.................................................................................................................................. x CHAPTER 1: INTRODUCTION................................................................................................... 1 1.1 OVERVIEW................................................................................................................. 1 1.2 ORIGIN, EVOLUTION AND DIVERSITY OF COTTON........................................ 3 1.3 CONTAMINATION OF AFLATOXINS IN COTTON............................................. 4 1.4 CONTROL MEASURES OF AFLATOXINS IN COTTON...................................... 5 1.5 DEVELOPMENT OF RNA-SEQ DATA ANALYSIS PIPELINE (COMPUTER PROGRAM/SOFTWARE).......................................................................................... 7 1.6 GOALS AND OBJECTIVES...................................................................................... 9 1.7 REFERENCES CITED.............................................................................................. 10 CHAPTER 2: IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN COTTON (GOSSYPIUM HIRSUTUM L.) IN RESPONSE TO INFECTION BY ASPERGILLUS FLAVUS ...................................................................................................................................................... 14 2.