Understanding the molecular basis of chromosome pairing and recombination during meiosis, particularly in polyploid crops such as wheat, is key to developing strategies for directly modulating recombination to expedite the development of novel germplasm. To facilitate a comprehensive analysis of gene expression dynamics during meiosis, we developed an optimized method termed MeioCapture for simultaneous isolation of uncontaminated meiocytes in prophase I substages of meiosis in wheat (Shunmugam et al., 2018. BMC Plant Biology 18: 293). Purified meiocytes from Chinese Spring anthers were collected from seven different meiotic stages, including pre-meiotic G2, leptotene, zygotene, pachytene, diplotene, metaphase I and metaphase II. Total RNA was isolated, and both mRNA and small RNA sequencing were performed using the Illumina platform. For comparison, RNA from whole anthers, pollens, flag leaf, and young leaves was isolated and sequenced. The analysis of mRNA and small RNA profiles of wheat meiocytes revealed general repression of transcription during meiosis. The comparison of RNA profiles between meiotic and non-meiotic tissues combined with weighted gene expression network analysis have uncovered differential gene expression patterns between different meiotic tissues and identified meiosisspecific genes and regulatory network modules. We are further leveraging these resources and PacBio isoform sequencing to determine the incidence and effects of de novo transcription and alternative splicing during different stages of meiosis. These findings along with our efforts to characterize and modulate gene regulatory networks governing homoeologous chromosome pairing and recombination will be discussed.