Genome-Wide Functional Analysis of the Cotton Transcriptome by Creating an Integrated EST Database

A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members. A total of 27,956 indel mutants and 149,616 single nucleotide polymorphisms (SNPs) were identified from consensus contigs. Interestingly, many contigs with significantly high frequencies of indels or SNPs encode transcription factors and protein kinases. In a comparison with six model plant species, cotton ESTs show the highest overall similarity to grape. A total of 87 cotton miRNAs were identified; 59 of these have not been reported previously from experimental or bioinformatics investigations. We also predicted 3,260 genes as miRNAs targets, which are associated with multiple biological functions, including stress response, metabolism, hormone signal transduction and fiber development. We identified 151 and 4,214 EST-simple sequence repeats (SSRs) from contigs and raw ESTs respectively. To make these data widely available, and to facilitate access to EST-related genetic information, we integrated our results into a comprehensive, fully downloadable web-based cotton EST database (www.leonxie.com)

In-vitro development of ovules obtained after pollination of cotton (Gossypium spp) flowers with pollen from okra (Abelmoschus esculentus L-Moench)

The in vitro response of ovules obtained after pollination of cotton flowers with pollen from Abelmoschus esculentus was studied. For this, 492 cotton flowers from five G. hirsutum varieties, four G. barbadense varieties and 10 F1 interspecific hybrids, were pollinated with pollen from A. esculentus and 5,069 ovules were cultured in vitro. From the cultured ovules, 69 embryos were isolated and 16 of them grew into plants. However, only three of them survived after transplantation. Finally, one plant which originated from the interspecific cross (B403 x Acala Sindos) x A. esculentus reached maturity. The mature plant (Pa0) had no morphological traits from A. esculentus. On the contrary, traits from both cotton species were observed. The flowcytometric analysis of the Pa0 plant indicated that it was hypoaneuploid. Root tip chromosome counts of its offsprings revealed a progressive chromosome increase from the Pa1 to Pa4 generation. Plants with 52 chromosomes or hypoaneuploids with a lower level of chromosomes (46-51) could be isolated from the Pa4 generation. These plants exhibited morphological traits from both cotton species and they were fertile. No signs of A. esculentus morphological characteristics were observed in these plants. It was concluded that aneuploid partial interspecific cotton plants could be produced after pollination of cotton interspecific hybrids with pollen from A. esculentus and application of an in-ovule embryo rescue technique