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Genome Biol. 2017 Feb 20;18(1):33. doi: 10.1186/s13059-017-1167-5.

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.

Author information

1
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
2
National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
3
Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.
4
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
5
Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Sciences, Xinjiang, 832000, China.
6
Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, the University of Texas at Austin, Austin, TX, 78712, USA.
7
State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
8
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China. cotton@njau.edu.cn.
9
Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310029, China. cotton@njau.edu.cn.
10
National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China. xhhuang@shnu.edu.cn.
11
College of life and environmental sciences, Shanghai Normal University, Shanghai, 200234, China. xhhuang@shnu.edu.cn.

Abstract

BACKGROUND:

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. 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.

RESULTS:

We 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.

CONCLUSIONS:

We 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.

KEYWORDS:

Allotetraploid cottons; Divergence; Domestication; Resequencing

PMID:
28219438
PMCID:
PMC5317056
DOI:
10.1186/s13059-017-1167-5
[Indexed for MEDLINE]
Free PMC Article

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