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Plant Biotechnol J. 2019 Jun 14. doi: 10.1111/pbi.13191. [Epub ahead of print]

Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population.

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State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan.
Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China.
Shandong Cotton Research Center, Jinan, China.
Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China.
Zhengzhou Research Institute of Agricultural and Forestry Sciences, Zhengzhou, China.
Shihezi Agricultural Science & Technology Research Center, Shihezi, China.
Institute of Cash Crops, Hubei Academy of Agricultural Science, Wuhan, China.
Institute of Agriculture, Bayingolin Mongol Autonomous Prefecture, Korla, Xinjiang, China.
Institute of Agricultural Science and Technology, Agricultural Production Division 1, Xinjiang Production and Construction Corps, Alar, Xinjiang, China.
College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of The Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.


Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.


QTL clusters; consensus genetic map; fibre quality; fibre yield; gene expression level; genetic correlation; upland cotton

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