Patterns of presence-absence variants in Upland cotton
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tterns of presence-absence variants in Upland cotton 1†
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Junfang Liu , Xianliang Zhang , Lingling Dou , Wei Li , Xiaojian Zhou , Yangai Liu , 1 1 1 2 2 Xiaoyu Pei , Zhongying Ren , Wensheng Zhang , Huaizhu Li , Wenbo Wang , 3 1 1 1 5 6* Changsong Zou , Kunlun He , Fei Zhang , Wenyu Ma , Haihong Shang , Hongbin Li , 1* 4* 1* Daigang Yang , Guanghui Xiao & Xiongfeng Ma 1
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; 2 School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang 712000, China; 3 Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University,
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Kaifeng 475004, China; Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal 5
University, Xi’an 710119, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; 6 College of Life Sciences, Shihezi University, Shihezi 832003, China Received November 12, 2019; accepted November 27, 2019; published online April 7, 2020
Citation:
Liu, J., Zhang, X., Dou, L., Li, W., Zhou, X., Liu, Y., Pei, X., Ren, Z., Zhang, W., Li, H., et al. (2020). Patterns of presence-absence variants in Upland cotton. Sci China Life Sci 63, https://doi.org/10.1007/s11427-019-1602-y
Dear Editor: Sources of genetic variations in genomes include small-scale sources (such as single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and simple sequence repeats and larger-scale structural variations (mainly presence-absence variants (PAVs)) and copy number variants). PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome. PAVs can have a much longer sequence than SNPs and InDels, as illustrated in the human genome (Conrad et al., 2010). PAVs are important genomic structural variations that can directly affect genomic structure and key functional genes in the genome (Kumar et al., 2007). Moreover, the use of PAVs for studying quantitative traits has been valuable (Lam et al., 2010).
†Contributed equally to this work *Corresponding authors (Hongbin Li, email: [email protected]; Daigang Yang, email: [email protected]; Guanghui Xiao, email: [email protected]; Xiongfeng Ma, email: [email protected])
PAVs have been extensively studied in plants. A large number of PAVs exist in the rice genome, and more than 20,000 PAVs have been detected among rice cultivars (Kumar et al., 2007). A study comparing the genomic sequences between two cultivars Nipponbare and Guang-lu-ai 4 revealed 641 structural variants, most of which were PAVs related to specific agronomic traits (Yu et al., 2011). Lam et al. identified 186,177 PAVs by resequencing 31 soybean cultivars; these structural v
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