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A high-density integrative linkage map for Gossypium hirsutum

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Abstract

Sequence-related amplified polymorphism (SRAP) combined with SSRs, RAPDs, and RGAPs was used to construct a high density genetic map for a F2 population derived from the cross DH962 (G. hirsutum accession) × Jimian5 (G. hirsutum cultivar). A total of 4,096 SRAP primer combinations, 6310 SSRs, 600 RAPDs, and 10 RGAPs produced 331, 156, 17 and 2 polymorphic loci, respectively. Among the 506 loci obtained, 471 loci (309 SRAPs, 144 SSRs, 16 RAPDs and 2 RGAPs) were assigned to 51 linkage groups. Of these, 29 linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 3070.2 cM with a mean density of 6.5 cM per locus. The segregation distortion in this population was 9.49%, and these distorted loci tend to cluster at the end of linkage groups or in minor clusters on linkage groups. The majority of SRAPs in this map provided an effective tool for map construction in G. hirsutum despite of its low polymorphism. This high-density linkage map will be useful for further genetic studies in Upland cotton, including mapping of loci controlling quantitative traits, and comparative and integrative analysis with other interspecific and intraspecific linkage maps in cotton.

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References

  • Abdalla AM, Reddy OUK, El-Zik KM, Pepper AE (2001) Genetic diversity and relationships of diploid and tetraploid cotton revealed using AFLP. Theor Appl Genet 103:547–554. doi:10.1007/PL00002908

    Article  Google Scholar 

  • Chen XM, Line RF, Leung H (1998) Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis. Theor Appl Genet 97:345–355. doi:10.1007/s001220050905

    Article  CAS  Google Scholar 

  • Guo WZ, Cai CP, Wang CB, Han ZG, Song XL, Wang K et al (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176:527–541. doi:10.1534/genetics.107.070375

    Article  PubMed  CAS  Google Scholar 

  • Han ZG, Guo WZ, Song XL, Zhang TZ (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboretum in allotetraploid cotton. Mol Genet Genomics 272:308–327. doi:10.1007/s00438-004-1059-8

    Article  PubMed  CAS  Google Scholar 

  • Han ZG, Wang CB, Song XL, Guo WZ, Gou JY, Li CH et al (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112:430–439. doi:10.1007/s00122-005-0142-9

    Article  PubMed  CAS  Google Scholar 

  • He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX et al (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153:181–197. doi:10.1007/s10681-006-9254-9

    Article  CAS  Google Scholar 

  • Iqbal MJ, Aziz N, Saeed NA, Zafar Y, Malik KA (1997) Genetic diversity evaluation of some elite cotton varieties by RAPD analysis. Theor Appl Genet 94:139–144. doi:10.1007/s001220050392

    Article  CAS  Google Scholar 

  • Iqbal MJ, Reddy OUK, El–Zik KM, Pepper AE (2001) A genetic bottleneck in the ‘evolution under domestication’ of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting. Theor Appl Genet 103:547–554. doi:10.1007/PL00002908

    Article  CAS  Google Scholar 

  • Jiang CX, Wright RJ, El-Zik K, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:1419–1424

    Google Scholar 

  • Kohel RJ, Yu J, Park YH, Lazo GR (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121:163–172. doi:10.1023/A:1012263413418

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP et al (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations. Crop Sci 45:123–140

    CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE et al (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181. doi:10.1016/0888-7543(87)90010-3

    Article  PubMed  CAS  Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461. doi:10.1007/s001220100570

    Article  CAS  Google Scholar 

  • Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C et al (2005) Linkage map construction and mapping QTL for cotton fiber quality using SRAP, SSR and RAPD. Plant Breed 124:180–187. doi:10.1111/j.1439-0523.2004.01039.x

    Article  CAS  Google Scholar 

  • Lu HJ, Myers GO (2002) Genetic relationships and discrimination of ten influential Upland cotton varieties using RAPD markers. Theor Appl Genet 105:325–331. doi:10.1007/s00122-002-0947-8

    Article  PubMed  CAS  Google Scholar 

  • Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM et al (2003) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291. doi:10.1007/s00122-003-1433-7

    Article  PubMed  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. doi:10.1007/s00122-004-1612-1

    Article  PubMed  CAS  Google Scholar 

  • Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J et al (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274:428–441. doi:10.1007/s00438-005-0037-0

