Transcriptome Profiling Of Upland Cotton Shoot Apex During Floral Induction

Cotton is a kind of important economic crop and strategic resource. The contradiction between large amount of people and small area of farmland as well as the conflict between grain and cotton for land is more and more serious. Precocious variety comes into being to meet the trend. The flower development is closely related to the early maturity, and the floral induction plays a vital role in the process of flower development. With application of the digital gene expression profiling technology, the gene expression profiling of different stages of CCRI36 (OTLS,1TLS,2TLS,3TLS) and TM-1 (1TLS,2TLS,3TLS) shoot apices was compared respectively. Then the entire gene expression profiling of CCRI36 and TM-1 shoot apices during the floral initiation process was compared. Through comparison and identification of differentially expressed genes, several important genes and biological pathways significantly related to the floral initiation process were identified. And many genes that were expressed differentially between the precocious variety CCRI36 and late-maturing variety TM-1 were also obtained. These results provided a large number of candidate genes for controlling the floral induction and also laid a solid foundation for exploring the induction mechanism of cotton flower bud initiation and molecular mechanism for early initiation in the precocious variety. The main results were as follows:1. Through histological observation of shoot apices of precocious variety CCRI36 and late-maturing variety TM-1, it turned out that CCRI36 started flower bud differentiation at the time point of two true-leaf stage, whereas TM-1 did so during three true-leaf stage. This indicated floral initiation of precocious variety was earlier than that of late-maturing variety.2. Tag-sequencing approach developed by Illumina/Solexa deep-sequencing technology was adopted to identify gene expression profiling of CCRI36 and TM-1 shoot apices during the floral initiation process. Seven tag libraries (0TLS,1TLS,2TLS,3TLS of CCRI36 and 1TLS,2TLS,3TLS of TM-1) were individually obtained by Tag-sequencing. Then to complete gene expression annotation, all tags in each library were mapped to the reference sequences database called the DFCI Cotton Gene Index database.3. Through identification and statistical analysis of differentially expressed genes, the result showed that the number of genes between OTLS vs 1TLS of CCRI36 was the most and for TM-1 the most was 2TLS vs 3TLS. Further analysis showed that homologous gene of the floral meristem identity gene API and GhSOCl were up-regulated in expression between OTLS vs 1TLS of CCRI36 and between 2TLS vs 3TLS of TM-1. Based on the above two points, it can be deduced that genes related to the floral induction were differentially expressed between OTLS vs 1TLS of CCRI36 and between 2TLS vs 3TLS of TM-1.4. Two groups were focused on, one was OTLS vs 1TLS of CCRI36, the other was 2TLS vs 3TLS of TM-1. The genes that had significant changes respectively in these two groups were compared. The related genes involving in GA biosynthesis and signal transduction were discovered from genes sharing the same expression pattern in two materials, and it can be postulated that GA pathway had a positive impact on the induction of flower bud differentiation of upland cotton. Subsequently, up-regulated genes sharing the same expression pattern was compared with up-regulated genes(TM-11TLS vs 3TLS), and it can be deduced that genes that were still up-regulated were involved in the floral induction of upland cotton. The VIP3 homolog was discovered in down-regulated genes sharing the same expression trend in the two groups (CRI36 OTLS vs 1TLS and TM-12TLS vs 3TLS), which indicated these genes might contain genes that negatively regulated the initiation of flower bud differentiation in upland cotton. These genes related to floral induction with the different expression pattern, such as homologous genes of SPL3,VRN1,FVE, can be chosen as the candidate genes for identifying genes related to flower bud differentiation in early maturing variety.5. Finally, six genes were selected at random from the genes which displayed significant changes. Then, quantitative RT-PCR assays were used to check the accuracy of the expression analysis. The result showed that there were just some subtle differences between the results of quantitative RT-PCR assays and Tag-seq data sets, but the whole trend was mainly same.