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Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum

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Abstract

Molecular markers associated with fiber development traits have the potential to play a key role in understanding of cotton fiber development. Seventeen SSRs out of 304 markers tested from MGHES (EST-SSR), JESPR (genomic SSR), and TMB (BAC-derived SSR) collections showed significant linkage associations (using a Kurskal-Wallis non-parametric test) with lint percentage QTL in a set of recombinant inbred cotton lines (RILs) segregating for lint percentage. The permutation test of these potential markers associated with lint percentage QTL(s) determined that 12 SSR markers have stable estimates, exceeding empirically chosen threshold significance values at or above α = 0.01. Interval mapping demonstrated that 9 SSRs with stable critical LOD threshold values at α = 0.01 have significant QTL effect. Multiple QTL-mapping (MQM) revealed that at least, two highly significant fiber development QTLs exist around regions TMB0471 and MGHES–31 (explained about 23–59% of the phenotypic variation of lint percentage) and around markers MGHES–31 and TMB0366 (accounted for 5.4–12.5% phenotypic variation of lint percentage). These markers, in particular fiber-specific EST-SSRs, might be the possible ‘candidate’ loci contributing for fiber development in cotton. BAC-derived SSRs associated with fiber trait are the possible markers that are useful for the identification of physical genomic contigs that contain fiber development genes. Several lint percentage trait associated SSR markers have been located to chromosomes 12, 18, 23, and 26 using deletion analysis in aneuploid chromosome substitution lines. Outcomes of the work may prove useful in understanding and revealing the molecular basis of the fiber development, and the utilization of these markers for development of superior cotton cultivars through marker-assisted selection (MAS) programs.

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References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Akkaya MS, Bhagwat AA, Cregan PB (1995) Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci35:1439–1445

    Article  Google Scholar 

  • 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 54:911–929

    Article  PubMed  CAS  Google Scholar 

  • Asnaghi C, Blewitt M, Guo Y, Lin D, Burr B (2001) Identification of genes involved in quality of cotton fiber by fiber cDNA microarray and QTL analysis. In: Plant and animal genomes IX conference, P5q_26.html. San Diego, California

  • Balls WL (1912) The cotton plant in Egypt. Macmillan, London

    Google Scholar 

  • Basra AS, Saha SS (1999) Growth regulation of cotton fibers. Food product press 47–63

  • Basra AS, Malik AC (1984) Development of the cotton fiber. Int rev Cytol 9:65–113

    Article  Google Scholar 

  • Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144

    Article  PubMed  CAS  Google Scholar 

  • Beavis WD (1994) The power and deceit of QTL experiments: lessons from comparative QTL studies. In: Proceedings of the 49th annual corn and sorghum industry research conference, American Seed Trade Association, Washington, DC, pp 250–266

  • Blenda, A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D (2006) CMD: a cotton microsatellite database resource for Gossypium genomics. BMC genomics 7:132 doi:10.1186/1471–2164–7–132

  • Brooks TD (2001) Mapping of cotton fiber length and strength quantitative trait loci using microsatellites. PhD Dissertation. Texas A&M University, USA

    Google Scholar 

  • Carver WA (1929) The inheritance of certain seed, leaf and flower characters in Gossypium hirsutum and their genetic interrelations. J Am Soc Agron 21:467–480

    Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971

    PubMed  CAS  Google Scholar 

  • Darvasi A (1997) The effect of selective genotyping on QTL mapping accuracy. Mamm Genome 8:67–68

    Article  PubMed  CAS  Google Scholar 

  • Darvasi A, Soller M (1992) Selective genotyping for determination of linkage between a marker locus and quantitative trait locus. Theor Appl Genet 85:353–359

    Article  Google Scholar 

  • Dellaporta SL, Wood J, Hicks JP (1983) A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1:19–21

    CAS  Google Scholar 

  • Du XM, Pan JJ, Wang RH, Zhang TZ, Shi Y (2001) Genetic analysis of presence and absence of lint and fuzz in cotton. Plant Breed 120:519–522

    Article  Google Scholar 

  • Endrizzi JE, Turcotte EL, Kohel RJ (1984) Quantitative genetics, cytology and cytogenetics. In: Cotton Kohel RJ, Lewis CF (eds) Amer Soc Agron Madison. WI, USA, pp 81–129

    Google Scholar 

  • Endrizzi JE, Turcotte EL, Kohel RJ (1985) Genetics, cytology, and evolution of Gossypium. Adv Genet 23:272–375

