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Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.)

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Abstract

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5–62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

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Acknowledgments

This study was financially supported by the Natural Science Foundation of China (31270037, 31271305, 30971827) and the “111” Project (B12006).

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    Authors and Affiliations

    1. Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People’s Republic of China

      Dexin Liu, Fang Liu, Xiaoru Shan, Jian Zhang, Shiyi Tang, Xiaomei Fang, Xueying Liu, Wenwen Wang, Zhaoyun Tan, Zhonghua Teng, Zhengsheng Zhang & Dajun Liu

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    1. Dexin Liu
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    Correspondence to Dajun Liu.

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    Communicated by J. Zhang.

    D. Liu and F. Liu have contributed equal work to this paper.

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    Liu, D., Liu, F., Shan, X. et al. Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 290, 1683–1700 (2015). https://doi.org/10.1007/s00438-015-1027-5

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