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However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole\u2010genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112\u00a0Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome\u2010wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.\n                  <\/jats:p>","DOI":"10.1111\/pbi.13446","type":"journal-article","created":{"date-parts":[[2020,7,11]],"date-time":"2020-07-11T17:08:21Z","timestamp":1594487301000},"page":"109-123","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":103,"title":["Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (\n                    <i>Gossypium hirsutum<\/i>\n                    L.)"],"prefix":"10.1111","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1138-134X","authenticated-orcid":false,"given":"Libei","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture Zhejiang A &amp; F University Lin'an, Hangzhou"},{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture Zhejiang A &amp; F University Lin'an, Hangzhou"},{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianqin","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture Zhejiang A &amp; F University Lin'an, Hangzhou"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qibao","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture Zhejiang A &amp; F University Lin'an, Hangzhou"},{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hengling","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hantao","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2811-108X","authenticated-orcid":false,"given":"Guoyuan","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijiao","family":"Gu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology Institute of Cotton Research of CAAS Anyang Henan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9715-3462","authenticated-orcid":false,"given":"Shuxun","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture Zhejiang A &amp; 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