    Google Scholar 

  • Giband, M, Pagant S, Pannetier C, Hofte H (2003) Arabidopsis thaliana as a source of candidate genes for cotton fiber quality. In: The proceedings of the 3rd World Cotton Research Conference. Cape Town, South Africa, pp 58–63

  • Griffee F, Ligon LL (1929) Occurrence of “lintless” cotton plants and inheritance of character “lintless”. J Am Soc Agron 21:711–717

    Google Scholar 

  • Haley CS, Knott SA (1992) A simple method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324

    PubMed  CAS  Google Scholar 

  • Han ZG, Guo WZ, Song XL, Zhang TZ (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Gen Genomics 272:308–327

    Article  CAS  Google Scholar 

  • Han ZG, Wang C, Song XL, Guo WZ, Gou J, Li C, Chen X, Zhang TZ (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112(3):430–439

    Article  PubMed  CAS  Google Scholar 

  • Harland SC (1939) The genetics of cotton. Jonathan Cape, London

    Google Scholar 

  • Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211

    PubMed  CAS  Google Scholar 

  • Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via Interval mapping. Genetics 136:1447–1455

    PubMed  CAS  Google Scholar 

  • Ji SS, Lu YC, Feng JX, Wei G, Li S, Shi YH, Fu Q, Liu D, JC Luo, Zhu YX (2003) Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and c DNA array. Nucleic Acid Res 31:2534–2543

    Article  PubMed  CAS  Google Scholar 

  • Karaca M, Saha S, Jenkins JN, Zipf A, Kohel RJ, Stelly MD (2002) Simple sequence Repeat (SSR) markers Linked to the ligon lintless (Li) mutant in cotton. J Hered 93:221–224

    Article  PubMed  CAS  Google Scholar 

  • Kearney TH, Harrison CJ (1927) The inheritance of smoothness seeds in cotton. J Agric Res 35:193–217

    Google Scholar 

  • Kohel RJ (1972) Linkage tests in upland cotton, Gossypium hirsutum L. II. Crop Sci 12:66–69

    Article  Google Scholar 

  • Kohel RJ (1973) Genetic nomenclature in cotton. J Hered 64:291–295

    Google Scholar 

  • Kohel RJ, Yu JZ, Park YH, Lazo GR (2001) Molecular mapping and characterization of genes controlling fiber quality in cotton. Euphytica 121:163–172

    Article  CAS  Google Scholar 

  • Knapp SJ (1991) Using molecular markers to map multiple quantitative trait loci: model for backcross, recombinant inbred and double haploid progeny. Theor Appl Genet 81:333–338

    Article  CAS  Google Scholar 

  • 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 x G. barbadense backcross population. Genome 46:612–626

    Article  PubMed  CAS  Google Scholar 

  • 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 x Gossypium barbadense backcross generations. Crop Sci 45:123–140

    CAS  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 134:943–951

    Google Scholar 

  • Lee JJ, Hassan OS, Gao W, Wei NE, Kohel RJ, Chen XY, Payton P, Sze SH, Stelly DM, Chen ZJ (2006) Developmental and gene expression analyses of a cotton naked seed mutant. Planta 223:418–432

    Article  PubMed  CAS  Google Scholar 

  • Lehmann EL (1975) Nonparametrics. McGraw-Hill, New York

    Google Scholar 

  • Li XB, Fan XP, Wang XL, Cai L, Yang WC (2005) The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17:859–875

    Article  PubMed  CAS  Google Scholar 

  • McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping applications in rice genetics and breeding. Plant Mol Biol 35:89–99

    Article  PubMed  CAS  Google Scholar 

  • Mc Lendon CA (1972) Mendelian inheritance in cotton hybrids. Georgia Sta Bull No 99

  • Musaev, JA, Abzalov MF (1972) Some questions concerning the inheritance of fuzzy in cotton seeds (G. hirsutum L.) Genetika 7–16 (in Russian)

  • Musaev JA (1979) Genetic collection of cotton. Fan UzSSR (in Russian)

  • Musaev JA, Abzalov MF, Almatov A, Sanamyan MF, Gubanova N, Nadjimov U (2000) Cotton genetics and genetic collection of isogenic, monosomic and translocation lines. Bulletins SCST of the republic of Uzbekistan (in Russian), p 28–39

