Identification Of Cotton Genes Related To Gland Development And Their Application Prospect In Low Gossypol Cotton Breeding

Cotton is an important economic crop in our country and considered as the source of fiber, protein and oil. Cottonseed is abundant in protein, carbohydrate and mineral element, and the linoleic content of its oil reach up to 55.6%. However, cottonseed cannot be exploited completely because of the presence of gossypol, which is a kind of sesquiterpene and protect plant from insects, fungus and diseases. Long-term consumption of gossypol will be toxic to monogastric animals and humans. Gossypol is mainly accumulated in glands, so it is a promising way to eliminate gossypol within cottonseed by removing the pigment in cottonseed. Now, the mechanism of gland formation is poorly understanded. Here, we, using Illumina sequencing of tanscriptome, analyzed the gene expression difference of ten materials related to gland trait to find the key genes and metabolic pathways associated with gland formation.A total of 219,187,389 reads, approximately 44.27 Gb, were obtained from the ten transcriptomes libraries, and the CycleQ20, evaluating sequencing quality, equal to 100%. By de novo assembly, these reads were assembled into 43,424 unigenes, of which 12,895 were longer than 1 kb. The average length and N50 length of unigenes were 874 bp and 1,467 bp, respectively. All of the unigenes were searched against NR、NT、Swiss-Prot、GO、COG and KEGG databases, and the result showed that of 43,424 unigenes, 30,062(69.23%), 28,576(65.81%),19,029(43.82%), 24,245(55.83%), 8,327(19.18%), and 5,943(13.69%) had at least one homologous sequence in each database.The 10 transcriptomes were divided into 6 pairs of combinations of which containing 4 pairs of NILs with a common genetic background but the contrasting pigment gland traits. Based on pairwise comparison, we obtained 3,838、306、1,264、393、512 and 722 differentially expressed genes from Z12/H1、Z12/Z12 YW 、Z12/Z12XW、Z17/Z17YW、L7/L7 XW 、TM-1/T582, respectively. Gene Ontology functional annotation showed that extracellular matrix part, extracellular matrix and cell killing had a higher enrichment percentage in the background of differentially expressed genes than that in the background of all genes, suggesting these biological function may be associated with gland formation. Cluster of Orthologous Groups functional annotation revealed that some genes participating in secondary metabolites biosynthesis, transport and catabolism presented significant expression difference between glanded and glandless materials, indicating that the metabolic activity of gossypol and other secondary compounds would be weak with the deletion of gland. KEGG pathway enrichment indicated that plant hormone signal transduction might play important role in the morphogenesis of gland.25 common differentially expressed genes were obtained from all six pairs of combinations, and all of them represented down-regulated in the glandless materials. Among these common differentially expressed genes, AP2/ERF domain-containing transcription factor and Basic helix-loop-helix DNA-binding family protein might play key role in the process of gland formation. Besides, three genes of unknown function were also screened, and their role in gland formation needed further research. KEGG pathway enrichment of differentially expressed genes from four pairs NILs found that the upstream key genes of mevalonate pathway might play significant role for the biosynthesis of gossypol and other terpene compounds.The common differentially expressed genes obtained from six pairs of combinations were the key candidate genes of gland formation and gossypol biosynthesis, and would have a spacious application foreground in low gossypol cotton breeding.