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Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton

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Abstract

Fiber length is one of the most important fiber quality traits in Upland cotton (Gossypium hirsutum L.), the most important fiber crop, and its improvement has been impeded in part by a lack of knowledge regarding its genetic basis. Introgressed backcross inbred lines (BILs) or near isogenic lines (NILs) differing in fiber length in the same genetic background, developed through advanced backcrossing between Upland cotton and extra-long staple cotton (G. barbadense L.), provide an important genomic resource for studying the molecular genetic basis of fiber length. In the present study, a long-fiber group and a short-fiber group, each with five BILs of Upland cotton, were selected from a BIL population between G. hirsutum and G. barbadense. Through a microarray-based comparative transcriptome analysis of developing fibers at 10 days postanthesis from the two groups, 1478 differentially expressed genes (DEGs) were identified. A total of 166 DEGs were then mapped to regions of fiber length quantitative trait loci (QTL), including 12 QTL hotspots and 2 QTL identified previously in the BIL population from which the two sets of BILs were selected. Several candidate genes possibly underlying the genetic control of fiber length differences between G. barbadense and G. hirsutum, including GhACX and GhKIF, were identified in this study. These results provide a list of positional candidate genes for the fine-scale mapping and map-based cloning of fiber length QTL, which will facilitate targeted gene transfer from G. barbadense to Upland cotton to further improve fiber quality.

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Abbreviations

LF:

Long-fiber

SF:

Short-fiber

LFP:

Long-fiber parent

SFP:

Short-fiber parent

DEGs:

Differentially expressed genes

BILs:

Backcross isogenic lines

DPA:

Days post-anthesis

QTLs:

Quantitative trait loci

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Acknowledgements

The research was sponsored by grants from the National Key Research and Development Program of China (Grant Nos. 2018YFD0100300 and 2016YFD0101400), the National Natural Science Foundation of China (Grant No. 31621005), and the National Research and Development Project of Transgenic Crops of China (Grant No. 2016ZX08005005). The research was also supported in part by the New Mexico Agricultural Experiment Station.

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Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China

    Man Wu, Longyun Li, Guoyuan Liu, Xihua Li, Wenfeng Pei, Xingli Li, Shuxun Yu & Jiwen Yu

  2. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 880033, USA

    Jinfa Zhang

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  1. Man Wu
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  2. Longyun Li
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Contributions

JFZ, SXY and JWY conceived the study. MW, LYL, GYL, XHL, WFP and XLL performed the experiments. MW wrote the manuscript. JWY and JFZ edited the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Jinfa Zhang, Shuxun Yu or Jiwen Yu.

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Supplementary Data 1. Primers used for qRT-PCR analyses. (XLSX 9 KB)

11033_2019_4589_MOESM2_ESM.xlsx

Supplementary Data 2. Variance analysis of fiber quality, the yield trait, boll size, and the lint percentage. (XLSX 11 KB)

11033_2019_4589_MOESM3_ESM.xls

Supplementary Data 3. Microarray results for the differentially expressed genes (DEGs) identified in the long- and short-fiber groups. (XLS 322 KB)

Supplementary Data 4. Mapping of DEGs in the G. hirsutum genome. (XLSX 58 KB)

11033_2019_4589_MOESM5_ESM.xlsx

Supplementary Data 5. Mapping of DEGs with the 4 fiber length QTLs and 13 fiber length QTL hotspots in the genome of G. hirsutum. (XLSX 67 KB)

Supplementary Data 6. 166 mapped DEGs with the 2 fiber length QTLs and 12 fiber length QTL hotspots. (XLSX 156 KB)

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Wu, M., Li, L., Liu, G. et al. Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton. Mol Biol Rep 46, 1199–1212 (2019). https://doi.org/10.1007/s11033-019-04589-x

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