  • Nadarajan N, Rangasamy SR (1988) Inheritance of the fuzzless-lintless character in cotton (Gossypium hirsutum). Theor Appl Genet 75:728–730

    Article  Google Scholar 

  • Narbuth EV, Kohel RJ (1990) Inheritance and linkage analysis of a new fiber mutant in cotton. J Hered 81:131–133

    Google Scholar 

  • Nelson JC (1997) QGene: software for marker–based genomic analysis breeding. Molecular Breeding 3:293–245

    Article  Google Scholar 

  • Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor Appl Genet 109:167–175

    Article  PubMed  CAS  Google Scholar 

  • Nolte KD, Hendrix DL, Radin JW, Koch KE (1995) Sucrose synthase localization during initiation of seed development and trichome differentiation in cotton ovules. Plant Physiol 109:1285–1293

    PubMed  CAS  Google Scholar 

  • Orford SJ, Timmis JN (1998) Specific expression of an expansin gene during elongation of cotton fibers. Biochim Biophys Acta 1398:342–346

    PubMed  CAS  Google Scholar 

  • Paterson AH, Saranga Y, Menz M, Ziang CX (2003) QTL analysis of genotype X environment interactions affecting cotton fiber quality. Theor Appl Genet 106:384–396

    PubMed  CAS  Google Scholar 

  • Pear JR, Kawagoe Y, Schreckengost WE, Delmer DP, Stalker DM (1996) Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc Natl Acad Sci USA 93:12637–12642

    Article  PubMed  CAS  Google Scholar 

  • Qureshi SN, Saha S, Kantety RV, Jenkins JN (2004) EST-SSR: a new class of genetic markers in cotton. J Cotton Sci 8:112–123

    CAS  Google Scholar 

  • Reddy OUK, Pepper AE, Abdurakhmonov IY, Saha S, Jenkins JN, Brooks TD, Bolek Y, El-Zik KM (2001) The identification of dinucleotide and trinucleotide microsatellite repeat loci from cotton G. hirsutum L. J Cotton Sci 5:103–113

    Google Scholar 

  • Richmond TR (1947) The genetics of certain factors responsible for lint quantity in American Upland cotton. Bull Tex Agric Sta vol 716

  • Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA et al. (2004) A3347–locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417

    Article  PubMed  CAS  Google Scholar 

  • Rong, J, Pierce GJ, Waghmare VN, Rogers CJ, Desai A, Chee PW, May OL, Gannaway JR, Wendel JF, Wilkins TA, Paterson AH (2005) Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor Appl Genet DOI 10.1007/s00122–005–0041–0

  • Ruan YL, Llewellyn DJ, Furbank RT (2001) The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin. Plant Cell 13:47–63

    Article  PubMed  CAS  Google Scholar 

  • Ruan YL, Llewellyn DJ, Furbank RT (2003) Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development. Plant Cell 15:952–964

    Article  PubMed  CAS  Google Scholar 

  • Saha S, Jenkins JN, Wu J, McCarty JC, Gutierrez OA, Percy RG, Cantrell RG, Stelly DM (2006) Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits. Genetics 172(3):1927–38

    Article  PubMed  CAS  Google Scholar 

  • Shen X, Guo W, Zhu X, Yuan Y, Yu JZ, Kohel RJ, Zhang T (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15:169–181

    Article  CAS  Google Scholar 

  • Soller M, Genizi A, Brody T (1976) On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theor Appl Genet 47:35–39

    Article  Google Scholar 

  • Stelly DM, Saha S, Raska DA, Jenkins JN Jr, McCarty JC, Gutiérrez OA (2005) Registration of 17 Upland (Gossypium hirsutum) Cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions. Crop Sci 45:2663–2665

    Article  Google Scholar 

  • Suo J, Liang X, Pu L, Zhang Y, Xue Y (2003) Identification of GhMYB109 encoding a R2R3 MYB transcription factor that expressed specifically in fiber initials and elongating fibers of cotton (Gossypium hirsutum L.). Biochim Biophys Acta 1630(1):25–34

    PubMed  CAS  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277:1063–1066

    Article  PubMed  CAS  Google Scholar 

  • Thadani KI (1923) Linkage relations in the cotton plant. Agric J India No 18

  • Thadani KI (1925) Inheritance of certain characters in Gossypium. Agric J India vol 20

  • Turley RB, Kloth RH (2002) Identification of a third fuzzless seed locus in Upland cotton (Gossypium hirsutum L.). J Hered 93:359–364

