Monogalactosyldiacylglycerol (MGDG) is the major lipid constituent of thylakoid membranes and is essential for chloroplast biogenesis in plants. In Arabidopsis (Arabidopsis thaliana), MGDG is predominantly synthesized by inner envelope-localized MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE1 (MGD1); its knockout causes albino seedlings. Because of the lethal phenotype of the null MGD1 mutant, functional details of MGDG synthesis at seedling development have remained elusive. In this study, we used an inducible gene-suppression system to investigate the impact of MGDG synthesis on cotyledon development. We created transgenic Arabidopsis lines that express an artificial microRNA targeting MGD1 (amiR-MGD1) under the control of a dexamethasone-inducible promoter. The induction of amiR-MGD1 resulted in up to 75% suppression of MGD1 expression, although the resulting phenotypes related to chloroplast development were diverse, even within a line. The strong MGD1 suppression by continuous dexamethasone treatment caused substantial decreases in galactolipid content in cotyledons, leading to severe defects in the formation of thylakoid membranes and impaired photosynthetic electron transport. Time-course analyses of the MGD1 suppression during seedling germination revealed that MGDG synthesis at the very early germination stage is particularly important for chloroplast biogenesis. The MGD1 suppression down-regulated genes associated with the photorespiratory pathway in peroxisomes and mitochondria as well as those responsible for photosynthesis in chloroplasts and caused high expression of genes for the glyoxylate cycle. MGD1 function may link galactolipid synthesis with the coordinated transcriptional regulation of chloroplasts and other organelles during cotyledon greening.In dicotyledonous plants, cotyledons, which are formed during embryogenesis, initially serve as storage organs during seed germination but mainly function in photosynthesis after seedling establishment. During the developmental switch from heterotrophic to autotrophic growth in germinated seedlings, metabolic activities change greatly in cotyledon cells. Before the development of photosynthetic capacity in cotyledons, the seedlings of oilseed plants such as Arabidopsis (Arabidopsis thaliana) grow heterotrophically depending on triacylglycerol (TAG) stored within oil bodies in cotyledon cells. In this stage, peroxisomes function as the glyoxysome, which converts fatty acids bound to TAG to succinate via b-oxidation and the glyoxylate cycle, to provide carbon sources and energy for growth. After chloroplast development, plants rely on photosynthesis, which converts solar energy into chemical energy and fixes carbon dioxide into carbohydrates. Concomitant with photosynthesis, photorespiration, performed by cooperation among chloroplasts, peroxisomes, and mitochondria, is activated to recycle 2-phosphoglycolate, the product of oxygenation reaction instead of carboxylation by Rubisco (Peterhansel et al., 2010).Chloroplast biogenesis involves the remarkable develop...