| Cotton (Gossypium spp.) is one of the most important economic crops due to its excellent natural fiber properties. China is the world’s largest producer and consumer of textiles, around the growing area of80million acres every year, the cotton textile industry in national economy plays an important part in our country. But, at present domestic raw cotton quality have not already met the demands of the market, and the superior quality raw cotton with a higher spinning performance almost all rely on imports. The domestic cotton fiber quality is poor because of low average span length and strength, which restrict sustainable development in cotton industry. Cotton fiber qualities including length, strength and fineness are controlled by genes that affect cell elongation and secondary cell wall (SCW) biosynthesis. Therefore, the research on cotton fiber development transcriptomics can be used to clarify gene expression patterns for crucial genes, and integratation of genetics and genetical genomics can help us understand the molecular mechanisms controlling the cotton fiber qualities, which will be remarkable significance for genetic improvement of fiber qualities.We developed AFLP, SAMPL, SABPL and EST molecular markers in BC1population of G. hirsutum acc. TM-1and G. barbadense cv. Hai7124, increasing244loci in our backbone BC1population, particular for EST functional markers, enriched types of molecular markers and dense area of chromosomes. The combination of four-year fiber trait data that were obtained from the same genetic materials revealed22QTL for fiber length (FL), strength (FS), micronaire reading (FM), elongation (FE), and uniformity (FU) involving genotype and interaction of genotype and environment [logarithm of odds (LOD)≥3.0] by multi-QTL joint analysis, including6main effect QTL,16QTL-by-environment interaction. QTL for FL and FS were mapped on A-subgenome (At) chromosomes (A1, A3, A5and All), whereas QTL for FU and FM were mainly mapped on D-subgenome (Dt) chromosomes (D1, D4, D7and D12). Stable or consistent QTL will provide foundation for identification of genes affecting fiber qualities.Cotton fiber is a highly elongated trichome from epidermal cell of cotton ovule that is one of the most important natural raw materials for the textile industry. Upland cotton (G hirsutum L.) accounts for about95%of the annual cotton production in the world. To reveal developmental features of upland cotton fiber cells, we combined11developmental stages (-3-25days post-anthesis, DPA) of microarray data in G. hirsutum acc.TM-1, and identified10,902effective genes during fiber cell initiation, elongation and secondary cell wall (SCW) synthesis. Of these genes, we determined6,186differentially expressed genes (DEGs) among11development times by SAM (significant analysis of microarray) multiclass. Several significant metabolic pathways from6,186DEGs were identified by Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis in fiber development, primarily including cytoskeleton proteins, flavonoid biosynthesis, oxidative phosphorylation, and glycolysis/gluconeogenesis. Comparative analyses of transcriptomes showed192specific-times expressed genes across a developmental time-course involving in4gene clusters, and many key genes were confirmed by real-time quantitative reverse transcription PCR (QRT-PCR) analysis. These specific-times expressed genes may determine that cotton fiber cell at a certain stage has its own unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript profiles. This study also gains new insights to understand the molecular mechanism of cultivated tetraploid cotton fiber development.Comparative analysis of gene expression in G. hirsutum and G. barbadense was conducted using the high-throughput microarray platform. To reveal the differential feature of fiber development that may account for fiber qualities, we measured dynamic change of fiber length of TM-1and Hai7124at different time points (5-38DPA), and observed that fiber length increased approximately linearly over the first15-20DPA in TM-1and23-28DPA in Hai7124, and plateaued as the fibers reached their final dimensions, great difference occurred between20-33DPA during elongation. To investigate differentially regulated genes in fiber developmental process, we hybridized a cotton fiber cDNA microarray (GPL2610) with RNA samples of TM-1and Hai7124fiber from five different developmental time-points,5,10,15,20and25DPA. We compare mRNA expression levels in developing fiber-cells using the empirical eBayes method in LIMMA, and revealed the numbers of DEGs between adjacent time-points during fiber development within and between species based on the criterion of false discovery rate (FDR)<0.05and fold change (FC)≥2. Within each species, the number of DEGs was unequally distributed between adjacent time points. In Hai7124,276(5vs.10DPA),2,402(10vs.15DPA),94(15vs.20DPA) and44(20vs.25DPA) genes were differentially expressed, whereas in TM-1,473,2,224,148and396genes were differentially expressed. Between Hai7124and TM-1, there were151,233,195,100and232genes differentially expressed at five time points (5-25DPA). Thus, the two periods10and25DPA with higher numbers of DEGs will be crucial for identification of fiber genes regulating elongation at fast elongation stage and determination G. barbadense fiber continuative elongation or the termination of G. hirsutum fiber elongation at the transition stage.To deeply identify fiber quality genes, we selected these two respective periods for further linkage analysis of expression profiles. We extensively investigated gene expression in fiber cells of66randomly selected BC1S1lines as well as the two parents TM-1and Hai7124using another cDNA microarray platform (GPL8569) with abundant probes. A total of13,760and13,411active transcripts at10and25DPA, respectively, were detected and142and302DEGs between TM-1and Hai7124were further identified. Furthermore,444expression traits in66cotton BC1S1lines were used to expression quantitative trait loci (eQTL) analysis. A total of916eQTL were statistically significant with a logarithm of odds (LOD) score exceeding permutation based thresholds (P<0.05), including293and623eQTL at10and25DPA, respectively. Many positional cis-/trans-acting eQTL could be estimated by comparing chromosomal location of each transcript and position of its eQTL A total of46eQTL hotspots were identified, of them,30on At and16on Dt, and some transcriptional factors were existed in the hotspot regions. By comparative analysis of eQTL and consistent or stable fiber QTL in the present study, especially for eQTL hotspots were observed within the intervals regions of fiber QTL, we identified functional fiber quality genes differentially espressed between G. hirsutum and G. barbadense. Most noteworthy, the fiber transcript abundance variation at25DPA predominantly affected fiber qualities. The temporal regulation of gene expression and QRT-PCR identified the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism of fiber difference between G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulation expression of ABA and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities. |
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