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen JW (1999) LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83:613–624

    Article  PubMed  Google Scholar 

  • Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C (2002) MapQTL@4.0, Software for the calculation of QTL positions of genetic maps. Plant Research International, Wageningen, The Netherlands

    Google Scholar 

  • Ware JO (1929) Inheritance of linted percentage in cotton. J Am Soc Agron 21:876–894

    Google Scholar 

  • Ware JO, Benedict LN, Rolfe WH (1947) A recessive naked seed character in Upland cotton. J Hered 38:313–331

    CAS  PubMed  Google Scholar 

  • Wilkins TA, Jernstedt JA (1999) Molecular genetics of developing cotton fibers. Food product press 231–269

  • Wu Y, Llewellyn DJ, Dennis ES (2001) Gene discovery in cotton fiber initiation using EST and microarray approaches. Plant and animal genomes IX conference abstract P01_76.html

  • Young DN (2000) Constructing a plant genetic linkage map with DNA markers. In: Philips RL, Vasil JK (eds) DNA-based Markers in plants. Kluwer Academic Publishers, Netherlands, pp 31–47

    Google Scholar 

  • Yu JZ, Kohel RJ, Dong J (2002) Development of integrative SSR markers from TM-1 BACs. In: Proceedings of beltwide cotton improvement conference, CDROM (2002) Altlanta, Georgia

  • Yu JZ, Kohel RJ, Zhang H, Stelly DM, Xu Z, Dong J, Covaleda L, Lee M, Cui P, Lazo GR, Gupta P, Ding K (2004a) Toward an integrated physical and genetic map of the cultivated allotetraploid cotton genome. In: Plant and animal genome conference XII, W147. San Diego, California

  • Yu JZ, Kohel RJ, Cantrell RG, Jones D, Saha S, Tomkins J, Main D, Palmer M, Pepper AE, Stelly DM, Ulloa M, Scheffler J (2004b) Establishment of standardized cotton microsatellite database (CMD) panel. In: The proceedings of cotton beltwide conference. San Antonio, Texas, p 1129

  • Zang T, Pan J (1991) Genetic analysis of fuzzless-lintless mutant in Gossypium hirsutum L. Jiangsu J Agric Sci 7:13–16

    Google Scholar 

  • Zhang J, Guo W, Zhang T (2002) Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L x Gossypium barbadense L.) with a haploid population. Theor Appl Genet 105:1166–117

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This work was supported in part by a research grant on cotton marker-assisted selection by the Science and Technology Center of Uzbekistan. We are grateful to the ARS-FSU Scientific Cooperation Program, Office of International Research Programs, USDA-ARS for financial support of cotton genomics research in Uzbekistan. We thank Dr. D. M. Stelly, Texas A&M University, for providing the aneuploid chromosome substitution lines of cotton. Disclaimer: Mention of trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.

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Authors and Affiliations

  1. Laboratory of Genetic Engineering and Biotechnology, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Yuqori Yuz, Qibray region Tashkent district, 702151, Uzbekistan

    I. Y. Abdurakhmonov, Z. T. Buriev, J. A. Musaev, A. Almatov, S. E. Shermatov, F. N. Kushanov, G. T. Mavlonov & A. Abdukarimov

  2. USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture, 8120 Highway 12E, P. O. Box 5367, Mississippi State, MS, 39762, USA

    S. Saha & J. N. Jenkins

  3. Department of Biology, Texas A&M University, College Station, TX, 77843, USA

    A. E. Pepper

  4. Department of Biology, West Virginia State University, 103 Hamblin Hall, WV, 25112, USA

    U. K. Reddy

  5. Crop Germplasm Research Unit, 2881 F&B Road, College Station, TX, 77845, USA

    J. Z. Yu & R. J. Kohel

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  1. I. Y. Abdurakhmonov
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  2. Z. T. Buriev
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  3. S. Saha
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  5. J. A. Musaev
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  8. F. N. Kushanov
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  9. G. T. Mavlonov
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  11. J. Z. Yu
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  12. J. N. Jenkins
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  14. A. Abdukarimov
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Correspondence to I. Y. Abdurakhmonov.

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I. Y. Abdurakhmonov and S. Saha contributed equally to the work

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Abdurakhmonov, I.Y., Buriev, Z.T., Saha, S. et al. Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum . Euphytica 156, 141–156 (2007). https://doi.org/10.1007/s10681-007-9361-2

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