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

  • Man Wu
  • Longyun Li
  • Guoyuan Liu
  • Xihua Li
  • Wenfeng Pei
  • Xingli Li
  • Jinfa ZhangEmail author
  • Shuxun YuEmail author
  • Jiwen YuEmail author
Original Article
  • 56 Downloads

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.

Keywords

Gossypium barbadense Gossypium hirsutum Fiber quality traits Affymetrix microarray Quantitative RT-PCR 

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

Notes

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.

Author 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.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11033_2019_4589_MOESM1_ESM.xlsx (10 kb)
Supplementary Data 1. Primers used for qRT-PCR analyses. (XLSX 9 KB)
11033_2019_4589_MOESM2_ESM.xlsx (11 kb)
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 (322 kb)
Supplementary Data 3. Microarray results for the differentially expressed genes (DEGs) identified in the long- and short-fiber groups. (XLS 322 KB)
11033_2019_4589_MOESM4_ESM.xlsx (58 kb)
Supplementary Data 4. Mapping of DEGs in the G. hirsutum genome. (XLSX 58 KB)
11033_2019_4589_MOESM5_ESM.xlsx (68 kb)
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)
11033_2019_4589_MOESM6_ESM.xlsx (35 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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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Cotton BiologyCotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of AgricultureAnyangChina
  2. 2.Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesUSA

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