Bioinformatics

Biography

Biography: Yinghong Pan

Abstract

Proteomics analysis of complex trait is useful to understand gene functions and trait mechanisms. But the reliability of proteomics analysis is affected by many factors, such as genetic background influences, sampling variations, and experimental conditions. In this strategy, four near isogenic lines (NILs) of dwarf male-sterile (DS) wheat with different genetic backgrounds were analyzed and a large mass spectrometry (MS) data from multiple batches were used to study the DS traits in wheat. At first, another and immature spike proteins from four NILs of DS wheat were prepared in different ways and detected with different mass spectrometry, and a total of 58170 protein groups were detected from sixteen independent experiments. Secondly the abundance distributions of proteins that detected at different frequencies and expressed types were analyzed. By using several simple formulae which were introduced to evaluate the reliability of protein expression, a database contained expression levels of 58170 protein groups and comprehensive evaluation values of 17187 proteins without duplications was established. As focusing on nuclear male sterile trait mechanism and the function of Taigu genie male-sterile wheat (TGMSW) gene ms2 in those NILs, proteomes of immature spike from three DS wheat NILs were analyzed under same conditions, and 160 differentially expressed proteins and 43 highly expressed proteins detected in this experiment were compared with database. Finally, it is determined that 28 proteins were closely related to male-sterile trait. The result show that large MS data from multiple batches is helpful for studying the complex traits and gene functions.