Abstract Next-generation sequencing （NGS） technologies provide enormous power and new potential to access the complex polyploid genomes and transcriptomes of major crops， including cotton. This article summarises the applications of NGS in cotton genomic studies， including genome sequencing and resequencing， transcriptomic analysis， small RNA sequencing and miRNA identification， and identification of single nucleotide polymorphisms. NGS has rapidly accelerated genomic studies in cotton and will further expand our understanding of the evolution and polyploidisation of cotton at the species level as well as our understanding of the biology of the development of the unique seed trichomes that characterise the commercial textile fibres produced by some members of the Gossypium genus. Realisation of substantial impacts on applied cotton genetics and breeding will largely depend on the formulation of novel applications of NGS and the development of handy bioinformatic tools for dealing with and interpretation of the vast amounts of data generated by this technology．
Zhu Qianhao， Danny Llewellyn， Iain Wilson. Use of next-generation sequencing in genomic studies of polyploid crops: Cotton as an example. Journal of Zhejiang University (Agriculture and Life Sciences), 2014, 40(4): 355-369.