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP and PCR analysis. Plant Mol Biol Rep 11:112–127. doi:10.1007/BF02670470

    Article  Google Scholar 

  • Pillen K, Steinrücken G, Wricke G, Herrmann RG, Jung C (1992) A linkage map of sugar beet (Beta vulgaris L.). Theor Appl Genet 84:129–135. doi:10.1007/BF00223992

    Article  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, Abudurakhmonov I, Saha S, Jenkins JN, Brooks TD et al (2001) New dinucleotide and trinucleotide microsatellite resources for cotton genome research. J Cotton Sci 5:103–113

    Google Scholar 

  • Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel JF, Paterson AH (1994) A detailed RFLP map of cotton Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847

    PubMed  CAS  Google Scholar 

  • Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang C, Peng WC et al (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417. doi:10.1534/genetics.166.1.389

    Article  PubMed  CAS  Google Scholar 

  • Slocum MK, Figdore SS, Kennard WC, Suzuki JY, Osborn TC (1990) Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. Theor Appl Genet 8:57–64

    Google Scholar 

  • Sun ZD, Wang ZN, Tu JX, Zhang JF, Yu FQ, McVetty PBE et al (2007) An ultradense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers. Theor Appl Genet 114:1305–1317. doi:10.1007/s00122-006-0483-z

    Article  PubMed  CAS  Google Scholar 

  • Taliercio E, Allen RD, Essenberg M, Klueva N, Nguyen H, Patil MA et al (2006) Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs. Genome 49:306–319. doi:10.1139/G05-115

    Article  PubMed  CAS  Google Scholar 

  • Tatineni V, Cantrell RG, Davis DD (1996) Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPDs. Crop Sci 36:186–192

    Google Scholar 

  • Ulloa M, Meredith WR (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161–170

    CAS  Google Scholar 

  • Ulloa M, Meredith WR, Shappley ZW, Kahler AL (2002) RFLP genetic linkage maps from F2.3 populations and a joinmap of Gossypium hirsutum. Theor Appl Genet 104:200–208. doi:10.1007/s001220100739

    Article  PubMed  CAS  Google Scholar 

  • Wagner H, Weber WE, Wricke G (1992) Estimating linkage relationship of isozyme markers and morphological markers in sugar beet (Beta vulgaris L.) including families with distorted segregations. Plant Breed 108:89–96. doi:10.1111/j.1439-0523.1992.tb00106.x

    Article  CAS  Google Scholar 

  • Wricke G, Wehling P (1985) Linkage between an incompatibility locus and a peroxidase locus (Prx 7) in rye. Theor Appl Genet 71:289–291

    Google Scholar 

  • Wu JL, Zhuang JY, Cai RY, Fan YY, Jin MZ, Li DB et al (2000) Molecular mapping of a gene conferring resistance to neck blast in rice. Acta Phytopathol Sin 30(2):111–115

    Google Scholar 

  • Zhang JF, Lu Y, Cantrell RG, Hughs E (2005a) Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the Southwestern USA. Crop Sci 45:1483–1490. doi:10.2135/cropsci2004.0581

    Article  CAS  Google Scholar 

  • Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L et al (2005b) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144:91–99. doi:10.1007/s10681-005-4629-x

    Article  CAS  Google Scholar 

  • Zuo K, Sun J, Zhang X, Nie Y, Liu J, Feng C (2000) Constructing a linkage map of upland cotton (Gossypium hirsutum L.) using RFLP, RAPD and SSR makers. J Huazhong Agric Univ 19:190–193

    CAS  Google Scholar 

Download references

Acknowledgments

We thank Professor Yongzhang Niu (Agricultural Science Institute of Shānxi province) who provides us the Upland cotton accession, DH962. We also appreciate the Ministry of Science and Technology of China (973 project, 2004 CB117301; 863 project, 2006AA100105) for supporting this work.

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  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China

    Zhongxu Lin, Yanxin Zhang, Xianlong Zhang & Xiaoping Guo

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  1. Zhongxu Lin
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  2. Yanxin Zhang
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  3. Xianlong Zhang
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  4. Xiaoping Guo
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Correspondence to Xianlong Zhang.

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Lin, Z., Zhang, Y., Zhang, X. et al. A high-density integrative linkage map for Gossypium hirsutum . Euphytica 166, 35–45 (2009). https://doi.org/10.1007/s10681-008-9822-2

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