بینش های اخیر در ژنومیک عملکرد پنبه Recent insights into cotton functional genomics: progress and future perspectives

Introduction Cotton (Gossypium hirsutum) is a foundation of the global economy, prized for its important renewable fiber resource. It serves as an ideal plant for different biological studies such as genome evolution, polyploidization and single-celled biological processes (Qin and Zhu, 2011; Shan et al., 2014). Decoding cotton’s genome provides useful understanding about the agronomic and functional importance of polyploidy and genome size variations within the genus Gossypium (Chen et al., 2007). However, evolution and function of allopolyploid cotton genome is complicated by the presence of two subgenomes (AT and DT) in its nucleus. About 5-10 million years ago (MYA), the African derived ‘A’ diploid genome diverged from the eudicot progenitor simultaneously with the diploid genome ‘D’ which was native to Mexican (Wendel, 1989; Wendel and Albert, 1992). Then around 1 -2 MYA, these two species were reunited together by the transoceanic dispersal of an A -genome ancestor (Gossypium arboreum ) to the New World and hybridized with a D -genome ancestor (Gossypium raimondii) followed by chromosome doubling, which produced the allotetraploid cotton (Wendel, 1989). These well -established relationships between the allotetraploid and diploid cotton genomes help us to explore the evolution of gene expression, because most of gene functions are highly conserved between wild as well as diploid and tetraploid cotton species. Whole genome sequencing is a fundamental component for comprehensive molecular analysis and for several thousands of plant species, genome sequencing projects are now complete or underway. Compared with model plants i.e. Arabidopsis, rice and maize , the whole genome sequencing of cotton was lack behind. During last decade, sequenced genomes of tetraploid cotton (Li et al., 2015; Liu et al., 2015; Yuan et al., 2015; Zhang et al., 2015 b ) and their diploid progenitors (Li et al., 2014b; Paterson et al., 2012; Wang et al., 2012), has been released that provide critical understanding of the evolution and differentiation of genome structures. Though, knowledge of the precise sequences and position of all the genes of an organism is an initial step to explore how biological systems work together. Previously, various studies have performed to compare the structural variations in genomes which showed the differences in the expression pattern rather than in the absence and presence of genes (Gingle et al., 2006). In this respect functional genomics is the main approach which is generally referred as “development and application of global experimental approaches to evaluate gene function s by using the information and reagents obtained from structural genomics”.