Apple SWATH-MS - Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value

Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 411 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substanial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected. We also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Overall, our work provide important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributed to the fruit skin color formation.

苹果是全球最受欢迎的果树作物之一，其果皮颜色是影响商业价值的核心品质性状。然而，当前针对红皮苹果的遗传育种策略，以及果皮颜色分化的遗传基础，相关研究仍极为有限，且在很大程度上尚未明晰。本研究报道了一株红皮着色且花青素积累增强的富士苹果芽变突变体。通过定量SWATH-MS（全理论谱序贯采集-质谱）蛋白质组学分析，我们揭示了红皮苹果芽变的蛋白质组变化，共在苹果果皮中鉴定出411个差异表达蛋白。该突变体中，光合作用相关蛋白、胁迫响应相关蛋白以及花青素生物合成通路相关蛋白的表达水平显著上调。另一方面，研究检测到丝裂原活化蛋白激酶4（MAPK4）与甲羟戊酸激酶（MVK）的表达显著下调。借助先进的SWATH-MS分析，我们还推测该突变体的果皮颜色形成过程存在转录后调控机制。总体而言，本研究为利用蛋白质组学方法分析富士苹果的蛋白质组变化提供了重要参考，并揭示了一组可能参与果实果皮颜色形成的调控蛋白。