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Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

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Abstract

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F2-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development.

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References

  • Burr B, Burr FA (1991) Recombinant inbred for molecular mapping in maize: theoretical and practical considerations. Trends Genet 7:55–60

    PubMed  CAS  Google Scholar 

  • Burr B, Burr FA, Thompson KH, Albertson MC, Stuber C (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526

    PubMed  CAS  Google Scholar 

  • Brubaker CL, Wendel JF (2001) RFLP diversity in cotton. In: Saha S, Jenkins JN (eds) Genetic improvement of cotton emerging technologies. Science Pulisher Inc, Enfield, CO, pp 3–31

    Google Scholar 

  • Fehr W (1987) Principles of cultivar development: volume one, theory and technique. Macmillan Publishing Co., New York

    Google Scholar 

  • Frelichowski JM, Palmer MB, Main D, Tomkins JP, Cantrell RG, Stelly DM et al (2006) Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends. Mol Genet Genomics 275:479–491. doi:10.1007/s00438-006-0106-z

    Article  PubMed  CAS  Google Scholar 

  • Gutierrez OA, Basu S, Saha S, Jenkins JN, Shoemaker DB, Cheatham CL et al (2002) Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Sci 42:1841–1847

    Google Scholar 

  • Han Z, Guo W, Song X, Zhang T (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Genet Genomics 272(3):308–327. doi:10.1007/s00438-004-1059-8

    Article  PubMed  CAS  Google Scholar 

  • Han Z, Wang C, Song X, Guo W, Gou J, Li C 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 

  • Horne EC, Kumpatla SP, Patterson KA, Gupta M, Thompson SA (2004) Improved protocols for high-throughput sunflower and cotton genomic DNA extraction and PCR fidelity. Plant Mol Biol Rep 22:83–84. doi:10.1007/BF02773352

    Article  Google Scholar 

  • Jenkins JN, Wu J, McCarty JC, Saha S, Gutiérrez OA, Hayes R et al (2006) Genetic effects of thirteen Gossypium barbadense L. chromosome substitution lines in topcrosses with upland cotton cultivars: I. yield and yield components. Crop Sci 46:1169–1178. doi:10.2135/cropsci2005.08-0269

    Article  Google Scholar 

  • Jenkins JN, McCarty JC, Wu J, Saha S, Gutiérrez OA, Hayes R et al (2007) Genetic effects of thirteen Gossypium barbadense L. chromosome substitution lines in topcrosses with upland cotton cultivars: II. fiber quality traits. Crop Sci 47:561–572

    Google Scholar 

  • Jiang C, Wright RJ, El-Zik KM, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:4419–4424. doi:10.1073/pnas.95.8.4419

    Article  PubMed  CAS  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, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG et al (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46:612–626. doi:10.1139/g03-050

    Article  PubMed  CAS  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 

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

    Article  CAS  Google Scholar 

  • Liu S, Cantrell G, McCarty JC, Stewart JM (2000a) Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions. Crop Sci 40:1459–1469

    CAS  Google Scholar 

  • Liu S, Saha S, Stelly D, Burr B, Cantrell RG (2000b) Chromosomal assignment of microsatellite loci in cotton. J Hered 91:326–332. doi:10.1093/jhered/91.4.326

    Article  PubMed  CAS  Google Scholar 

  • Miller RG (1974) The jackknife: a review. Biometrika 61:1–15

    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 

  • 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 

  • Rao CR (1971) Estimation of variance and covariance components MINQUE theory. J Multivariate Anal 1:257–275. doi:10.1016/0047-259X(71)90001-7

    Article  Google Scholar 

  • Reinisch AJ, Dong J, 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 polyploidy genome. Genetics 138:829–847

    PubMed  CAS  Google Scholar 

  • Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW 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 

  • Saha S, Callahan FE, Dollar DA, Creech JB (1997) Effect of lyophilization of cotton tissue on quality of extractable DNA, RNA, and protein. J Cotton Sci 1:10–14

    CAS  Google Scholar 

  • Saha S, Wu J, Jenkins JN, McCarty JC, Gutiérrez O, Stelly DM et al (2004) Effects of chromosome substitution from Gossypium barbadense L. into G. hirsutum L. TM-1 on agronomic and fiber traits. J Cotton Sci 8:162–169

    CAS  Google Scholar 

  • Saha S, Jenkins JN, Wu J, McCarty JC, Gutiérrez O, Percy RG et al (2006) Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits. Genetics 172:1927–1938. doi:10.1534/genetics.105.053371

    Article  PubMed  CAS  Google Scholar 

  • SAS Institute Inc (1999) SAS software Version 8.0. SAS Institute, Cary, NC

    Google Scholar 

  • Shappley ZW, Jenkins JN, Meredith WR, McCarty JC (1998a) An RFLP linkage map of upland cotton (Gossypium hirsutum L.). Theor Appl Genet 97:756–761. doi:10.1007/s001220050952

    Article  CAS  Google Scholar 

  • Shappley ZW, Jenkins JN, Zhu McCarty JC (1998b) Quantitative traits loci associated with agronomic and fiber traits of upland cotton. J Cotton Sci 4:153–163

    Google Scholar 

  • Shen X, Guo W, Zhu X, Yuan Y, Yu J, Kohel R et al (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15:169–181. doi:10.1007/s11032-004-4731-0

    Article  CAS  Google Scholar 

  • Shen X, Zhang T, Guo W, Zhu X, Zhang X (2006) Mapping fiber and yield QTLs with main, epistatic, and QTL × Environment interaction effects in recombinant inbred lines of upland cotton. Crop Sci:61–66.

