Cotton (Gossypium spp.) fibers are single-celled trichomes of the seed epidermis. This fiber is a major, and the only natural, staple for the textile industry. Its production is of key economic importance for millions of people in the developed and developing world. Cultivated species, mostly G hirsutum and G barbadense, are allotetraploid species with 2 resident genomes ‘A’ and ‘D’. The sequence of the ‘D’ genome (eg of the diploid species G raimondii) has been published by 2 groups from China and the USA in 2012.

Most molecular breedingi work (marker development, QTL mapping, marker-assisted selection or MAS) developed at Cirad have concentrated on the analysis of progenies from G hirsutum x G barbadense crosses and on the study of genetic diversity within the species and beyond within the genus, with focus on fiber quality and resistances to pest, disease and nematode, as targetted traits. Important progresses in sequencing technologies (and their reduced cost) are offering larger opportunities for identifying higher numbers of polymorphic markers (in particular SNPs). Some applications of these technologies (RNAseq) are explored at Cirad, including through comparative genomics between the wild and cultivated pools of G hirsutum (Arcad project), for an accelerated identification of markers linked to traits on interest for their utilization in MAS.

Marker development and utilization in molecular breeding

In the recent years, the cotton group of Cirad and its collaborators has contributed several important ouputs and publications in the areas of marker development (SSRs of the series ‘mghCIR’, SNPs), genetic mapping (several bi-parental populations and a consensus map as an integration of 6 published maps), QTL mapping (fiber quality, leaf hairiness, disease and nematode resistance). A number of data and results have been deposited and are now centralized on the different tools of SouthGreen platform for public access.

Links between South Green and Cotton

The South Green Bioinformatics platform is proposing different tools and interfaces for facilitating the access to a large variety of data and information, including:

- TropGeneDB, as a repository for cotton marker sequences and for cotton genetic and QTL linkage maps, including the most updated integrated high density consensus, HDC, map published in 2012 (Blenda et al, 2012). Maps are displayable with CMap.

- SNiPlay: for SNPs between G hirsutum and G barbadense (Lacape et al, 2012)

- A browser for the genome of G raimondii  proposing a track with genetic markers mapped on the consensus map (HDC) and fully interfaced with CMap displays in TropGeneDB