Development of genomic resources for cotton (Gossypium hirsutum L.): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development

We have constructed a cotton (Gossypium hirsutum L.) BAC library using the elite Acala-type cultivar Maxxa. The BAC library contains 129 024 clones comprising 8.3 haploid genome equivalents based on a AD genome size of 2118 Mb. A random sampling of 435 BACs indicated an average insert length of 137 kb with a range of 80 to 275 kb, and 1.4% of the BACs do not contain inserts. Of the BAC clones in the sample 99% had an average insert length equal to or greater than 100 kb. Contamination of the genomic library with chloroplast clones was low (1.5%). To evaluate the library for genome representation and to identify clones associated with cotton fiber development, six BAC colony filters (7.2× representation) were screened with PCR-generated gene-specific probes for the GhMYB class of transcription factor genes giving an average of 12 positive signals per probe (range 6–20). To gain a glimpse into the cotton genome and evaluate the library for sequence-tagged connector (STC) development, 1536 BAC clones were end sequenced in both forward and reverse direction. The STCs were queried against the SwissProt and MIPS Arabidopsis databases and significant hits were sorted according to putative function.