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Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton
- Xu, Peng, Gao, Jin, Cao, Zhibin, Chee, Peng W., Guo, Qi, Xu, Zhenzhen, Paterson, Andrew H., Zhang, Xianggui, Shen, Xinlian
- Theoretical and applied genetics 2017 v.130 no.6 pp. 1309-1319
- 1-aminocyclopropane-1-carboxylate synthase, Gossypium barbadense, Gossypium hirsutum, chromosomes, cotton, gene expression, genes, heterozygosity, introgression, microsatellite repeats, phenotype, polymerase chain reaction, quantitative trait loci
- KEY MESSAGE: 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. 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.