Local Haplotyping Analysis for Flowering Time in Soybean Using Crosshap

The vast amount of genomic data available for various plant species has enabled a greater understanding of genomic regions associated with phenotypic variation, mainly through approaches such as Genome-Wide Association Studies (GWAS). However, relying solely on GWAS results limits our understanding of trait variation, as it focuses on individual SNPs without considering the linked variants that may also influence the trait. As a follow-up to GWAS, haplotype analysis focusing on local regions of the genome can provide detailed insights into the genetic variants associated with a trait. crosshap, a local haplotyping R-package, identifies and visualises haplotype structures, allowing users to explore allelic diversity and associated phenotypic variation in targeted genomic regions. This chapter demonstrates local haplotyping analysis using crosshap to understand the genetic control of flowering time in domesticated and wild soybean, informing breeding strategies and crop improvement efforts; however, crosshap can be applied to any species where suitable data is available.