An initial count on the surface of developing ovules at 0 dpa is a useful, overall non destructive way to estimate mature fibre FD. When comparing genotypes, it was able to identify differences in FD. SEM is used routinely by cotton researchers to visualise and count the number of initials on developing ovules to study the effect of genetic manipulation of fibre-related genes on the development of fibre cells (Machado et al., 2009). However, in a large scale breeding programme, initial counts are impractical unless reliable imaging software is available to automatically count fibre initial cells. SEM provides a way to estimate FD before harvest although it has been suggested that mature lint fibres/SSA needs to be correlated with ovule counts to determine its usefulness (Bowman et al., 2001). We have demonstrated that association in these data and mid-zone flowers are preferred for sampling.