  • Tanksley SD, McCough SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066. doi:10.1126/science.277.5329.1063

    Article  PubMed  CAS  Google Scholar 

  • Tomkins JP, Peterson DG, Yang TJ, Main D, Wilkins TA, Paterson AH et al (2001) Development of genomic resources for cotton (Gossypium hirsutum L.): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development. Mol Breed 8(3):255–261. doi:10.1023/A:1013798716098

    Article  CAS  Google Scholar 

  • Ulloa M, Meredith WR (2000) Genetic linkage map and QTL analysis of agronomic and fiber 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 four F2.3 populations and a joinmap of Gossypium hirsutum L. Theor Appl Genet 104:200–208. doi:10.1007/s001220100739

    Article  PubMed  CAS  Google Scholar 

  • Ulloa M, Saha S, Jenkins JN, Meredith WR, McCarty JC, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) joinmap. J Hered 96:132–144. doi:10.1093/jhered/esi020

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands

    Google Scholar 

  • Wang D, Zhu J, Li Z, Paterson AH (1999) Mapping QTLs with epistatic effects and QTL × environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255–1264. doi:10.1007/s001220051331

    Article  Google Scholar 

  • Wu J (2001) Comparisons on properties of marker linkage and QTL mapping between two methods of recombinant line development. Ph.D. dissertation, Zhejiang University, Hangzhou, China

  • Wu J (2003) Genetic variation, conditional analysis, and QTL mapping for agronomic and fiber traits in upland cotton. Ph.D. diss. Diss. Abstra. Int. 64-09B:4119), Mississippi State Univ., Mississippi State, MS

  • Wu J, Jenkins JN, Zhu J, McCarty JC, Watson CE (2003a) Comparisons of QTL mapping properties for two methods of recombinant inbred line development. Euphytica 132:159–166. doi:10.1023/A:1024690711867

    Article  CAS  Google Scholar 

  • Wu J, Zhu J, Jenkins JN (2003b) Mixed linear model approaches in quantitative genetic models (book chapter) In: Formulars, software, and techniques for genetics and breeders. The Haworth Reference Press Inc., New York

  • Wu J, Jenkins JN, Zhu J, McCarty JC, Watson CE (2003c) Monte Carlo simulations on marker grouping and ordering. Theor Appl Genet 107:568–573. doi:10.1007/s00122-003-1283-3

    Article  PubMed  CAS  Google Scholar 

  • Wu J, Jenkins JN, McCarty JC, Zhu J (2004) Genetic association of yield with its component traits for upland cotton recombinant inbred lines. Euphytica 140:171–179. doi:10.1007/s10681-004-2897-5

    Article  Google Scholar 

  • Zhang T, Yuan Y, Yu J, Guo W, Kohel RJ (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor Appl Genet 106:262–268

    PubMed  CAS  Google Scholar 

  • Zhang Z, Xiao Y, Luo M, Li X, Luo X, Hou L et al (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144(1):91–99. doi:10.1007/s10681-005-4629-x

    Article  CAS  Google Scholar 

  • Zhu J (1989) Estimation of genetic variance components in the general mixed model. Ph.D. Dissertation, North Carolina State University, Raleigh, NC

  • Zhu J (1993) Methods of predicting genotype value and heterosis for offspring of hybrids. J Biomathematics Chin 8(1):32–44

    Google Scholar 

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Authors and Affiliations

  1. Department of Plant and Soil Sciences, Mississippi State University, P.O. Box 9555, Mississippi State, MS, 39762, USA

    Jixiang Wu & Osman Ariel Gutierrez

  2. Crop Science Research Laboratory, USDA-ARS, P.O. Box 5367, Mississippi State, MS, 39762, USA

    Johnie N. Jenkins & Jack C. McCarty

  3. Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, 310029, China

    Jun Zhu

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  1. Jixiang Wu
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  2. Osman Ariel Gutierrez
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  3. Johnie N. Jenkins
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  4. Jack C. McCarty
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  5. Jun Zhu
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Correspondence to Jixiang Wu or Johnie N. Jenkins.

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Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.

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Wu, J., Gutierrez, O.A., Jenkins, J.N. et al. Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton. Euphytica 165, 231–245 (2009). https://doi.org/10.1007/s10681-008-9748-8

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