What do we know about the cotton genome so far

Not much, compared to Arabidopsis and rice, and even maize; but we have much more resources compared to other crop species like melon or banana. If you ask me, i think cotton genome research has not get as much attention as it deserves.

Genetic mapping for the whole genome has been done for the AD, A and D genome cotton species. This is mainly contributed by four different resources: the PGML (Plant Genome Mapping Laboratory, UGA),  USDA-ARS, Nanjing Acriculture University in China, and a French group under Dr. JM Lacape. Physical mapping of tetraploid cotton is been approached by USDA-ARS in colaboration with Hongbin Zhang's lab in TAMU, and for the diploid D genome cotton, in PGML by Dr. Andrew Paterson and me. You can find information about the D genome physical map here. BAC libraries resources and ESTs databases are also quite abundant, for the A, D and AD genome that is. Sadly, for other genomes, relatively less is known.

Much research about the evolution of genome size has been done using cotton as a model system, for obvious reasons: cotton genomes diverged from each other relatively recently, and huge variation in genome size among different diploid genomes have already been detected. Relating to the research on genome size evolution, the profiling of transposible elements in the cotton genomes has been done by the Wendel lab. More detail can be found in the bookchapter i wrote for Andy's book on the physical composition of the cotton genomes here.

Cloning a gene from a genome whose genomic mapping and sequence data is lacking is a tedious and painful process. That is probably the reason why still no genes has been cloned in cotton. But the good news is, given the huge boost in genomic sequences, EST sequences and BAC library information in recent genomic analysis, new doors into cloning cotton genes has been opened. This include using BAC library and physical mapping data in selecting interesting BAC clones; developing new markers from BAC end sequences; developing new markers from already sequenced genomes such as Arabidopsis using synteny and colinearity relationships and even direct gene prediction using already sequenced genomes. I am interested in these new approaches, and is actually  trying to clone a gene using all the available resources. Please refer to my project description page for more details.