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Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton

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A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length.

Abstract

Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC4F2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC4F3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F2 population, supporting these genes as candidates for qFL-chr1.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (NSFC) (No. 31171595, 31471545), Natural science fund for colleges and universities in Jiangsu Province (BK20160580), Jiangsu Collaborative Innovation Center for Modern Crop Production.

Author contributions

X.P. contributed to genotyping, data analysis, and writing; G.J. contributed to genotyping and data collection; C.Z.B. contributed to genotyping; C.P. provided material and reviewed manuscript; G.Q. contributed to population construction; X.Z.Z. contributed to q-PCR analysis; P.A. provided material and reviewed manuscript; Z.X.G. contributed to population construction; and S.X.L. contributed to experiment design and writing.

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    1. Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People’s Republic of China

      Peng Xu, Jin Gao, Zhibin Cao, Qi Guo, Zhenzhen Xu, Xianggui Zhang & Xinlian Shen

    2. The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People’s Republic of China

      Peng Xu, Jin Gao, Zhibin Cao, Qi Guo, Zhenzhen Xu, Xianggui Zhang & Xinlian Shen

    3. Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 3179, USA

      Peng W. Chee

    4. Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA

      Andrew H. Paterson

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    Xu, P., Gao, J., Cao, Z. et al. Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton. Theor Appl Genet 130, 1309–1319 (2017). https://doi.org/10.1007/s00122-017-2890-8

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