Abstract
Meiosis is of crucial importance in agriculture because it provides the genetic variation required for breeding programs. Many cytological techniques have thus been developed to study meiosis in plants. Maize provides a powerful system for cytogenetic analysis due to its large conspicuous chromosomes. This protocol outlines a method for the simultaneous visualization of specific chromosomes or their segments, alongside proteins involved in meiosis in maize germ cells. The workflow combines fluorescence in situ hybridization (FISH) of oligonucleotide probe cocktails (oligo-FISH) covering entire specific chromosomes, or large chromosome segments, with immunostaining of chromosomal proteins. This method enables the examination of chromosome location, structure, dynamics, and protein distribution during key meiotic events. Immuno-FISH reveals how chromosome structure and meiotic proteins interact to shape recombination, providing mechanistic insight into meiotic progression, and enabling strategies to adjust recombination patterns for plant breeding.