High-resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets |
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Authors: | Nian Wang Yuanxue Li Chao Shen Yang Yang Hongya Wang Tian Yao Xianlong Zhang Keith Lindsey Zhongxu Lin |
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Institution: | 1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China;2. College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 Guangdong, China;3. Department of Biosciences, Durham University, Durham, DH1 3LE UK |
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Abstract: | Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s–2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88–1.47 × 104 SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high-throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton. |
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Keywords: | upland cotton SV inversion haplotype adaptability genetic improvement |
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