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


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.


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







Long-fiber parent


Short-fiber parent


Differentially expressed genes


Backcross isogenic lines


Days post-anthesis


Quantitative trait loci



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)


  1. 1.
    Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 54:911–929CrossRefGoogle Scholar
  2. 2.
    Basra AS, Malik CP (1984) Development of the cotton fiber. Int Rev Cytol 89:65–113CrossRefGoogle Scholar
  3. 3.
    Bennett J, Hondred D, Register JC (2015) Keeping qRT-PCR rigorous and biologically relevant. Plant Cell Rep 34:1–3CrossRefGoogle Scholar
  4. 4.
    Brubaker CL, Paterson AH, Wendel JF (1999) Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42(2):184–203CrossRefGoogle Scholar
  5. 5.
    Chee PW, Draye X, Jiang CX, Decanini L, Dehnonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor Appl Genet 111(4):757–763CrossRefGoogle Scholar
  6. 6.
    Chee PW, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length. Theor Appl Genet 111(4):772–781CrossRefGoogle Scholar
  7. 7.
    Dong J, Wei LB, Yan H, Guo WZ (2013) Molecular cloning and characterization of three novel genes related to fatty acid degradation and their responses to abiotic stresses in Gossypium hirsutum L. J Integ Agric. 12(4):582–588CrossRefGoogle Scholar
  8. 8.
    Draye X, Chee PW, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Wayne SC, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum. and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness. Theor Appl Genet 111(4):764–771CrossRefGoogle Scholar
  9. 9.
    Fang L, Tian R, Li XH, Chen JD, Wang S, Wang P, Zhang TZ (2014) Cotton fiber elongation network revealed by expression profiling of longer fiber lines introgressed with different Gossypium barbadense chromosome segments. BMC Genom 15:838–853CrossRefGoogle Scholar
  10. 10.
    Guo LX, Shi YZ, Gong JW, Liu AY, Tan YN, Gong WK, Li JW, Chen TT, Shang HH, Ge Q, Lu QW, Sun J, Yuan YL (2018) Genetic analysis of the fiber quality and yield traits in G. hirsutum background using chromosome segments substitution lines (CSSLs) from Gossypium barbadense. Euphytica 214:82CrossRefGoogle Scholar
  11. 11.
    Guo WZ, Cai CP, Wang CB, Han ZG, Song XL, Wang K, Niu XW, Wang C, Lu KY, Shi B, Zhang TZ (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176:527–541CrossRefGoogle Scholar
  12. 12.
    Hande AS, Katageri IS, Jadhav MP, Adiger S, Gamanagatti S, Padmalatha KV, Dhandapani G, Kanakachari M, Kumar PA, Reddy VS (2017) Transcript profiling of genes expressed during fibre development in diploid cotton (Gossypium arboreum L.). BMC Genom 18:675CrossRefGoogle Scholar
  13. 13.
    Hayashi H, De Bellis L, Ciurli A, Kondo M, Hayashi M, Nishimura M (1999) A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes. J Biol Chem 274:12715–12721CrossRefGoogle Scholar
  14. 14.
    Hiltunen JK, Mursula AM, Rottensteiner H, Wierenga RK, Kastaniotis AJ, Gurvitz A (2003) The biochemistry of peroxisomal b-oxidat ion in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 27(1):35–64CrossRefGoogle Scholar
  15. 15.
    Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC, Zhu YX (2003) Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucl Acids Res 31(10):2534–2543CrossRefGoogle Scholar
  16. 16.
    John ME (1996) Structural characterization of genes corresponding to cotton fiber mRNA, E6: reduced E6 protein in transgenic plants by antisense gene. Plant Mol Biol 30(2):297–306CrossRefGoogle Scholar
  17. 17.
    Kim MC, Kim TH, Park JH, Moon BY, Lee CH, Cho SH (2007) Expression of rice acyl-CoA oxidase isoenzymes in response to wounding. J Plant Physiol 164(5):665–668CrossRefGoogle Scholar
