Abstract
BackgroundCotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.ResultsWe resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.ConclusionsWe report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.
Highlights
Cotton has been cultivated and used to make fabrics for at least 7000 years
Modern Upland cotton has been further improved in the southern United States from domesticated early-cropping perennials through extensive human selection to produce a common set of agronomic features known as “domestication syndrome” traits [12]
Close relatives of the allotetraploid cotton species, Gossypium tomentosum (AD)3, Gossypium mustelinum (AD)4, and Gossypium darwinii (AD)5, as well as Thespesia populneoides (Roxb.) Kostelas, which is closely related to the genus Gossypium in the Malvaceae family, were all included as outgroups
Summary
Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Fang et al Genome Biology (2017) 18:33 selection of a wide range of morphological and physiological traits, the two tetraploid species, G. hirsutum and G. barbadense, have been domesticated and cultivated. Modern Upland cotton has been further improved in the southern United States from domesticated early-cropping perennials through extensive human selection to produce a common set of agronomic features known as “domestication syndrome” traits [12]. These traits include an annual growth habit and photoperiod insensitivity [5], decreased seed dormancy [6], a large boll size and number per plant [1], and superior fiber quality [13]. The present research provides genome-wide level insights into genetic divergence and dual domestication of cultivated tetraploid cottons
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