean using next-generation sequencing
Year: 2025
Type: article
Abstract: Selected genes are genomic regions shaped by selection pressure and are often associated with important agronomic traits. Here, we present a protocol for identifying selected genes using genome resequencing data, followed by haplotype analysis of these genes. We describe steps for sequencing data collection and preprocessing, detection of genomic regions under selection, and haplotype construction based on sequence variation. The selected genes and haplotypes identified using this protocol provide insights into the genetic basis of soybean adaptation and improvement. For complete details on the use and execution of this protocol, please refer to Zhu et al. 1 • Protocol for genome-wide identification of selective sweeps in soybean • Workflow for prioritizing selected genes and resolving key haplotypes • Framework for cross-population mining of elite functional haplotypes Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Selected genes are genomic regions shaped by selection pressure and are often associated with important agronomic traits. Here, we present a protocol for identifying selected genes using genome resequencing data, followed by haplotype analysis of these genes. We describe steps for sequencing data collection and preprocessing, detection of genomic regions under selection, and haplotype construction based on sequence variation. The selected genes and haplotypes identified using this protocol provide insights into the genetic basis of soybean adaptation and improvement.
Source: STAR Protocols
Authors: Zhou Zhu, Zhixi Tian
Institution: University of Chinese Academy of Sciences
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $1,550
Award: G7023501448
OpenAlex ID: W7117103164