  18. 18.
    Kong ZS, Ioki M, Braybrook S, Li S, Ye ZH, Lee YRJ, Hotta T, Chang A, Tian J, Wang GD, Liu B (2015) Kinesin-4 functions in vesicular transport on cortical microtubules and regulates cell wall mechanics during cell elongation in plants. Mol Plant 8:1011–1023CrossRefGoogle Scholar
  19. 19.
    Lacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimaraes Pereira GA, Ruiz M, Pre M, LIewellyn D, AI-Ghazi Y, Jacobs J, Dereeper A, Huquet S, Giband M, Lanaud C (2012) Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS ONE 7(11):e48855CrossRefGoogle Scholar
  20. 20.
    Lacape JM, Llewellyn D, Jacobs J, Arioli T, Becker D, Calhoun S, AI-Ghazi Y, Liu SM, Palai O, Georges S, Giband M, Assuncao H, Barroso PAV, Claverie M, Gawryziak G, Jean J, Vialle M, Viot C (2010) Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population. BMC Plant Biol 10:132CrossRefGoogle Scholar
  21. 21.
    Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations. Crop Sci 45(1):123–140CrossRefGoogle Scholar
  22. 22.
    Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46(4):612–626CrossRefGoogle Scholar
  23. 23.
    Li DD, Ruan XM, Zhang J, Wu YJ, Wang XL, Li XB (2013) Cotton plasma membrane intrinsic protein 2 s (PIP2s) selectively interact to regulate their water channel activities and are required for fiber development. New Phytol 199(3):695–707CrossRefGoogle Scholar
  24. 24.
    Li FG, Fan GY, Lu CR, Xiao GH, Zou CS, Kohel RJ, Ma ZY, Shang HH, Ma XF, Wu JY, Ling XM, Huang G, Percy RG, Liu K, Yang WH, Chen WB, Du XM, Shi CC, Yuan YL, Ye WW, Liu X, Zhang XY, Liu WQ, Wei HL, Wei SJ, Huang GD, Zhang XL, Zhu SJ, Zhang H, Sun FM, Wang XF, Liang J, Wang JH, He Q, Huang LH, Wang J, Cui JJ, Song GL, Wang KB, Xu X, Yu JZ, Zhu YX, Yu SX (2015) Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33(5):524–529CrossRefGoogle Scholar
  25. 25.
    Li XH, Wu M, Liu GY, Pei WF, Zhai HH, Yu JW, Zhang JF, Yu SX (2017) Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkge and physical mapping in cotton. BMC Genom 18:427CrossRefGoogle Scholar
  26. 26.
    Liu BL, Zhu YC, Zhang TZ (2015) The R3-MYB gene GhCPC negatively regulates cotton fiber elongation. PLoS ONE 10(2):e0116272CrossRefGoogle Scholar
  27. 27.
    Pang MX, Stewart JM, Zhang JF (2013) A mini-scale hot borate method for the isolation of total RNA from a large number of cotton tissue samples. Afr J Biotechnol 10(68):15430–15437Google Scholar
  28. 28.
    Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype x environment interactions affecting cotton fiber quality. Theor Appl Genet 106(3):384–396CrossRefGoogle Scholar
  29. 29.
    Preuss ML, Delmer DP, Liu B (2003) The cotton kinesin-like calmodulin-binding protein associates with cortical microtubules in cotton fibers. Plant Physiol 132(1):154–160CrossRefGoogle Scholar
  30. 30.
    Preuss ML, Kovar DR, Lee YR, Staiger CJ, Delmer DP, Liu B (2004) A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibers. Plant Physiol 136(4):3945–3955CrossRefGoogle Scholar
  31. 31.
    Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, Zhu YX (2007) Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell 19(11):3692–3704CrossRefGoogle Scholar
  32. 32.
    Said JI, Knapka JA, Song MZ, Zhang JF (2015) Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum x G. barbadense populations. Mol Genet Genom 290(4):1615–1625CrossRefGoogle Scholar
  33. 33.
    Said JI, Lin ZX, Zhang XL, Song MZ, Zhang JF (2013) A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genom 14:776–798CrossRefGoogle Scholar
  34. 34.
    Said JI, Song MZ, Wang HT, Lin ZX, Zhang XL, Fang DD, Zhang JF (2015) A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. Mol Genet Genom 290(3):1003–1025CrossRefGoogle Scholar
  35. 35.
