Abstract
Key message
Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage.
Abstract
Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion–deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology (GB_D11G3437), WDL2 orthology (GB_D11G3460) and TUBA1 orthology (GB_D11G3471), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 (GB_A07G1034) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.
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Data availability
The genomic resequencing datasets generated during the current study are available in the NCBI Sequence Read Archive repository under accession number PRJNA728217.
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Funding
We are grateful to Xinjiang Tarim River Seed Co., Ltd. for kindly helping us with the investigation works of traits in the field. This work was supported by the National Key Technology R&D program of China (2016YFD0101404), China Agriculture Research System (CARS-18–25) and Jiangsu Collaborative Innovation Center for Modern Crop Production.
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Yu, J., Hui, Y., Chen, J. et al. Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage. Theor Appl Genet 134, 3249–3261 (2021). https://doi.org/10.1007/s00122-021-03889-w
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DOI: https://doi.org/10.1007/s00122-021-03889-w