# Protocol for the identification of selected genes and haplotype analysis in soybean using next-generation sequencing

## TL;DR

This paper outlines a protocol for identifying selected genes and analyzing haplotypes in soybean using next-generation sequencing to understand genetic adaptation and improvement.

## Contribution

A detailed protocol for identifying selected genes and haplotypes in soybean using genome resequencing data.

## Key findings

- Steps for sequencing data collection and preprocessing are described.
- Methods for detecting genomic regions under selection and constructing haplotypes are outlined.
- The protocol provides insights into the genetic basis of soybean adaptation and improvement.

## 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

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.