    Shan CM, Shangguan XX, Zhao B, Zhang XF, Chao LM, Yang CQ, Wang LJ, Zhu HY, Zeng YD, Guo WZ, Zhou BL, Hu GJ, Guan XY, Chen ZJ, Wendel JF, Zhang TZ, Chen XY (2014) Control of cotton fiber elongation by a homeodomain transcription factor GhHOX3. Nat Commun 21(5):5519CrossRefGoogle Scholar
  36. 36.
    Tang WX, Tu LL, Yang XY, Tan JF, Deng FL, Hao J et al (2014) The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating reactive oxygen species (ROS) production. New Phytol 202(2):509–520CrossRefGoogle Scholar
  37. 37.
    Tiwari SC, Wilkins TA (1995) Cotton (Gossypium hirsutum) seed trichomes expand via diffuse growing mechanism. Can J Bot 73(5):746–757CrossRefGoogle Scholar
  38. 38.
    Wanjie SW, Welti R, Moreau RA, Chapman KD (2005) Identification and quantification of glycerolipids in cotton fibers: reconciliation with metabolic pathway predictions from DNA databases. Lipids 40(8):773–785CrossRefGoogle Scholar
  39. 39.
    Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42(1):225–249CrossRefGoogle Scholar
  40. 40.
    Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78(2):139–186CrossRefGoogle Scholar
  41. 41.
    Wu M, Zhang LY, Li XH, Xie XB, Pei WF, Yu JW, Yu SX, Zhang JF (2016) A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint–yield derived from a Gossypium hirsutum × Gossypium barbadense population. Mol Genet Genom 291(4):1749–1767CrossRefGoogle Scholar
  42. 42.
    Yang ZR, Zhang CJ, Yang XJ, Liu K, Wu ZX, Zhang XY, Wu Z, Xun QQ, Liu CL, Lu LL, Yang ZE, Qian YY, Xu ZZ, Li CF, Li J, Li FG (2014) PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. New Phytol 203(2):437–448CrossRefGoogle Scholar
  43. 43.
    Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D (2014) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res 42:1229–1236CrossRefGoogle Scholar
  44. 44.
    Yu JW, Yu SX, Fan SL, Song MZ, Zhai HH, Li XX, Zhang JF (2012) Mapping quantitative trait loci for cottonseed oil, protein and gossypol content in a Gossypium hirsutum x Gossypium barbadense backcross inbred line population. Euphytica 187(2):191–201CrossRefGoogle Scholar
  45. 45.
    Yu JW, Yu SX, Gore M, Wu M, Zhai HH, Li XL, Song MZ, Zhang JF (2013) Identification of quantitative trait loci across interspecific F2, F2:3 and testcross populations for agronomic and fiber traits in tetraploid cotton. Euphytica 191(3):375–389CrossRefGoogle Scholar
  46. 46.
    Yu JW, Zhang K, Yu SX, Fan SL, Song MZ, Zhai HH, Wu M, Li XL, Fan SL, Song MZ, Yang DG, Li YH, Zhang JF (2013) Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum x Gossypium barbadense backcross inbred line population. Theor Appl Genet 126(1):275–287CrossRefGoogle Scholar
  47. 47.
    Zhang JF, Percy RG, McCarty JC (2014) Introgression genetics and breeding between Upland and Pima cotton: a review. Euphytica 198(1):1–12CrossRefGoogle Scholar
  48. 48.
    Zhang M, Zheng XL, Song SQ, Zeng QW, Hou L, Li DM, Zhao J, Wei Y, Li XB, Luo M, Xiao YH, Luo XY, Zhang JF, Xiang CB, Pei Y (2011) Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat Biotechnol 29(5):453–458CrossRefGoogle Scholar
  49. 49.
    Zhang TZ, Hu Y, Jiang WK, Fang L, Guan XY, Chen JD, Zhang JB, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu BL, Liu CX, Wang S, Pan MQ, Wang YK, Wang D, Ye WX, Chang LJ, Zhang WP, Song QX, Kirkbride RC, Chen XY, Dennis E, LIewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu XY, Zhang H, Wu HT, Zhou L, Mei CF, Chen SQ, Tian Y, Xiang D, Li XH, Ding J, Zuo QY, Tao LN, Liu YC, Li J, Lin Y, Hui YY, Cao ZS, Cai CP, Zhu XF, Jiang Z, Zhou BL, Guo WZ, Li RQ, Chen ZJ (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33(5):531–537CrossRefGoogle Scholar

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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