Gene Co-Expression Network Analysis Reveals AsAMS as a Key Regulator of Gametophyte Fertility in Garlic

The reproductive cycle of plants features a crucial transition between diploid sporophytic and haploid gametophytic generations. In garlic (Allium sativum L.), a lack of gametophyte fertility poses significant challenges for breeding. This study conducted a comprehensive comparative transcriptomic analysis across three developmental stages of garlic floral buds from three genotypes with varied fertility profiles to unravel the genetic underpinnings of gametophyte development. Through differential expression analysis and weighted gene co-expression network analysis, we identified key pathways and genes influencing gametophyte fertility. Our findings provided a comprehensive framework that reveals both shared and sex-specific regulatory mechanisms in garlic gametophyte development. Lipid metabolism appeared to be a common pathway influencing the fertility of both male and female gametes, whereas ribosome biogenesis was crucial for female gametophyte development. Furthermore, we identified the AsAMS gene as a key regulator of male gametophyte fertility, likely orchestrating tapetal development and microspore formation by modulating lipid metabolism through a conserved tapetum network. The first functional validation using virus-induced gene silencing in garlic further substantiated the role of AsAMS, which demonstrated its critical impact on pollen viability and morphological integrity of reproductive structures. Taken together, these findings not only deepen our understanding of the genetic mechanisms underlying gametophyte development in garlic but also shed light on potential genetic interventions to overcome fertility barriers. By delineating the pathways and key regulators such as AsAMS, this study opens new avenues for enhancing reproductive efficiency in garlic.